BJ-DNA-QC v2.1.0

The report aggregates all metrics from BJ-DNA-QC pipeline to help evaluate the performance of single-cell libraries.

session_id: d1cf5c64-c154-46e0-b82f-aaa9eeae7dc7
read_length: 50
n_reads: 2000000
genome: GRCh38
instrument: None
skip_fastqc: True
skip_kraken: True
skip_qualimap: True
skip_CNV: False
bin_size: 1000000
min_ploidy: 1.5
max_ploidy: 6

JavaScript Disabled

MultiQC reports use JavaScript for plots and toolbox functions. It looks like you have JavaScript disabled in your web browser. Please note that many of the report functions will not work as intended.

Report generated on 2025-11-03, 17:24 UTC

General Statistics

Showing ¹⁰/₁₀ rows and ⁷/₇ columns.

Sample Name	% Duplication	% > Q30	Mb Q30 bases	Reads After Filtering	GC content	% PF	% Adapter
ResolveOMEv2.0-384-DNA-QC-B4	13.6%	94.4%	93.2Mb	2.0M	39.7%	99.4%	0.6%
ResolveOMEv2.0-384-DNA-QC-D3	11.9%	93.3%	92.2Mb	2.0M	39.5%	99.3%	0.5%
ResolveOMEv2.0-384-DNA-QC-D6	11.5%	94.0%	93.0Mb	2.0M	39.7%	99.4%	0.5%
ResolveOMEv2.0-384-DNA-QC-F22	23.1%	94.2%	93.3Mb	2.0M	40.5%	99.5%	0.3%
ResolveOMEv2.0-384-DNA-QC-G22	23.5%	94.3%	82.8Mb	1.7M	39.8%	99.6%	0.3%
ResolveOMEv2.0-384-DNA-QC-H5	11.1%	93.5%	92.4Mb	2.0M	39.6%	99.3%	0.5%
ResolveOMEv2.0-384-DNA-QC-K3	7.1%	93.6%	92.7Mb	2.0M	39.6%	99.4%	0.3%
ResolveOMEv2.0-384-DNA-QC-M4	7.9%	93.4%	91.6Mb	2.0M	39.6%	98.5%	0.7%
ResolveOMEv2.0-384-DNA-QC-O7	10.5%	94.0%	93.1Mb	2.0M	39.9%	99.3%	0.4%
ResolveOMEv2.0-384-DNA-QC-O11	9.7%	94.7%	93.9Mb	2.0M	39.5%	99.6%	0.4%

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: general_stats_table_table

Sort	Group	Column	Description	ID	Scale
\|\|	fastp	% Duplication	Duplication rate before filtering	`fastp-pct_duplication`
\|\|	fastp	% > Q30	Percentage of reads > Q30 after filtering	`fastp-after_filtering_q30_rate`
\|\|	fastp	Mb Q30 bases	Bases > Q30 after filtering (millions)	`fastp-after_filtering_q30_bases`	base_count
\|\|	fastp	Reads After Filtering	Total reads after filtering (millions)	`fastp-filtering_result_passed_filter_reads`	read_count
\|\|	fastp	GC content	GC content after filtering	`fastp-after_filtering_gc_content`
\|\|	fastp	% PF	Percent reads passing filter	`fastp-pct_surviving`
\|\|	fastp	% Adapter	Percentage adapter-trimmed reads	`fastp-pct_adapter`

Selected Metrics

Selected metrics are subset of all metrics that provides overview of the sample quality assessment.

Showing ¹⁰/₁₀ rows and ¹⁵/₁₅ columns.

sample_name	PreSeq Count	% chrM	% Chimeras	% Aligned	% Error	Insert Size	Total Reads	Adapter Trimmed Reads	Adapter Trimmed Bases	Gini coefficient	Average ploidy	Number of segments	CN-Aware MAD	MAPD CNV Log2	SKEW CNV
ResolveOMEv2.0-384-DNA-QC-B4	4277889373	0.24	8.51	99.82	0.30	350	2156730	12208	125683	0.04	2.00	17	0.191	0.1256	0.1281
ResolveOMEv2.0-384-DNA-QC-D3	4163860302	0.30	8.17	99.85	0.32	351	2389264	9768	107828	0.04	2.00	7	0.177	0.1305	0.0712
ResolveOMEv2.0-384-DNA-QC-D6	4205181705	0.16	8.65	99.83	0.31	371	2277812	9680	104691	0.04	2.00	7	0.179	0.1229	0.1075
ResolveOMEv2.0-384-DNA-QC-F22	4041824467	0.16	8.45	99.88	0.33	385	1974650	6312	70130	0.02	2.00	12	0.388	0.2336	0.1634
ResolveOMEv2.0-384-DNA-QC-G22	4112028582	0.12	7.77	99.88	0.34	384	1749274	5946	68542	0.02	2.00	7	0.199	0.1295	0.0992
ResolveOMEv2.0-384-DNA-QC-H5	4051637120	0.27	8.04	99.85	0.33	361	2568144	9444	101982	0.03	2.00	14	0.183	0.1192	0.0700
ResolveOMEv2.0-384-DNA-QC-K3	4027887378	0.28	9.54	99.87	0.33	387	2518868	6270	70176	0.03	2.00	10	0.263	0.1719	0.1320
ResolveOMEv2.0-384-DNA-QC-M4	4158273878	0.27	8.90	99.86	0.33	391	2301682	14427	429232	0.03	2.00	16	0.200	0.1207	0.0894
ResolveOMEv2.0-384-DNA-QC-O7	4239754595	0.20	9.09	99.87	0.32	368	2326878	7080	75080	0.03	2.00	8	0.173	0.1157	0.1016
ResolveOMEv2.0-384-DNA-QC-O11	4123097286	0.11	8.69	99.87	0.30	372	2393006	7094	78374	0.03	2.00	9	0.170	0.1177	0.0662

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: selected_metrics_table

Sort	Column	Description	ID
\|\|	PreSeq Count	Expected number of bases covered >= 1 for theoretical larger experiment.	`preseq_count`
\|\|	% chrM	Percent of reads mapping to chrM.	`chrM`
\|\|	% Chimeras	Percent of reads with two ends mapping to different chromosomes or with long insert size.	`PCT_CHIMERAS`
\|\|	% Aligned	Percent of trimmed reads that aligned to reference genome.	`pct_trimmed_aligned`
\|\|	% Error	Percent of bases that mismatch the reference in aligned reads.	`PF_HQ_ERROR_RATE`
\|\|	Insert Size	Median Insert Size estimated from sampled reads.	`MEDIAN_INSERT_SIZE`
\|\|	Total Reads	Total number of reads.	`total_reads`
\|\|	Adapter Trimmed Reads	Total number of adapter trimmed reads.	`adapter_trimmed_reads`
\|\|	Adapter Trimmed Bases	Total number of adapter trimmed bases.	`adapter_trimmed_bases`
\|\|	Gini coefficient	Gini coefficient ranges 0 to 1 where 0 is prefect uniformity and 1 is perfect non-uniformity in genomic coverage.	`gini_coefficient_index`
\|\|	Average ploidy	Estimated ploidy at the genome-wide level. This value represents this genome-wide ploidy	`cnv_genome_ploidy`
\|\|	Number of segments	Number of genome-wide copy changes (gain or loss)	`cnv_number_of_segments`
\|\|	CN-Aware MAD	CN-Aware Median absolute deviation (MAD) of cnv-segment.	`SegmentMAD_Aware`
\|\|	MAPD CNV Log2	MAPD CNV Log2 measurement from ginkgo segment summary	`MAPD_CNV_Log2`
\|\|	SKEW CNV	SKEW CNV measurement from ginkgo segment summary	`SKEW_CNV`

All Metrics

All metrics generated by the BJ-DNA-QC pipeline.

Showing ¹⁰/₁₀ rows and ¹⁸⁹/₁₈₉ columns.

sample_name	Total Reads	Unpaired Reads Examined	Read Pairs Examined	Secondary Reads	Unmapped Reads	Unpaired Read Duplicates	Read Pair Duplicates	Read Pair Optical Duplicates	Proportion Duplication	Estimated Library Size	Mean Read Length	Sampled Reads	PF Reads	Proportion PF Reads	PF Reads Aligned	Proportion PF Reads Aligned	PF Aligned Bases	PF HQ Aligned Reads	PF HQ Aligned Bases	PF HQ Aligned Q20 Bases	PF Mismatch Rate	PF HQ Error Rate	PF Indel Rate	Reads Aligned in Pairs	Proportion Reads Aligned in Pairs	Stand Balance	Proportion Chimeras	Gini coefficient	ROC Lorenz curve	Total covered positions of genome	Total investigated genomic positions	Total sequenced bases	chr1	chr2	chr3	chr4	chr5	chr6	chr7	chr8	chr9	chr10	chr11	chr12	chr13	chr14	chr15	chr16	chr17	chr18	chr19	chr20	chr21	chr22	chrX	chrY	chrM	Genome Territory	Mean Coverage	SD Coverage	Proportion Bases with low MAPQ	Proportion Bases Unpaired	Proportion Bases with low BASEQ	Proportion Bases with Overlap	Proportion Bases Excluded in Total	Proportion Bases > 1x	HET SNP Sensitivity	Window Size on the genome	Total Clusters seen in GC Bias	Reads Used by GC Bias Algo	AT Dropout	GC Dropout	NC GC 0-19	NC GC 20-39	NC GC 40-59	NC GC 60-79	NC GC 80-100	Median Insert Size	Median Absolute Deviation	Min Insert Size	Max Insert Size	Mean Insert Size	Standard Deviation	Read Pairs	Pair Orientation	Preseq Count	Preseq Input Read Count	Custom Proportion Chimeras	MAPD Score	MAPD CNV Log2	SKEW CNV	Adapter Trimmed Reads	Adapter Trimmed Bases	Average ploidy	Number of segments	Segment score of MAD	CN-Aware MAD	Preseq Count_NonDedup	Sampled Reads Non dedup	PF Reads Non dedup	Proportion PF Reads Non dedup	PF Reads Aligned Non dedup	Proportion PF Reads Aligned Non dedup	PF Aligned Bases Non dedup	PF HQ Aligned Reads Non dedup	PF HQ Aligned Bases Non dedup	PF HQ Aligned Q20 Bases Non dedup	PF Mismatch Rate Non dedup	PF HQ Error Rate Non dedup	PF Indel Rate Non dedup	Mean Read Length Non dedup	Reads Aligned in Pairs Non dedup	Proportion Reads Aligned in Pairs Non dedup	Stand Balance Non dedup	Proportion Chimeras Non dedup	Proportion Adapters Non dedup	chr1 Non dedup	chr2 Non dedup	chr3 Non dedup	chr4 Non dedup	chr5 Non dedup	chr6 Non dedup	chr7 Non dedup	chr8 Non dedup	chr9 Non dedup	chr10 Non dedup	chr11 Non dedup	chr12 Non dedup	chr13 Non dedup	chr14 Non dedup	chr15 Non dedup	chr16 Non dedup	chr17 Non dedup	chr18 Non dedup	chr19 Non dedup	chr20 Non dedup	chr21 Non dedup	chr22 Non dedup	chrX Non dedup	chrY Non dedup	chrM Non dedup	Genome Territory Non dedup	Mean Coverage Non dedup	SD Coverage Non dedup	Proportion Bases with low MAPQ Non dedup	Proportion Bases Unpaired Non dedup	Proportion Bases with low BASEQ Non dedup	Proportion Bases with Overlap Non dedup	Proportion Bases Excluded in Total Non dedup	Proportion Bases > 1x Non dedup	HET SNP Sensitivity Non dedup	Window Size on the genome Non dedup	Total Clusters seen in GC Bias Non dedup	Reads Used by GC Bias Algo Non dedup	AT Dropout Non dedup	GC Dropout Non dedup	NC GC 0-19 Non dedup	NC GC 20-39 Non dedup	NC GC 40-59 Non dedup	NC GC 60-79 Non dedup	NC GC 80-100 Non dedup	Median Insert Size Non dedup	Median Absolute Deviation Non dedup	Min Insert Size Non dedup	Max Insert Size Non dedup	Mean Insert Size Non dedup	Standard Deviation Non dedup	Read Pairs Non dedup	Pair Orientation Non dedup	Flag
ResolveOMEv2.0-384-DNA-QC-B4	2156730	5993	984320	13745	12555	2732	131313	8576	0.134	3545956	50	1679101	1679101	1.00	1676153	1.00	81157194	1470191	71504922	70166933	0.0036	0.0030	0.0003	1673205	0.9982	0.5007	0.0851	0.04	0.458	76041008.000	3185560356.000	83218708.000	0.087	0.086	0.070	0.069	0.063	0.060	0.053	0.050	0.042	0.046	0.045	0.045	0.036	0.030	0.026	0.034	0.023	0.027	0.013	0.021	0.019	0.011	0.029	0.013	0.002	2923732648	0.024	0.183	0.119	0.001	0.016	0.008	0.144	0.023	0.0109	100	839690	1676482	0.67	6.02	0.85	1.11	0.95	0.45	1.22	350	87.0	2	244823552	356	147.0	770649	FR	4277889373	1731268	0.0613	0.3908	0.1256	0.1281	12208	125683	2.00	17	0.198	0.191	519397759	1943635	1943635	1.00	1938009	1.00	93849026	1715208	83416542	81703966	0.0037	0.0030	0.0003	50	1932383	0.9971	0.5011	0.0829	0.0010	0.086	0.087	0.071	0.070	0.064	0.060	0.053	0.050	0.041	0.046	0.045	0.045	0.036	0.030	0.026	0.034	0.023	0.027	0.013	0.021	0.018	0.011	0.029	0.012	0.002	2923732648	0.028	0.222	0.111	0.001	0.018	0.008	0.139	0.023	0.0103	100	971990	1938368	0.67	6.02	0.85	1.11	0.94	0.45	2.29	347	86.0	2	244823552	352	145.5	891875	FR	NA
ResolveOMEv2.0-384-DNA-QC-D3	2389264	5706	985516	12665	9430	2942	119112	11690	0.122	4083117	50	1705906	1705906	1.00	1703365	1.00	82785965	1507353	73523205	71761261	0.0038	0.0032	0.0002	1700824	0.9985	0.5009	0.0817	0.04	0.463	78382280.000	3189506119.000	84779407.000	0.086	0.086	0.071	0.071	0.064	0.059	0.053	0.051	0.041	0.045	0.044	0.045	0.036	0.030	0.027	0.034	0.022	0.027	0.013	0.020	0.018	0.010	0.030	0.013	0.003	2923732648	0.024	0.186	0.112	0.001	0.021	0.004	0.138	0.024	0.0112	100	853079	1703673	1.23	6.71	0.87	1.13	0.92	0.43	1.67	351	74.0	2	206726521	361	130.4	785920	FR	4163860302	1753360	0.0608	0.4532	0.1305	0.0712	9768	107828	2.00	7	0.193	0.177	582388842	1947042	1947042	1.00	1941597	1.00	94373404	1730836	84419065	82207720	0.0038	0.0033	0.0002	50	1936152	0.9972	0.5014	0.0796	0.0012	0.086	0.088	0.071	0.072	0.064	0.060	0.054	0.051	0.041	0.045	0.044	0.045	0.036	0.030	0.027	0.034	0.022	0.027	0.013	0.020	0.017	0.010	0.030	0.012	0.003	2923732648	0.028	0.220	0.105	0.001	0.023	0.004	0.134	0.024	0.0106	100	973647	1941927	1.24	6.70	0.88	1.13	0.92	0.43	2.90	348	73.0	2	206726521	358	129.1	896596	FR	NA
ResolveOMEv2.0-384-DNA-QC-D6	2277812	4648	987827	12787	8950	1481	113202	6681	0.115	4185245	50	1723589	1723589	1.00	1720678	1.00	83302271	1522962	74013486	72468863	0.0037	0.0031	0.0003	1717767	0.9983	0.5004	0.0865	0.04	0.465	79166804.000	3191391899.000	85274276.000	0.086	0.087	0.072	0.070	0.064	0.061	0.054	0.050	0.040	0.046	0.044	0.045	0.036	0.029	0.027	0.034	0.023	0.028	0.013	0.021	0.017	0.010	0.029	0.013	0.002	2923732648	0.025	0.183	0.112	0.001	0.018	0.004	0.135	0.024	0.0114	100	862040	1721048	0.82	6.01	0.85	1.11	0.94	0.46	1.02	371	82.0	2	230986810	384	142.9	789567	FR	4205181705	1771447	0.0657	0.4196	0.1229	0.1075	9680	104691	2.00	7	0.193	0.179	608875885	1950116	1950116	1.00	1945766	1.00	94208428	1734856	84309838	82404483	0.0037	0.0031	0.0003	50	1941416	0.9978	0.5006	0.0849	0.0005	0.086	0.087	0.072	0.070	0.064	0.062	0.054	0.050	0.040	0.046	0.044	0.045	0.036	0.030	0.027	0.034	0.023	0.028	0.013	0.021	0.017	0.010	0.029	0.012	0.002	2923732648	0.028	0.215	0.105	0.001	0.020	0.004	0.131	0.024	0.0108	100	975301	1946157	0.81	5.98	0.85	1.11	0.94	0.46	1.52	368	81.0	2	230986810	381	141.3	893768	FR	NA
ResolveOMEv2.0-384-DNA-QC-F22	1974650	3136	978186	8673	5228	1204	229915	33985	0.235	1948066	50	1480150	1480150	1.00	1478395	1.00	72482302	1332776	65526621	64298805	0.0037	0.0033	0.0002	1476640	0.9988	0.5004	0.0845	0.02	0.476	70189735.000	3186760950.000	73718740.000	0.089	0.087	0.072	0.064	0.064	0.061	0.053	0.049	0.042	0.046	0.045	0.047	0.032	0.031	0.030	0.031	0.027	0.026	0.016	0.022	0.016	0.012	0.028	0.008	0.002	2923732648	0.022	0.161	0.096	0.001	0.017	0.003	0.117	0.021	0.0102	100	740322	1478861	0.31	3.63	0.75	1.05	0.99	0.59	1.12	385	85.0	2	228810234	404	150.1	678976	FR	4041824467	1509397	0.0652	0.3995	0.2336	0.1634	6312	70130	2.00	12	0.420	0.388	314928864	1938376	1938376	1.00	1935468	1.00	94906826	1769252	86983626	85062511	0.0038	0.0034	0.0002	50	1932560	0.9985	0.5006	0.0808	0.0003	0.088	0.087	0.072	0.065	0.064	0.061	0.054	0.050	0.042	0.046	0.046	0.047	0.032	0.032	0.030	0.031	0.027	0.026	0.016	0.022	0.016	0.012	0.027	0.007	0.002	2923732648	0.029	0.232	0.083	0.001	0.020	0.003	0.108	0.021	0.0093	100	969472	1936003	0.25	3.60	0.76	1.05	0.99	0.59	1.27	380	83.0	2	228810234	398	146.0	891888	FR	NA
ResolveOMEv2.0-384-DNA-QC-G22	1749274	2682	867380	9200	4314	1004	205108	33414	0.237	1736659	50	1307937	1307937	1.00	1306432	1.00	64173107	1165219	57394471	56346111	0.0038	0.0034	0.0002	1304927	0.9988	0.5001	0.0777	0.02	0.476	62206147.000	3185839670.000	65419594.000	0.087	0.087	0.073	0.072	0.064	0.063	0.054	0.040	0.042	0.046	0.045	0.045	0.037	0.030	0.027	0.032	0.024	0.028	0.013	0.021	0.016	0.010	0.030	0.011	0.001	2923732648	0.019	0.152	0.106	0.001	0.016	0.003	0.126	0.019	0.0090	100	654171	1306810	1.08	5.79	0.85	1.11	0.94	0.49	0.91	384	86.0	2	214178248	405	150.4	604936	FR	4112028582	1336900	0.0600	0.4648	0.1295	0.0992	5946	68542	2.00	7	0.215	0.199	262973363	1715967	1715967	1.00	1713502	1.00	84181657	1552374	76468127	74817363	0.0039	0.0035	0.0002	50	1711037	0.9986	0.5003	0.0740	0.0003	0.086	0.088	0.074	0.073	0.065	0.063	0.054	0.040	0.042	0.047	0.045	0.045	0.037	0.030	0.027	0.031	0.024	0.028	0.013	0.021	0.015	0.010	0.030	0.010	0.001	2923732648	0.025	0.220	0.092	0.001	0.020	0.003	0.115	0.019	0.0083	100	858218	1713957	1.04	5.73	0.86	1.11	0.94	0.49	1.08	379	83.0	2	214178248	398	146.1	796071	FR	NA
ResolveOMEv2.0-384-DNA-QC-H5	2568144	5128	986070	12197	8942	2226	111202	11154	0.114	4419169	50	1725173	1725173	1.00	1722511	1.00	83580733	1532235	74603858	72863122	0.0039	0.0033	0.0002	1719849	0.9985	0.5007	0.0804	0.03	0.466	79638067.000	3193167071.000	85461758.000	0.085	0.085	0.072	0.071	0.063	0.060	0.053	0.050	0.042	0.046	0.045	0.044	0.036	0.030	0.027	0.033	0.023	0.028	0.013	0.021	0.017	0.011	0.030	0.011	0.003	2923732648	0.025	0.185	0.107	0.001	0.021	0.004	0.133	0.024	0.0115	100	862758	1722811	1.00	6.20	0.85	1.12	0.93	0.46	1.30	361	76.0	2	226330348	373	134.1	795636	FR	4051637120	1770358	0.0608	0.5064	0.1192	0.0700	9444	101982	2.00	14	0.190	0.183	628846848	1949468	1949468	1.00	1944624	1.00	94355940	1741525	84791837	82639922	0.0039	0.0034	0.0002	50	1939780	0.9975	0.5011	0.0785	0.0009	0.085	0.086	0.072	0.072	0.064	0.060	0.053	0.050	0.042	0.046	0.045	0.045	0.036	0.030	0.027	0.033	0.023	0.028	0.013	0.021	0.017	0.011	0.030	0.011	0.003	2923732648	0.028	0.216	0.101	0.001	0.023	0.004	0.129	0.024	0.0109	100	974914	1944945	1.00	6.18	0.85	1.12	0.93	0.46	2.18	358	76.0	2	226330348	370	132.9	899033	FR	NA
ResolveOMEv2.0-384-DNA-QC-K3	2518868	3636	990112	9665	5548	1098	72719	16484	0.074	8100716	50	1814295	1814295	1.00	1811970	1.00	87640837	1642007	79631647	77764135	0.0037	0.0033	0.0002	1809645	0.9987	0.4970	0.0954	0.03	0.473	84366863.000	3189180795.000	89204635.000	0.083	0.091	0.076	0.072	0.065	0.061	0.051	0.055	0.040	0.047	0.046	0.046	0.035	0.030	0.026	0.031	0.022	0.027	0.011	0.020	0.017	0.010	0.026	0.010	0.003	2923732648	0.027	0.183	0.091	0.001	0.021	0.002	0.116	0.026	0.0122	100	907375	1812433	1.06	6.16	0.88	1.12	0.93	0.47	1.11	387	82.0	2	227047533	409	144.2	822339	FR	4027887378	1850836	0.0498	0.4788	0.1719	0.1320	6270	70176	2.00	10	0.288	0.263	934691395	1960542	1960542	1.00	1957142	1.00	94663606	1779967	86318213	84164615	0.0037	0.0033	0.0002	50	1953742	0.9983	0.4972	0.0943	0.0004	0.082	0.091	0.076	0.072	0.065	0.061	0.051	0.055	0.040	0.047	0.046	0.046	0.035	0.030	0.025	0.031	0.022	0.027	0.011	0.020	0.017	0.010	0.026	0.010	0.003	2923732648	0.029	0.204	0.088	0.001	0.023	0.002	0.114	0.026	0.0118	100	980509	1957623	1.05	6.15	0.89	1.12	0.93	0.46	1.52	385	81.0	2	227047533	406	142.7	888771	FR	NA
ResolveOMEv2.0-384-DNA-QC-M4	2301682	3346	981067	10110	5414	568	79849	17745	0.082	7146571	50	1779939	1779939	1.00	1777374	1.00	86043058	1596510	77503905	75626452	0.0037	0.0033	0.0002	1774809	0.9986	0.5011	0.0890	0.03	0.471	82556119.000	3188209881.000	87739626.000	0.084	0.089	0.072	0.071	0.065	0.062	0.054	0.051	0.039	0.046	0.045	0.045	0.037	0.030	0.027	0.032	0.022	0.028	0.013	0.020	0.017	0.010	0.029	0.010	0.003	2923732648	0.026	0.184	0.099	0.001	0.022	0.002	0.124	0.025	0.0119	100	890153	1777775	1.18	6.24	0.87	1.12	0.93	0.46	2.56	391	83.0	2	223224393	412	145.6	812622	FR	4158273878	1819465	0.0691	0.4725	0.1207	0.0894	14427	429232	2.00	16	0.191	0.200	850049845	1938959	1938959	1.00	1935862	1.00	93719375	1747325	84823905	82630268	0.0038	0.0034	0.0002	50	1932765	0.9984	0.5011	0.0877	0.0000	0.084	0.089	0.072	0.072	0.065	0.062	0.054	0.050	0.039	0.046	0.045	0.045	0.037	0.030	0.027	0.032	0.022	0.028	0.013	0.020	0.017	0.010	0.029	0.010	0.003	2923732648	0.028	0.206	0.095	0.001	0.023	0.002	0.121	0.025	0.0115	100	969671	1936274	1.17	6.23	0.87	1.12	0.92	0.46	2.57	388	82.0	2	223224393	409	144.0	886108	FR	NA
ResolveOMEv2.0-384-DNA-QC-O7	2326878	6808	985311	9787	9990	4232	103150	6760	0.106	4635284	50	1744504	1744504	1.00	1742155	1.00	84137773	1565532	75815035	74250502	0.0036	0.0032	0.0002	1739806	0.9987	0.4993	0.0909	0.03	0.473	81047841.000	3194550458.000	85663523.000	0.085	0.086	0.072	0.071	0.064	0.062	0.054	0.051	0.042	0.046	0.045	0.046	0.037	0.030	0.027	0.031	0.023	0.028	0.013	0.021	0.016	0.010	0.030	0.010	0.002	2923732648	0.025	0.179	0.099	0.001	0.019	0.002	0.121	0.025	0.0117	100	872469	1742603	0.94	5.70	0.83	1.11	0.94	0.49	1.88	368	88.0	2	241241043	391	149.8	794686	FR	4239754595	1781482	0.0606	0.4537	0.1157	0.1016	7080	75080	2.00	8	0.182	0.173	688027523	1957262	1957262	1.00	1950709	1.00	94217021	1760698	85264515	83377602	0.0036	0.0032	0.0002	50	1944156	0.9966	0.5002	0.0892	0.0020	0.084	0.088	0.072	0.071	0.064	0.062	0.054	0.051	0.041	0.046	0.045	0.046	0.037	0.030	0.027	0.031	0.023	0.028	0.013	0.020	0.015	0.010	0.030	0.009	0.002	2923732648	0.028	0.209	0.095	0.001	0.020	0.002	0.118	0.025	0.0112	100	978861	1951186	0.93	5.72	0.83	1.11	0.94	0.48	3.90	365	86.0	2	241241043	387	148.0	889623	FR	NA
ResolveOMEv2.0-384-DNA-QC-O11	2393006	3428	991190	10207	6320	924	94790	6329	0.096	5148914	50	1772624	1772624	1.00	1770349	1.00	85522257	1590847	77065954	75670309	0.0035	0.0030	0.0002	1768074	0.9987	0.5003	0.0869	0.03	0.474	82426567.000	3190450125.000	87080649.000	0.085	0.086	0.074	0.070	0.064	0.062	0.054	0.051	0.041	0.046	0.045	0.045	0.037	0.030	0.027	0.032	0.023	0.028	0.013	0.020	0.016	0.010	0.030	0.010	0.001	2923732648	0.026	0.181	0.099	0.001	0.016	0.002	0.118	0.025	0.0120	100	886541	1770796	1.11	6.21	0.81	1.12	0.93	0.46	0.80	372	87.0	2	201598009	396	149.9	811387	FR	4123097286	1810079	0.0691	0.4916	0.1177	0.0662	7094	78374	2.00	9	0.183	0.170	754290530	1962246	1962246	1.00	1959079	1.00	94640526	1770067	85744767	84093016	0.0035	0.0031	0.0002	50	1955912	0.9984	0.5005	0.0854	0.0003	0.085	0.087	0.074	0.071	0.065	0.062	0.054	0.051	0.041	0.046	0.045	0.045	0.037	0.030	0.027	0.032	0.023	0.028	0.013	0.020	0.016	0.010	0.030	0.010	0.001	2923732648	0.029	0.208	0.094	0.001	0.017	0.002	0.115	0.025	0.0115	100	981360	1959557	1.08	6.20	0.82	1.12	0.93	0.46	1.09	369	86.0	2	201598009	392	148.2	898874	FR	NA

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: all_metrics_table

Sort	Column	Description	ID
\|\|	Total Reads	Total number of reads from fastq file(s)	`total_reads`
\|\|	Unpaired Reads Examined	Picard DuplicationMetrics: The number of mapped reads examined which did not have a mapped mate pair, either because the read is unpaired, or the read is paired to an unmapped mate.	`UNPAIRED_READS_EXAMINED`
\|\|	Read Pairs Examined	Picard DuplicationMetrics: The number of mapped read pairs examined. (Primary, non-supplemental)	`READ_PAIRS_EXAMINED`
\|\|	Secondary Reads	Picard DuplicationMetrics: The number of reads that were either secondary or supplementary	`SECONDARY_OR_SUPPLEMENTARY_RDS`
\|\|	Unmapped Reads	Picard DuplicationMetrics: The total number of unmapped reads examined. (Primary, non-supplemental)	`UNMAPPED_READS`
\|\|	Unpaired Read Duplicates	Picard DuplicationMetrics: The number of fragments that were marked as duplicates.	`UNPAIRED_READ_DUPLICATES`
\|\|	Read Pair Duplicates	Picard DuplicationMetrics: The number of read pairs that were marked as duplicates.	`READ_PAIR_DUPLICATES`
\|\|	Read Pair Optical Duplicates	Picard DuplicationMetrics: The number of read pairs duplicates that were caused by optical duplication. Value is always < READ_PAIR_DUPLICATES, which counts all duplicates regardless of source.	`READ_PAIR_OPTICAL_DUPLICATES`
\|\|	Proportion Duplication	Picard DuplicationMetrics: The fraction of mapped sequence that is marked as duplicate.	`PERCENT_DUPLICATION`
\|\|	Estimated Library Size	Picard DuplicationMetrics: The estimated number of unique molecules in the library based on PE duplication.	`ESTIMATED_LIBRARY_SIZE`
\|\|	Mean Read Length	AlignmentStat: The mean read length of the set of reads examined. When looking at the data for a single lane with equal length reads this number is just the read length. When looking at data for merged lanes with differing read lengths this is the mean read length of all reads.	`MEAN_READ_LENGTH`
\|\|	Sampled Reads	AlignmentStat: The total number of reads including all PF and non-PF reads. When CATEGORY equals PAIR this value will be 2x the number of clusters.	`TOTAL_READS`
\|\|	PF Reads	AlignmentStat: The number of PF reads where PF is defined as passing Illumina's filter.	`PF_READS`
\|\|	Proportion PF Reads	AlignmentStat: The fraction of reads that are PF (PF_READS / TOTAL_READS)	`PCT_PF_READS`
\|\|	PF Noise Reads	AlignmentStat: The number of PF reads that are marked as noise reads. A noise read is one which is composed entirely of A bases and/or N bases. These reads are marked as they are usually artifactual and are of no use in downstream analysis.	`PF_NOISE_READS`
\|\|	PF Reads Aligned	AlignmentStat: The total number of aligned bases, in all mapped PF reads, that are aligned to the reference sequence.	`PF_READS_ALIGNED`
\|\|	Proportion PF Reads Aligned	AlignmentStat: The percentage of PF reads that aligned to the reference sequence. PF_READS_ALIGNED / PF_READS	`PCT_PF_READS_ALIGNED`
\|\|	PF Aligned Bases	AlignmentStat: The total number of aligned bases, in all mapped PF reads, that are aligned to the reference sequence.	`PF_ALIGNED_BASES`
\|\|	PF HQ Aligned Reads	AlignmentStat: The number of PF reads that were aligned to the reference sequence with a mapping quality of Q20 or higher signifying that the aligner estimates a 1/100 (or smaller) chance that the alignment is wrong.	`PF_HQ_ALIGNED_READS`
\|\|	PF HQ Aligned Bases	AlignmentStat: The number of bases aligned to the reference sequence in reads that were mapped at high quality. Will usually approximate PF_HQ_ALIGNED_READS * READ_LENGTH but may differ when either mixed read lengths are present or many reads are aligned with gaps.	`PF_HQ_ALIGNED_BASES`
\|\|	PF HQ Aligned Q20 Bases	AlignmentStat: The subset of PF_HQ_ALIGNED_BASES where the base call quality was Q20 or higher.	`PF_HQ_ALIGNED_Q20_BASES`
\|\|	PF HQ Median Mismatches	AlignmentStat: The median number of mismatches versus the reference sequence in reads that were aligned to the reference at high quality (i.e. PF_HQ_ALIGNED READS).	`PF_HQ_MEDIAN_MISMATCHES`
\|\|	PF Mismatch Rate	AlignmentStat: The rate of bases mismatching the reference for all bases aligned to the reference sequence.	`PF_MISMATCH_RATE`
\|\|	PF HQ Error Rate	AlignmentStat: The fraction of bases that mismatch the reference in PF HQ aligned reads.	`PF_HQ_ERROR_RATE`
\|\|	PF Indel Rate	AlignmentStat: The number of insertion and deletion events per 100 aligned bases. Uses the number of events as the numerator, not the number of inserted or deleted bases.	`PF_INDEL_RATE`
\|\|	Reads Aligned in Pairs	AlignmentStat: The number of aligned reads whose mate pair was also aligned to the reference.	`READS_ALIGNED_IN_PAIRS`
\|\|	Proportion Reads Aligned in Pairs	AlignmentStat: The fraction of reads whose mate pair was also aligned to the reference. READS_ALIGNED_IN_PAIRS / PF_READS_ALIGNED	`PCT_READS_ALIGNED_IN_PAIRS`
\|\|	Bad Cycles	AlignmentStat: The number of instrument cycles in which 80% or more of base calls were no-calls.	`BAD_CYCLES`
\|\|	Stand Balance	AlignmentStat: The number of PF reads aligned to the positive strand of the genome divided by the number of PF reads aligned to the genome.	`STRAND_BALANCE`
\|\|	Proportion Chimeras	AlignmentStat: The fraction of reads that map outside of a maximum insert size (usually 100kb) or that have the two ends mapping to different chromosomes.	`PCT_CHIMERAS`
\|\|	Proportion Adapters	AlignmentStat: The fraction of PF reads that are unaligned and match to a known adapter sequence right from the start of the read.	`PCT_ADAPTER`
\|\|	Gini coefficient	bam-lorenz-coverage: Gini coefficient ranges 0 to 1 where 0 is prefect uniformity and 1 is perfect non-uniformity in genomic coverage.	`gini_coefficient_index`
\|\|	ROC Lorenz curve	bam-lorenz-coverage: ROC Lorenz curve	`ROC_Lorenz_curve`
\|\|	Total covered positions of genome	bam-lorenz-coverage: Total covered positions of genome	`total_covered_positions_of_genome`
\|\|	Total investigated genomic positions	bam-lorenz-coverage: Total investigated genomic position	`total_investigated_genomic_positions`
\|\|	Total sequenced bases	bam-lorenz-coverage: Total sequenced bases	`total_sequenced_bases`
\|\|	chr1	Proportion of reads mapping to chr1	`chr1`
\|\|	chr2	Proportion of reads mapping to chr2	`chr2`
\|\|	chr3	Proportion of reads mapping to chr3	`chr3`
\|\|	chr4	Proportion of reads mapping to chr4	`chr4`
\|\|	chr5	Proportion of reads mapping to chr5	`chr5`
\|\|	chr6	Proportion of reads mapping to chr6	`chr6`
\|\|	chr7	Proportion of reads mapping to chr7	`chr7`
\|\|	chr8	Proportion of reads mapping to chr8	`chr8`
\|\|	chr9	Proportion of reads mapping to chr9	`chr9`
\|\|	chr10	Proportion of reads mapping to chr10	`chr10`
\|\|	chr11	Proportion of reads mapping to chr11	`chr11`
\|\|	chr12	Proportion of reads mapping to chr12	`chr12`
\|\|	chr13	Proportion of reads mapping to chr13	`chr13`
\|\|	chr14	Proportion of reads mapping to chr14	`chr14`
\|\|	chr15	Proportion of reads mapping to chr15	`chr15`
\|\|	chr16	Proportion of reads mapping to chr16	`chr16`
\|\|	chr17	Proportion of reads mapping to chr17	`chr17`
\|\|	chr18	Proportion of reads mapping to chr18	`chr18`
\|\|	chr19	Proportion of reads mapping to chr19	`chr19`
\|\|	chr20	Proportion of reads mapping to chr20	`chr20`
\|\|	chr21	Proportion of reads mapping to chr21	`chr21`
\|\|	chr22	Proportion of reads mapping to chr22	`chr22`
\|\|	chrX	Proportion of reads mapping to chrX	`chrX`
\|\|	chrY	Proportion of reads mapping to chrY	`chrY`
\|\|	chrM	Proportion of reads mapping to chrM	`chrM`
\|\|	Genome Territory	WgsMetricsAlgo: The number of non-N bases in the genome reference over which coverage will be evaluated.	`GENOME_TERRITORY`
\|\|	Mean Coverage	WgsMetricsAlgo: The mean coverage in bases of the genome territory, after all filters are applied.	`MEAN_COVERAGE`
\|\|	SD Coverage	WgsMetricsAlgo: The standard deviation of coverage of the genome after all filters are applied.	`SD_COVERAGE`
\|\|	Median Coverage	WgsMetricsAlgo: The median coverage in bases of the genome territory, after all filters are applied.	`MEDIAN_COVERAGE`
\|\|	MAD Coverage	WgsMetricsAlgo: The median absolute deviation of coverage of the genome after all filters are applied.	`MAD_COVERAGE`
\|\|	Proportion Bases with low MAPQ	WgsMetricsAlgo: The fraction of aligned bases that were filtered out because they were in reads with low mapping quality (default is < 20).	`PCT_EXC_MAPQ`
\|\|	Proportion Bases with Duplicates	WgsMetricsAlgo: The fraction of aligned bases that were filtered out because they were in reads marked as duplicates.	`PCT_EXC_DUPE`
\|\|	Proportion Bases Unpaired	WgsMetricsAlgo: The fraction of aligned bases that were filtered out because they were in reads without a mapped mate pair.	`PCT_EXC_UNPAIRED`
\|\|	Proportion Bases with low BASEQ	WgsMetricsAlgo: The fraction of aligned bases that were filtered out because they were of low base quality (default is < 20).	`PCT_EXC_BASEQ`
\|\|	Proportion Bases with Overlap	WgsMetricsAlgo: The fraction of aligned bases that were filtered out because they were the second observation from an insert with overlapping reads.	`PCT_EXC_OVERLAP`
\|\|	Proportion Bases above Capped	WgsMetricsAlgo: The fraction of aligned bases that were filtered out because they would have raised coverage above the capped value (default cap = 250x).	`PCT_EXC_CAPPED`
\|\|	Proportion Bases Excluded in Total	WgsMetricsAlgo: The total fraction of aligned bases excluded due to all filters.	`PCT_EXC_TOTAL`
\|\|	Proportion Bases > 1x	WgsMetricsAlgo: The fraction of bases that attained at least 1X sequence coverage in post-filtering bases.	`PCT_1X`
\|\|	Proportion Bases > 5x	WgsMetricsAlgo: The fraction of bases that attained at least 5X sequence coverage in post-filtering bases.	`PCT_5X`
\|\|	HET SNP Sensitivity	WgsMetricsAlgo: The theoretical HET SNP sensitivity.	`HET_SNP_SENSITIVITY`
\|\|	HET SNP Phred Scaled Q Score	WgsMetricsAlgo: The Phred Scaled Q Score of the theoretical HET SNP sensitivity.	`HET_SNP_Q`
\|\|	Window Size on the genome	GCBias: The window size on the genome used to calculate the GC of the sequence.	`WINDOW_SIZE`
\|\|	Total Clusters seen in GC Bias	GCBias: The total number of clusters that were seen in the gc bias calculation.	`TOTAL_CLUSTERS`
\|\|	Reads Used by GC Bias Algo	GCBias: The total number of aligned reads used to compute the gc bias metrics.	`ALIGNED_READS`
\|\|	AT Dropout	GCBias: Illumina-style AT dropout metric. Calculated by taking each GC bin independently and calculating (%ref_at_gc - %reads_at_gc) and summing all positive values for GC=[0..50].	`AT_DROPOUT`
\|\|	GC Dropout	GCBias: Illumina-style GC dropout metric. Calculated by taking each GC bin independently and calculating (%ref_at_gc - %reads_at_gc) and summing all positive values for GC=[50..100].	`GC_DROPOUT`
\|\|	NC GC 0-19	GCBias: Normalized coverage over quintile of GC content ranging from 0 - 19.	`GC_NC_0_19`
\|\|	NC GC 20-39	GCBias: Normalized coverage over quintile of GC content ranging from 20 - 39.	`GC_NC_20_39`
\|\|	NC GC 40-59	GCBias: Normalized coverage over quintile of GC content ranging from 40 - 59.	`GC_NC_40_59`
\|\|	NC GC 60-79	GCBias: Normalized coverage over quintile of GC content ranging from 60 - 79.	`GC_NC_60_79`
\|\|	NC GC 80-100	GCBias: Normalized coverage over quintile of GC content ranging from 80 - 100.	`GC_NC_80_100`
\|\|	Median Insert Size	InsertSizeMetricAlgo: The MEDIAN insert size of all paired end reads where both ends mapped to the same chromosome.	`MEDIAN_INSERT_SIZE`
\|\|	Median Absolute Deviation	InsertSizeMetricAlgo: The median absolute deviation of the distribution. If the distribution is essentially normal then the standard deviation can be estimated as ~1.4826 * MAD.	`MEDIAN_ABSOLUTE_DEVIATION`
\|\|	Min Insert Size	InsertSizeMetricAlgo: The minimum measured insert size. This is usually 1 and not very useful as it is likely artifactual.	`MIN_INSERT_SIZE`
\|\|	Max Insert Size	InsertSizeMetricAlgo: The maximum measure insert size by alignment. This is usually very high representing either an artifact or possibly the presence of a structural re-arrangement.	`MAX_INSERT_SIZE`
\|\|	Mean Insert Size	InsertSizeMetricAlgo: The mean insert size of the'core' of the distribution. Artefactual outliers in the distribution often cause calculation of nonsensical mean and stdev values. To avoid this the distribution is first trimmed to a 'core' distribution of +/- N median absolute deviations around the median insert size. By default N=10, but this is configurable.	`MEAN_INSERT_SIZE`
\|\|	Standard Deviation	InsertSizeMetricAlgo: Standard deviation of insert sizes over the 'core' of the distribution.	`STANDARD_DEVIATION`
\|\|	Read Pairs	InsertSizeMetricAlgo: The total number of read pairs that were examined in the entire distribution.	`READ_PAIRS`
\|\|	Pair Orientation	InsertSizeMetricAlgo: The pair orientation of the reads in this data category.	`PAIR_ORIENTATION`
\|\|	Preseq Count	Preseq: Expected number of bases covered >= 1 for theoretical larger experiment.	`preseq_count`
\|\|	Preseq Input Read Count	Total number of reads used to estimate library complexiby by Preseq tool	`preseq_input_read_count`
\|\|	Custom Proportion Chimeras	PCT_POL_chimeras	`PCT_POL_chimeras`
\|\|	MAPD Score	Median Absolute deviation of Pairwise Differences (MAPD) is a measurement of the bin-to-bin variability of the coverage. A lower number represents higher uniformity of the whole genome amplification.	`MAPD_Score`
\|\|	MAPD CNV Log2	MAPD CNV Log2 measurement from ginkgo segment summary	`MAPD_CNV_Log2`
\|\|	SKEW CNV	SKEW CNV measurement from ginkgo segment summary	`SKEW_CNV`
\|\|	Adapter Trimmed Reads	fastp: Total number of adapter trimmed reads.	`adapter_trimmed_reads`
\|\|	Adapter Trimmed Bases	fastp: Total number of adapter trimmed bases.	`adapter_trimmed_bases`
\|\|	Average ploidy	Estimated ploidy at the genome-wide level. This value represents this genome-wide ploidy	`cnv_genome_ploidy`
\|\|	Number of segments	Number of genome-wide copy changes (gain or loss)	`cnv_number_of_segments`
\|\|	Segment score of MAD	Median absolute deviation (MAD) of cnv-segment. A lower number represents data with less amount of noise	`cnv_segment_MAD`
\|\|	CN-Aware MAD	CN-Aware Median absolute deviation (MAD) of cnv-segment.	`SegmentMAD_Aware`
\|\|	Preseq Count_NonDedup	Preseq: Expected number of bases covered >= 1 for theoretical larger experiment.	`preseq_count_nondedup`
\|\|	Sampled Reads Non dedup	AlignmentStat: The total number of reads including all PF and non-PF reads. When CATEGORY equals PAIR this value will be 2x the number of clusters.	`TOTAL_READS_ndd`
\|\|	PF Reads Non dedup	AlignmentStat: The number of PF reads where PF is defined as passing Illumina's filter.	`PF_READS_ndd`
\|\|	Proportion PF Reads Non dedup	AlignmentStat: The fraction of reads that are PF (PF_READS / TOTAL_READS)	`PCT_PF_READS_ndd`
\|\|	PF Noise Reads Non dedup	AlignmentStat: The number of PF reads that are marked as noise reads. A noise read is one which is composed entirely of A bases and/or N bases. These reads are marked as they are usually artifactual and are of no use in downstream analysis.	`PF_NOISE_READS_ndd`
\|\|	PF Reads Aligned Non dedup	AlignmentStat: The total number of aligned bases, in all mapped PF reads, that are aligned to the reference sequence.	`PF_READS_ALIGNED_ndd`
\|\|	Proportion PF Reads Aligned Non dedup	AlignmentStat: The percentage of PF reads that aligned to the reference sequence. PF_READS_ALIGNED / PF_READS	`PCT_PF_READS_ALIGNED_ndd`
\|\|	PF Aligned Bases Non dedup	AlignmentStat: The total number of aligned bases, in all mapped PF reads, that are aligned to the reference sequence.	`PF_ALIGNED_BASES_ndd`
\|\|	PF HQ Aligned Reads Non dedup	AlignmentStat: The number of PF reads that were aligned to the reference sequence with a mapping quality of Q20 or higher signifying that the aligner estimates a 1/100 (or smaller) chance that the alignment is wrong.	`PF_HQ_ALIGNED_READS_ndd`
\|\|	PF HQ Aligned Bases Non dedup	AlignmentStat: The number of bases aligned to the reference sequence in reads that were mapped at high quality. Will usually approximate PF_HQ_ALIGNED_READS * READ_LENGTH but may differ when either mixed read lengths are present or many reads are aligned with gaps.	`PF_HQ_ALIGNED_BASES_ndd`
\|\|	PF HQ Aligned Q20 Bases Non dedup	AlignmentStat: The subset of PF_HQ_ALIGNED_BASES where the base call quality was Q20 or higher.	`PF_HQ_ALIGNED_Q20_BASES_ndd`
\|\|	PF HQ Median Mismatches Non dedup	AlignmentStat: The median number of mismatches versus the reference sequence in reads that were aligned to the reference at high quality (i.e. PF_HQ_ALIGNED READS).	`PF_HQ_MEDIAN_MISMATCHES_ndd`
\|\|	PF Mismatch Rate Non dedup	AlignmentStat: The rate of bases mismatching the reference for all bases aligned to the reference sequence.	`PF_MISMATCH_RATE_ndd`
\|\|	PF HQ Error Rate Non dedup	AlignmentStat: The fraction of bases that mismatch the reference in PF HQ aligned reads.	`PF_HQ_ERROR_RATE_ndd`
\|\|	PF Indel Rate Non dedup	AlignmentStat: The number of insertion and deletion events per 100 aligned bases. Uses the number of events as the numerator, not the number of inserted or deleted bases.	`PF_INDEL_RATE_ndd`
\|\|	Mean Read Length Non dedup	AlignmentStat: The mean read length of the set of reads examined. When looking at the data for a single lane with equal length reads this number is just the read length. When looking at data for merged lanes with differing read lengths this is the mean read length of all reads.	`MEAN_READ_LENGTH_ndd`
\|\|	Reads Aligned in Pairs Non dedup	AlignmentStat: The number of aligned reads whose mate pair was also aligned to the reference.	`READS_ALIGNED_IN_PAIRS_ndd`
\|\|	Proportion Reads Aligned in Pairs Non dedup	AlignmentStat: The fraction of reads whose mate pair was also aligned to the reference. READS_ALIGNED_IN_PAIRS / PF_READS_ALIGNED	`PCT_READS_ALIGNED_IN_PAIRS_ndd`
\|\|	Bad Cycles Non dedup	AlignmentStat: The number of instrument cycles in which 80% or more of base calls were no-calls.	`BAD_CYCLES_ndd`
\|\|	Stand Balance Non dedup	AlignmentStat: The number of PF reads aligned to the positive strand of the genome divided by the number of PF reads aligned to the genome.	`STRAND_BALANCE_ndd`
\|\|	Proportion Chimeras Non dedup	AlignmentStat: The fraction of reads that map outside of a maximum insert size (usually 100kb) or that have the two ends mapping to different chromosomes.	`PCT_CHIMERAS_ndd`
\|\|	Proportion Adapters Non dedup	AlignmentStat: The fraction of PF reads that are unaligned and match to a known adapter sequence right from the start of the read.	`PCT_ADAPTER_ndd`
\|\|	chr1 Non dedup	Proportion of reads mapping to chr1	`chr1_ndd`
\|\|	chr2 Non dedup	Proportion of reads mapping to chr2	`chr2_ndd`
\|\|	chr3 Non dedup	Proportion of reads mapping to chr3	`chr3_ndd`
\|\|	chr4 Non dedup	Proportion of reads mapping to chr4	`chr4_ndd`
\|\|	chr5 Non dedup	Proportion of reads mapping to chr5	`chr5_ndd`
\|\|	chr6 Non dedup	Proportion of reads mapping to chr6	`chr6_ndd`
\|\|	chr7 Non dedup	Proportion of reads mapping to chr7	`chr7_ndd`
\|\|	chr8 Non dedup	Proportion of reads mapping to chr8	`chr8_ndd`
\|\|	chr9 Non dedup	Proportion of reads mapping to chr9	`chr9_ndd`
\|\|	chr10 Non dedup	Proportion of reads mapping to chr10	`chr10_ndd`
\|\|	chr11 Non dedup	Proportion of reads mapping to chr11	`chr11_ndd`
\|\|	chr12 Non dedup	Proportion of reads mapping to chr12	`chr12_ndd`
\|\|	chr13 Non dedup	Proportion of reads mapping to chr13	`chr13_ndd`
\|\|	chr14 Non dedup	Proportion of reads mapping to chr14	`chr14_ndd`
\|\|	chr15 Non dedup	Proportion of reads mapping to chr15	`chr15_ndd`
\|\|	chr16 Non dedup	Proportion of reads mapping to chr16	`chr16_ndd`
\|\|	chr17 Non dedup	Proportion of reads mapping to chr17	`chr17_ndd`
\|\|	chr18 Non dedup	Proportion of reads mapping to chr18	`chr18_ndd`
\|\|	chr19 Non dedup	Proportion of reads mapping to chr19	`chr19_ndd`
\|\|	chr20 Non dedup	Proportion of reads mapping to chr20	`chr20_ndd`
\|\|	chr21 Non dedup	Proportion of reads mapping to chr21	`chr21_ndd`
\|\|	chr22 Non dedup	Proportion of reads mapping to chr22	`chr22_ndd`
\|\|	chrX Non dedup	Proportion of reads mapping to chrX	`chrX_ndd`
\|\|	chrY Non dedup	Proportion of reads mapping to chrY	`chrY_ndd`
\|\|	chrM Non dedup	Proportion of reads mapping to chrM	`chrM_ndd`
\|\|	Genome Territory Non dedup	WgsMetricsAlgo: The number of non-N bases in the genome reference over which coverage will be evaluated.	`GENOME_TERRITORY_ndd`
\|\|	Mean Coverage Non dedup	WgsMetricsAlgo: The mean coverage in bases of the genome territory, after all filters are applied.	`MEAN_COVERAGE_ndd`
\|\|	SD Coverage Non dedup	WgsMetricsAlgo: The standard deviation of coverage of the genome after all filters are applied.	`SD_COVERAGE_ndd`
\|\|	Median Coverage Non dedup	WgsMetricsAlgo: The median coverage in bases of the genome territory, after all filters are applied.	`MEDIAN_COVERAGE_ndd`
\|\|	MAD Coverage Non dedup	WgsMetricsAlgo: The median absolute deviation of coverage of the genome after all filters are applied.	`MAD_COVERAGE_ndd`
\|\|	Proportion Bases with low MAPQ Non dedup	WgsMetricsAlgo: The fraction of aligned bases that were filtered out because they were in reads with low mapping quality (default is < 20).	`PCT_EXC_MAPQ_ndd`
\|\|	Proportion Bases with Duplicates Non dedup	WgsMetricsAlgo: The fraction of aligned bases that were filtered out because they were in reads marked as duplicates.	`PCT_EXC_DUPE_ndd`
\|\|	Proportion Bases Unpaired Non dedup	WgsMetricsAlgo: The fraction of aligned bases that were filtered out because they were in reads without a mapped mate pair.	`PCT_EXC_UNPAIRED_ndd`
\|\|	Proportion Bases with low BASEQ Non dedup	WgsMetricsAlgo: The fraction of aligned bases that were filtered out because they were of low base quality (default is < 20).	`PCT_EXC_BASEQ_ndd`
\|\|	Proportion Bases with Overlap Non dedup	WgsMetricsAlgo: The fraction of aligned bases that were filtered out because they were the second observation from an insert with overlapping reads.	`PCT_EXC_OVERLAP_ndd`
\|\|	Proportion Bases above Capped Non dedup	WgsMetricsAlgo: The fraction of aligned bases that were filtered out because they would have raised coverage above the capped value (default cap = 250x).	`PCT_EXC_CAPPED_ndd`
\|\|	Proportion Bases Excluded in Total Non dedup	WgsMetricsAlgo: The total fraction of aligned bases excluded due to all filters.	`PCT_EXC_TOTAL_ndd`
\|\|	Proportion Bases > 1x Non dedup	WgsMetricsAlgo: The fraction of bases that attained at least 1X sequence coverage in post-filtering bases.	`PCT_1X_ndd`
\|\|	Proportion Bases > 5x Non dedup	WgsMetricsAlgo: The fraction of bases that attained at least 5X sequence coverage in post-filtering bases.	`PCT_5X_ndd`
\|\|	HET SNP Sensitivity Non dedup	WgsMetricsAlgo: The theoretical HET SNP sensitivity.	`HET_SNP_SENSITIVITY_ndd`
\|\|	HET SNP Phred Scaled Q Score Non dedup	WgsMetricsAlgo: The Phred Scaled Q Score of the theoretical HET SNP sensitivity.	`HET_SNP_Q_ndd`
\|\|	Window Size on the genome Non dedup	GCBias: The window size on the genome used to calculate the GC of the sequence.	`WINDOW_SIZE_ndd`
\|\|	Total Clusters seen in GC Bias Non dedup	GCBias: The total number of clusters that were seen in the gc bias calculation.	`TOTAL_CLUSTERS_ndd`
\|\|	Reads Used by GC Bias Algo Non dedup	GCBias: The total number of aligned reads used to compute the gc bias metrics.	`ALIGNED_READS_ndd`
\|\|	AT Dropout Non dedup	GCBias: Illumina-style AT dropout metric. Calculated by taking each GC bin independently and calculating (%ref_at_gc - %reads_at_gc) and summing all positive values for GC=[0..50].	`AT_DROPOUT_ndd`
\|\|	GC Dropout Non dedup	GCBias: Illumina-style GC dropout metric. Calculated by taking each GC bin independently and calculating (%ref_at_gc - %reads_at_gc) and summing all positive values for GC=[50..100].	`GC_DROPOUT_ndd`
\|\|	NC GC 0-19 Non dedup	GCBias: Normalized coverage over quintile of GC content ranging from 0 - 19.	`GC_NC_0_19_ndd`
\|\|	NC GC 20-39 Non dedup	GCBias: Normalized coverage over quintile of GC content ranging from 20 - 39.	`GC_NC_20_39_ndd`
\|\|	NC GC 40-59 Non dedup	GCBias: Normalized coverage over quintile of GC content ranging from 40 - 59.	`GC_NC_40_59_ndd`
\|\|	NC GC 60-79 Non dedup	GCBias: Normalized coverage over quintile of GC content ranging from 60 - 79.	`GC_NC_60_79_ndd`
\|\|	NC GC 80-100 Non dedup	GCBias: Normalized coverage over quintile of GC content ranging from 80 - 100.	`GC_NC_80_100_ndd`
\|\|	Median Insert Size Non dedup	InsertSizeMetricAlgo: The MEDIAN insert size of all paired end reads where both ends mapped to the same chromosome.	`MEDIAN_INSERT_SIZE_ndd`
\|\|	Median Absolute Deviation Non dedup	InsertSizeMetricAlgo: The median absolute deviation of the distribution. If the distribution is essentially normal then the standard deviation can be estimated as ~1.4826 * MAD.	`MEDIAN_ABSOLUTE_DEVIATION_ndd`
\|\|	Min Insert Size Non dedup	InsertSizeMetricAlgo: The minimum measured insert size. This is usually 1 and not very useful as it is likely artifactual.	`MIN_INSERT_SIZE_ndd`
\|\|	Max Insert Size Non dedup	InsertSizeMetricAlgo: The maximum measure insert size by alignment. This is usually very high representing either an artifact or possibly the presence of a structural re-arrangement.	`MAX_INSERT_SIZE_ndd`
\|\|	Mean Insert Size Non dedup	InsertSizeMetricAlgo: The mean insert size of the'core' of the distribution. Artefactual outliers in the distribution often cause calculation of nonsensical mean and stdev values. To avoid this the distribution is first trimmed to a 'core' distribution of +/- N median absolute deviations around the median insert size. By default N=10, but this is configurable.	`MEAN_INSERT_SIZE_ndd`
\|\|	Standard Deviation Non dedup	InsertSizeMetricAlgo: Standard deviation of insert sizes over the 'core' of the distribution.	`STANDARD_DEVIATION_ndd`
\|\|	Read Pairs Non dedup	InsertSizeMetricAlgo: The total number of read pairs that were examined in the entire distribution.	`READ_PAIRS_ndd`
\|\|	Pair Orientation Non dedup	InsertSizeMetricAlgo: The pair orientation of the reads in this data category.	`PAIR_ORIENTATION_ndd`
\|\|	Flag	Flag highlights potential issue processing the biosample.	`Flag`

fastp

All-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...).URL: https://github.com/OpenGene/fastpDOI: 10.1093/bioinformatics/bty560

Fastp goes through fastq files in a folder and perform a series of quality control and filtering. Quality control and reporting are displayed both before and after filtering, allowing for a clear depiction of the consequences of the filtering process. Notably, the latter can be conducted on a variety of parameters including quality scores, length, as well as the presence of adapters, polyG, or polyX tailing.

Filtered Reads

Filtering statistics of sampled reads.

Created with MultiQC

Duplication Rates

Duplication rates of sampled reads.

Created with MultiQC

Insert Sizes

Insert size estimation of sampled reads.

Created with MultiQC

Sequence Quality

Average sequencing quality over each base of all reads.

Created with MultiQC

GC Content

Average GC content over each base of all reads.

Created with MultiQC

N content

Average N content over each base of all reads.

Created with MultiQC

QC composition

CNV Quadrants

Software Versions

Software Versions lists versions of software tools extracted from file contents.

Pipeline	Software	Version
BJ-DNA-QC	Ginkgo	`0.0.2`
	Preseq	`2.0.3`
	Sentieon	`202308.01`
	Seqtk	`1.3-r106`
	bam-lorenz-coverage	`2.3.0 GNU`
	bedtools	`v2.28.0`
	fastp	`0.20.1`

v1.28

MultiQC Toolbox

Highlight Samples

Rename Samples

Show / Hide Samples

Explain with AI

Export Plots

Choose Plots

Save Settings

Load Settings

Tool Citations

About MultiQC

BJ-DNA-QC v2.1.0

General Statistics

Selected Metrics

All Metrics

fastp

Filtered Reads

Duplication Rates

Insert Sizes

Sequence Quality

GC Content

N content

QC composition

CNV Quadrants

Software Versions

Toggle navigation v1.28

MultiQC Toolbox

Apply Highlight Samples

Apply Rename Samples

Apply Show / Hide Samples

Explain with AI

Export Plots

Choose Plots

Save Settings

Load Settings

Tool Citations

About MultiQC

BJ-DNA-QC v2.1.0

General Statistics

General Statistics: Columns

Selected Metrics

Selected Metrics: Columns

All Metrics

All Metrics: Columns

fastp

Filtered Reads

Duplication Rates

Insert Sizes

Sequence Quality

GC Content

N content

QC composition

CNV Quadrants

Software Versions

v1.28

Highlight Samples

Rename Samples

Show / Hide Samples