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MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

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MultiQC is published in Bioinformatics:

MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

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Report generated on 2026-02-28, 03:24 UTC based on data in: /tmp/nxf.LobybUAFbw

hap.py

Benchmarks variant calls against gold standard truth datasets.URL: https://github.com/Illumina/hap.py

INDEL

The default shown fields should give the best overview of quality, but there are many other hidden fields available.

No plots are generated, as hap.py is generally run on single control samples (NA12878, etc.)

Ideally, precision, recall and F1 Score should all be as close to 1 as possible.

Showing ⁶⁰/₆₀ rows and ⁴/₁₆ columns.

Sample Name	Recall	Precision	Fraction NA	F1 Score	Truth: Total	Truth: True Positive	Truth: False Negative	Query: Total	Query: False Positive	Query: Unknown	False Positive genotype	False Positive allele	Truth: Total het/hom ratio	Query: Total het/hom ratio
exome-2_HG003.happy_INDEL_ALL	0.9743	0.9924	0.2896	0.9833	1051	1024	27	1485	8	430	5	2	1.7473	1.7969
exome-2_HG003.happy_INDEL_PASS	0.9743	0.9924	0.2896	0.9833	1051	1024	27	1485	8	430	5	2	1.7473	1.7969
exome-3_HG003.happy_INDEL_ALL	0.9743	0.9924	0.2896	0.9833	1051	1024	27	1485	8	430	5	2	1.7473	1.7969
exome-3_HG003.happy_INDEL_PASS	0.9743	0.9924	0.2896	0.9833	1051	1024	27	1485	8	430	5	2	1.7473	1.7969
exome-4_HG003.happy_INDEL_ALL	0.9743	0.9924	0.2896	0.9833	1051	1024	27	1485	8	430	5	2	1.7473	1.7969
exome-4_HG003.happy_INDEL_PASS	0.9743	0.9924	0.2896	0.9833	1051	1024	27	1485	8	430	5	2	1.7473	1.7969
exome-5_HG003.happy_INDEL_ALL	0.9743	0.9924	0.2896	0.9833	1051	1024	27	1485	8	430	5	2	1.7473	1.7969
exome-5_HG003.happy_INDEL_PASS	0.9743	0.9924	0.2896	0.9833	1051	1024	27	1485	8	430	5	2	1.7473	1.7969
exome_HG003.happy_INDEL_ALL	0.9743	0.9924	0.2896	0.9833	1051	1024	27	1485	8	430	5	2	1.7473	1.7969
exome_HG003.happy_INDEL_PASS	0.9743	0.9924	0.2896	0.9833	1051	1024	27	1485	8	430	5	2	1.7473	1.7969
hybrid-pacbio-illumina-2_HG003.happy_INDEL_ALL	0.9975	0.9961	0.4690	0.9968	504501	503264	1237	998274	2052	468220	546	1406	1.4898	2.1566
hybrid-pacbio-illumina-2_HG003.happy_INDEL_PASS	0.9975	0.9961	0.4690	0.9968	504501	503264	1237	998274	2052	468220	546	1406	1.4898	2.1566
hybrid-pacbio-illumina-3_HG003.happy_INDEL_ALL	0.9975	0.9961	0.4690	0.9968	504501	503264	1237	998274	2052	468220	546	1406	1.4898	2.1566
hybrid-pacbio-illumina-3_HG003.happy_INDEL_PASS	0.9975	0.9961	0.4690	0.9968	504501	503264	1237	998274	2052	468220	546	1406	1.4898	2.1566
hybrid-pacbio-illumina-4_HG003.happy_INDEL_ALL	0.9975	0.9961	0.4690	0.9968	504501	503264	1237	998274	2052	468220	546	1406	1.4898	2.1566
hybrid-pacbio-illumina-4_HG003.happy_INDEL_PASS	0.9975	0.9961	0.4690	0.9968	504501	503264	1237	998274	2052	468220	546	1406	1.4898	2.1566
hybrid-pacbio-illumina-5_HG003.happy_INDEL_ALL	0.9975	0.9961	0.4690	0.9968	504501	503264	1237	998274	2052	468220	546	1406	1.4898	2.1566
hybrid-pacbio-illumina-5_HG003.happy_INDEL_PASS	0.9975	0.9961	0.4690	0.9968	504501	503264	1237	998274	2052	468220	546	1406	1.4898	2.1566
hybrid-pacbio-illumina_HG003.happy_INDEL_ALL	0.9975	0.9961	0.4690	0.9968	504501	503264	1237	998274	2052	468220	546	1406	1.4898	2.1566
hybrid-pacbio-illumina_HG003.happy_INDEL_PASS	0.9975	0.9961	0.4690	0.9968	504501	503264	1237	998274	2052	468220	546	1406	1.4898	2.1566
ont-r104-2_HG003.happy_INDEL_ALL	0.9125	0.9487	0.3971	0.9302	504501	460355	44146	830072	25676	329618	11428	8972	1.4898	1.5087
ont-r104-2_HG003.happy_INDEL_PASS	0.9125	0.9487	0.3971	0.9302	504501	460355	44146	830072	25676	329618	11428	8972	1.4898	1.5087
ont-r104-3_HG003.happy_INDEL_ALL	0.9125	0.9487	0.3971	0.9302	504501	460355	44146	830072	25676	329618	11428	8972	1.4898	1.5087
ont-r104-3_HG003.happy_INDEL_PASS	0.9125	0.9487	0.3971	0.9302	504501	460355	44146	830072	25676	329618	11428	8972	1.4898	1.5087
ont-r104-4_HG003.happy_INDEL_ALL	0.9125	0.9487	0.3971	0.9302	504501	460355	44146	830072	25676	329618	11428	8972	1.4898	1.5087
ont-r104-4_HG003.happy_INDEL_PASS	0.9125	0.9487	0.3971	0.9302	504501	460355	44146	830072	25676	329618	11428	8972	1.4898	1.5087
ont-r104-5_HG003.happy_INDEL_ALL	0.9125	0.9487	0.3971	0.9302	504501	460355	44146	830072	25676	329618	11428	8972	1.4898	1.5087
ont-r104-5_HG003.happy_INDEL_PASS	0.9125	0.9487	0.3971	0.9302	504501	460355	44146	830072	25676	329618	11428	8972	1.4898	1.5087
ont-r104_HG003.happy_INDEL_ALL	0.9125	0.9487	0.3971	0.9302	504501	460355	44146	830072	25676	329618	11428	8972	1.4898	1.5087
ont-r104_HG003.happy_INDEL_PASS	0.9125	0.9487	0.3971	0.9302	504501	460355	44146	830072	25676	329618	11428	8972	1.4898	1.5087
pacbio-2_HG003.happy_INDEL_ALL	0.9942	0.9942	0.4711	0.9942	504501	501567	2934	989958	3057	466322	1561	1062	1.4898	1.9155
pacbio-2_HG003.happy_INDEL_PASS	0.9942	0.9942	0.4711	0.9942	504501	501567	2934	989958	3057	466322	1561	1062	1.4898	1.9155
pacbio-3_HG003.happy_INDEL_ALL	0.9942	0.9942	0.4711	0.9942	504501	501567	2934	989958	3057	466322	1561	1062	1.4898	1.9155
pacbio-3_HG003.happy_INDEL_PASS	0.9942	0.9942	0.4711	0.9942	504501	501567	2934	989958	3057	466322	1561	1062	1.4898	1.9155
pacbio-4_HG003.happy_INDEL_ALL	0.9942	0.9942	0.4711	0.9942	504501	501567	2934	989958	3057	466322	1561	1062	1.4898	1.9155
pacbio-4_HG003.happy_INDEL_PASS	0.9942	0.9942	0.4711	0.9942	504501	501567	2934	989958	3057	466322	1561	1062	1.4898	1.9155
pacbio-5_HG003.happy_INDEL_ALL	0.9942	0.9942	0.4711	0.9942	504501	501567	2934	989958	3057	466322	1561	1062	1.4898	1.9155
pacbio-5_HG003.happy_INDEL_PASS	0.9942	0.9942	0.4711	0.9942	504501	501567	2934	989958	3057	466322	1561	1062	1.4898	1.9155
pacbio_HG003.happy_INDEL_ALL	0.9942	0.9942	0.4711	0.9942	504501	501567	2934	989958	3057	466322	1561	1062	1.4898	1.9155
pacbio_HG003.happy_INDEL_PASS	0.9942	0.9942	0.4711	0.9942	504501	501567	2934	989958	3057	466322	1561	1062	1.4898	1.9155
rnaseq-2_HG005.happy_INDEL_ALL	0.8032	0.8105	0.3333	0.8068	188	151	37	285	36	95	5	3	1.4865	1.8218
rnaseq-2_HG005.happy_INDEL_PASS	0.8032	0.8105	0.3333	0.8068	188	151	37	285	36	95	5	3	1.4865	1.8218
rnaseq-3_HG005.happy_INDEL_ALL	0.8032	0.8105	0.3333	0.8068	188	151	37	285	36	95	5	3	1.4865	1.8218
rnaseq-3_HG005.happy_INDEL_PASS	0.8032	0.8105	0.3333	0.8068	188	151	37	285	36	95	5	3	1.4865	1.8218
rnaseq-4_HG005.happy_INDEL_ALL	0.8032	0.8105	0.3333	0.8068	188	151	37	285	36	95	5	3	1.4865	1.8218
rnaseq-4_HG005.happy_INDEL_PASS	0.8032	0.8105	0.3333	0.8068	188	151	37	285	36	95	5	3	1.4865	1.8218
rnaseq-5_HG005.happy_INDEL_ALL	0.8032	0.8105	0.3333	0.8068	188	151	37	285	36	95	5	3	1.4865	1.8218
rnaseq-5_HG005.happy_INDEL_PASS	0.8032	0.8105	0.3333	0.8068	188	151	37	285	36	95	5	3	1.4865	1.8218
rnaseq_HG005.happy_INDEL_ALL	0.8032	0.8105	0.3333	0.8068	188	151	37	285	36	95	5	3	1.4865	1.8218
rnaseq_HG005.happy_INDEL_PASS	0.8032	0.8105	0.3333	0.8068	188	151	37	285	36	95	5	3	1.4865	1.8218
wgs-2_HG003.happy_INDEL_ALL	0.9942	0.9977	0.4414	0.9960	504501	501594	2907	937937	1190	414010	765	212	1.4898	1.9334
wgs-2_HG003.happy_INDEL_PASS	0.9942	0.9977	0.4414	0.9960	504501	501594	2907	937937	1190	414010	765	212	1.4898	1.9334
wgs-3_HG003.happy_INDEL_ALL	0.9942	0.9977	0.4414	0.9960	504501	501594	2907	937937	1190	414010	765	212	1.4898	1.9334
wgs-3_HG003.happy_INDEL_PASS	0.9942	0.9977	0.4414	0.9960	504501	501594	2907	937937	1190	414010	765	212	1.4898	1.9334
wgs-4_HG003.happy_INDEL_ALL	0.9942	0.9977	0.4414	0.9960	504501	501594	2907	937937	1190	414010	765	212	1.4898	1.9334
wgs-4_HG003.happy_INDEL_PASS	0.9942	0.9977	0.4414	0.9960	504501	501594	2907	937937	1190	414010	765	212	1.4898	1.9334
wgs-5_HG003.happy_INDEL_ALL	0.9942	0.9977	0.4414	0.9960	504501	501594	2907	937937	1190	414010	765	212	1.4898	1.9334
wgs-5_HG003.happy_INDEL_PASS	0.9942	0.9977	0.4414	0.9960	504501	501594	2907	937937	1190	414010	765	212	1.4898	1.9334
wgs_HG003.happy_INDEL_ALL	0.9942	0.9977	0.4414	0.9960	504501	501594	2907	937937	1190	414010	765	212	1.4898	1.9334
wgs_HG003.happy_INDEL_PASS	0.9942	0.9977	0.4414	0.9960	504501	501594	2907	937937	1190	414010	765	212	1.4898	1.9334

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

Sort	Column	Description	ID
\|\|	Recall	Recall for truth variant representation = TRUTH.TP / (TRUTH.TP + TRUTH.FN)	`METRIC_Recall_indel`
\|\|	Precision	Precision of query variants = QUERY.TP / (QUERY.TP + QUERY.FP)	`METRIC_Precision_indel`
\|\|	Fraction NA	Fraction of non-assessed query calls = QUERY.UNK / QUERY.TOTAL	`METRIC_Frac_NA_indel`
\|\|	F1 Score	Harmonic mean of precision and recall = 2METRIC.RecallMetric.Precision/(METRIC.Recall + METRIC.Precision)	`METRIC_F1_Score_indel`
\|\|	Truth: Total	Total number of truth variants	`TRUTH_TOTAL_indel`
\|\|	Truth: True Positive	Number of true-positive calls in truth representation (counted via the truth sample column)	`TRUTH_TP_indel`
\|\|	Truth: False Negative	Number of false-negative calls = calls in truth without matching query call	`TRUTH_FN_indel`
\|\|	Query: Total	Total number of query calls	`QUERY_TOTAL_indel`
\|\|	Query: False Positive	Number of false-positive calls in the query file (mismatched query calls within the confident regions)	`QUERY_FP_indel`
\|\|	Query: Unknown	Number of query calls outside the confident regions	`QUERY_UNK_indel`
\|\|	False Positive genotype	Number of genotype mismatches (alleles match, but different zygosity)	`FP_gt_indel`
\|\|	False Positive allele	Number of allele mismatches (variants matched by position and not by haplotype)	`FP_al_indel`
\|\|	Truth: Total TiTv ratio	Transition / Transversion ratio for all truth variants	`TRUTH_TOTAL_TiTv_ratio_indel`
\|\|	Truth: Total het/hom ratio	Het/Hom ratio for all truth variants	`TRUTH_TOTAL_het_hom_ratio_indel`
\|\|	Query: total TiTv ratio	Transition / Transversion ratio for all query variants	`QUERY_TOTAL_TiTv_ratio_indel`
\|\|	Query: Total het/hom ratio	Het/Hom ratio for all query variants	`QUERY_TOTAL_het_hom_ratio_indel`

SNP

The default shown fields should give the best overview of quality, but there are many other hidden fields available.

No plots are generated, as hap.py is generally run on single control samples (NA12878, etc.)

Ideally, precision, recall and F1 Score should all be as close to 1 as possible.

Showing ⁶⁰/₆₀ rows and ⁴/₁₆ columns.

Sample Name	Recall	Precision	Fraction NA	F1 Score	Truth: Total	Truth: True Positive	Truth: False Negative	Query: Total	Query: False Positive	Query: Unknown	False Positive genotype	False Positive allele	Truth: Total TiTv ratio	Truth: Total het/hom ratio	Query: total TiTv ratio	Query: Total het/hom ratio
exome-2_HG003.happy_SNP_ALL	0.9883	0.9976	0.0962	0.9929	25279	24983	296	27709	60	2665	36	4	2.8547	1.6230	2.7613	1.6288
exome-2_HG003.happy_SNP_PASS	0.9883	0.9976	0.0962	0.9929	25279	24983	296	27709	60	2665	36	4	2.8547	1.6230	2.7613	1.6288
exome-3_HG003.happy_SNP_ALL	0.9883	0.9976	0.0962	0.9929	25279	24983	296	27709	60	2665	36	4	2.8547	1.6230	2.7613	1.6288
exome-3_HG003.happy_SNP_PASS	0.9883	0.9976	0.0962	0.9929	25279	24983	296	27709	60	2665	36	4	2.8547	1.6230	2.7613	1.6288
exome-4_HG003.happy_SNP_ALL	0.9883	0.9976	0.0962	0.9929	25279	24983	296	27709	60	2665	36	4	2.8547	1.6230	2.7613	1.6288
exome-4_HG003.happy_SNP_PASS	0.9883	0.9976	0.0962	0.9929	25279	24983	296	27709	60	2665	36	4	2.8547	1.6230	2.7613	1.6288
exome-5_HG003.happy_SNP_ALL	0.9883	0.9976	0.0962	0.9929	25279	24983	296	27709	60	2665	36	4	2.8547	1.6230	2.7613	1.6288
exome-5_HG003.happy_SNP_PASS	0.9883	0.9976	0.0962	0.9929	25279	24983	296	27709	60	2665	36	4	2.8547	1.6230	2.7613	1.6288
exome_HG003.happy_SNP_ALL	0.9883	0.9976	0.0962	0.9929	25279	24983	296	27709	60	2665	36	4	2.8547	1.6230	2.7613	1.6288
exome_HG003.happy_SNP_PASS	0.9883	0.9976	0.0962	0.9929	25279	24983	296	27709	60	2665	36	4	2.8547	1.6230	2.7613	1.6288
hybrid-pacbio-illumina-2_HG003.happy_SNP_ALL	0.9990	0.9994	0.1821	0.9992	3327495	3324021	3474	4068058	1856	740734	779	480	2.1026	1.5351	1.9217	1.5780
hybrid-pacbio-illumina-2_HG003.happy_SNP_PASS	0.9990	0.9994	0.1821	0.9992	3327495	3324021	3474	4068058	1856	740734	779	480	2.1026	1.5351	1.9217	1.5780
hybrid-pacbio-illumina-3_HG003.happy_SNP_ALL	0.9990	0.9994	0.1821	0.9992	3327495	3324021	3474	4068058	1856	740734	779	480	2.1026	1.5351	1.9217	1.5780
hybrid-pacbio-illumina-3_HG003.happy_SNP_PASS	0.9990	0.9994	0.1821	0.9992	3327495	3324021	3474	4068058	1856	740734	779	480	2.1026	1.5351	1.9217	1.5780
hybrid-pacbio-illumina-4_HG003.happy_SNP_ALL	0.9990	0.9994	0.1821	0.9992	3327495	3324021	3474	4068058	1856	740734	779	480	2.1026	1.5351	1.9217	1.5780
hybrid-pacbio-illumina-4_HG003.happy_SNP_PASS	0.9990	0.9994	0.1821	0.9992	3327495	3324021	3474	4068058	1856	740734	779	480	2.1026	1.5351	1.9217	1.5780
hybrid-pacbio-illumina-5_HG003.happy_SNP_ALL	0.9990	0.9994	0.1821	0.9992	3327495	3324021	3474	4068058	1856	740734	779	480	2.1026	1.5351	1.9217	1.5780
hybrid-pacbio-illumina-5_HG003.happy_SNP_PASS	0.9990	0.9994	0.1821	0.9992	3327495	3324021	3474	4068058	1856	740734	779	480	2.1026	1.5351	1.9217	1.5780
hybrid-pacbio-illumina_HG003.happy_SNP_ALL	0.9990	0.9994	0.1821	0.9992	3327495	3324021	3474	4068058	1856	740734	779	480	2.1026	1.5351	1.9217	1.5780
hybrid-pacbio-illumina_HG003.happy_SNP_PASS	0.9990	0.9994	0.1821	0.9992	3327495	3324021	3474	4068058	1856	740734	779	480	2.1026	1.5351	1.9217	1.5780
ont-r104-2_HG003.happy_SNP_ALL	0.9983	0.9986	0.2437	0.9985	3327495	3321799	5696	4400475	4611	1072196	636	852	2.1026	1.5351	1.7445	1.1180
ont-r104-2_HG003.happy_SNP_PASS	0.9983	0.9986	0.2437	0.9985	3327495	3321799	5696	4400475	4611	1072196	636	852	2.1026	1.5351	1.7445	1.1180
ont-r104-3_HG003.happy_SNP_ALL	0.9983	0.9986	0.2437	0.9985	3327495	3321799	5696	4400475	4611	1072196	636	852	2.1026	1.5351	1.7445	1.1180
ont-r104-3_HG003.happy_SNP_PASS	0.9983	0.9986	0.2437	0.9985	3327495	3321799	5696	4400475	4611	1072196	636	852	2.1026	1.5351	1.7445	1.1180
ont-r104-4_HG003.happy_SNP_ALL	0.9983	0.9986	0.2437	0.9985	3327495	3321799	5696	4400475	4611	1072196	636	852	2.1026	1.5351	1.7445	1.1180
ont-r104-4_HG003.happy_SNP_PASS	0.9983	0.9986	0.2437	0.9985	3327495	3321799	5696	4400475	4611	1072196	636	852	2.1026	1.5351	1.7445	1.1180
ont-r104-5_HG003.happy_SNP_ALL	0.9983	0.9986	0.2437	0.9985	3327495	3321799	5696	4400475	4611	1072196	636	852	2.1026	1.5351	1.7445	1.1180
ont-r104-5_HG003.happy_SNP_PASS	0.9983	0.9986	0.2437	0.9985	3327495	3321799	5696	4400475	4611	1072196	636	852	2.1026	1.5351	1.7445	1.1180
ont-r104_HG003.happy_SNP_ALL	0.9983	0.9986	0.2437	0.9985	3327495	3321799	5696	4400475	4611	1072196	636	852	2.1026	1.5351	1.7445	1.1180
ont-r104_HG003.happy_SNP_PASS	0.9983	0.9986	0.2437	0.9985	3327495	3321799	5696	4400475	4611	1072196	636	852	2.1026	1.5351	1.7445	1.1180
pacbio-2_HG003.happy_SNP_ALL	0.9983	0.9988	0.2308	0.9985	3327495	3321765	5730	4329942	4125	999338	552	415	2.1026	1.5351	1.7823	1.2405
pacbio-2_HG003.happy_SNP_PASS	0.9983	0.9988	0.2308	0.9985	3327495	3321765	5730	4329942	4125	999338	552	415	2.1026	1.5351	1.7823	1.2405
pacbio-3_HG003.happy_SNP_ALL	0.9983	0.9988	0.2308	0.9985	3327495	3321765	5730	4329942	4125	999338	552	415	2.1026	1.5351	1.7823	1.2405
pacbio-3_HG003.happy_SNP_PASS	0.9983	0.9988	0.2308	0.9985	3327495	3321765	5730	4329942	4125	999338	552	415	2.1026	1.5351	1.7823	1.2405
pacbio-4_HG003.happy_SNP_ALL	0.9983	0.9988	0.2308	0.9985	3327495	3321765	5730	4329942	4125	999338	552	415	2.1026	1.5351	1.7823	1.2405
pacbio-4_HG003.happy_SNP_PASS	0.9983	0.9988	0.2308	0.9985	3327495	3321765	5730	4329942	4125	999338	552	415	2.1026	1.5351	1.7823	1.2405
pacbio-5_HG003.happy_SNP_ALL	0.9983	0.9988	0.2308	0.9985	3327495	3321765	5730	4329942	4125	999338	552	415	2.1026	1.5351	1.7823	1.2405
pacbio-5_HG003.happy_SNP_PASS	0.9983	0.9988	0.2308	0.9985	3327495	3321765	5730	4329942	4125	999338	552	415	2.1026	1.5351	1.7823	1.2405
pacbio_HG003.happy_SNP_ALL	0.9983	0.9988	0.2308	0.9985	3327495	3321765	5730	4329942	4125	999338	552	415	2.1026	1.5351	1.7823	1.2405
pacbio_HG003.happy_SNP_PASS	0.9983	0.9988	0.2308	0.9985	3327495	3321765	5730	4329942	4125	999338	552	415	2.1026	1.5351	1.7823	1.2405
rnaseq-2_HG005.happy_SNP_ALL	0.9389	0.9646	0.1047	0.9516	11349	10656	693	12336	391	1291	111	9	3.1019	1.3861	3.0127	1.2990
rnaseq-2_HG005.happy_SNP_PASS	0.9389	0.9646	0.1047	0.9516	11349	10656	693	12336	391	1291	111	9	3.1019	1.3861	3.0127	1.2990
rnaseq-3_HG005.happy_SNP_ALL	0.9389	0.9646	0.1047	0.9516	11349	10656	693	12336	391	1291	111	9	3.1019	1.3861	3.0127	1.2990
rnaseq-3_HG005.happy_SNP_PASS	0.9389	0.9646	0.1047	0.9516	11349	10656	693	12336	391	1291	111	9	3.1019	1.3861	3.0127	1.2990
rnaseq-4_HG005.happy_SNP_ALL	0.9389	0.9646	0.1047	0.9516	11349	10656	693	12336	391	1291	111	9	3.1019	1.3861	3.0127	1.2990
rnaseq-4_HG005.happy_SNP_PASS	0.9389	0.9646	0.1047	0.9516	11349	10656	693	12336	391	1291	111	9	3.1019	1.3861	3.0127	1.2990
rnaseq-5_HG005.happy_SNP_ALL	0.9389	0.9646	0.1047	0.9516	11349	10656	693	12336	391	1291	111	9	3.1019	1.3861	3.0127	1.2990
rnaseq-5_HG005.happy_SNP_PASS	0.9389	0.9646	0.1047	0.9516	11349	10656	693	12336	391	1291	111	9	3.1019	1.3861	3.0127	1.2990
rnaseq_HG005.happy_SNP_ALL	0.9389	0.9646	0.1047	0.9516	11349	10656	693	12336	391	1291	111	9	3.1019	1.3861	3.0127	1.2990
rnaseq_HG005.happy_SNP_PASS	0.9389	0.9646	0.1047	0.9516	11349	10656	693	12336	391	1291	111	9	3.1019	1.3861	3.0127	1.2990
wgs-2_HG003.happy_SNP_ALL	0.9938	0.9985	0.1322	0.9961	3327496	3306720	20776	3817962	4880	504695	1444	490	2.1026	1.5351	1.9783	1.4436
wgs-2_HG003.happy_SNP_PASS	0.9938	0.9985	0.1322	0.9961	3327496	3306720	20776	3817962	4880	504695	1444	490	2.1026	1.5351	1.9783	1.4436
wgs-3_HG003.happy_SNP_ALL	0.9938	0.9985	0.1322	0.9961	3327496	3306720	20776	3817962	4880	504695	1444	490	2.1026	1.5351	1.9783	1.4436
wgs-3_HG003.happy_SNP_PASS	0.9938	0.9985	0.1322	0.9961	3327496	3306720	20776	3817962	4880	504695	1444	490	2.1026	1.5351	1.9783	1.4436
wgs-4_HG003.happy_SNP_ALL	0.9938	0.9985	0.1322	0.9961	3327496	3306720	20776	3817962	4880	504695	1444	490	2.1026	1.5351	1.9783	1.4436
wgs-4_HG003.happy_SNP_PASS	0.9938	0.9985	0.1322	0.9961	3327496	3306720	20776	3817962	4880	504695	1444	490	2.1026	1.5351	1.9783	1.4436
wgs-5_HG003.happy_SNP_ALL	0.9938	0.9985	0.1322	0.9961	3327496	3306720	20776	3817962	4880	504695	1444	490	2.1026	1.5351	1.9783	1.4436
wgs-5_HG003.happy_SNP_PASS	0.9938	0.9985	0.1322	0.9961	3327496	3306720	20776	3817962	4880	504695	1444	490	2.1026	1.5351	1.9783	1.4436
wgs_HG003.happy_SNP_ALL	0.9938	0.9985	0.1322	0.9961	3327496	3306720	20776	3817962	4880	504695	1444	490	2.1026	1.5351	1.9783	1.4436
wgs_HG003.happy_SNP_PASS	0.9938	0.9985	0.1322	0.9961	3327496	3306720	20776	3817962	4880	504695	1444	490	2.1026	1.5351	1.9783	1.4436

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

Sort	Column	Description	ID
\|\|	Recall	Recall for truth variant representation = TRUTH.TP / (TRUTH.TP + TRUTH.FN)	`METRIC_Recall_snp`
\|\|	Precision	Precision of query variants = QUERY.TP / (QUERY.TP + QUERY.FP)	`METRIC_Precision_snp`
\|\|	Fraction NA	Fraction of non-assessed query calls = QUERY.UNK / QUERY.TOTAL	`METRIC_Frac_NA_snp`
\|\|	F1 Score	Harmonic mean of precision and recall = 2METRIC.RecallMetric.Precision/(METRIC.Recall + METRIC.Precision)	`METRIC_F1_Score_snp`
\|\|	Truth: Total	Total number of truth variants	`TRUTH_TOTAL_snp`
\|\|	Truth: True Positive	Number of true-positive calls in truth representation (counted via the truth sample column)	`TRUTH_TP_snp`
\|\|	Truth: False Negative	Number of false-negative calls = calls in truth without matching query call	`TRUTH_FN_snp`
\|\|	Query: Total	Total number of query calls	`QUERY_TOTAL_snp`
\|\|	Query: False Positive	Number of false-positive calls in the query file (mismatched query calls within the confident regions)	`QUERY_FP_snp`
\|\|	Query: Unknown	Number of query calls outside the confident regions	`QUERY_UNK_snp`
\|\|	False Positive genotype	Number of genotype mismatches (alleles match, but different zygosity)	`FP_gt_snp`
\|\|	False Positive allele	Number of allele mismatches (variants matched by position and not by haplotype)	`FP_al_snp`
\|\|	Truth: Total TiTv ratio	Transition / Transversion ratio for all truth variants	`TRUTH_TOTAL_TiTv_ratio_snp`
\|\|	Truth: Total het/hom ratio	Het/Hom ratio for all truth variants	`TRUTH_TOTAL_het_hom_ratio_snp`
\|\|	Query: total TiTv ratio	Transition / Transversion ratio for all query variants	`QUERY_TOTAL_TiTv_ratio_snp`
\|\|	Query: Total het/hom ratio	Het/Hom ratio for all query variants	`QUERY_TOTAL_het_hom_ratio_snp`

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