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# This file was generated by vcf-compare.
#
#VN 'Venn-Diagram Numbers'. Use `grep ^VN | cut -f 2-` to extract this part.
#VN The columns are:
#VN 1 .. number of sites unique to this particular combination of files
#VN 2- .. combination of files and space-separated number, a fraction of sites in the file
VN 6 cmp-test-a.vcf.gz (100.0%) cmp-test-b.vcf.gz (100.0%)
#SN Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.
SN Number of REF matches: 6
SN Number of ALT matches: 5
SN Number of REF mismatches: 0
SN Number of ALT mismatches: 1
SN Number of samples in GT comparison: 2
#GS Genotype Comparison Summary. Use `grep ^GS | cut -f 2-` to extract this part.
#GS The columns are:
#GS 1 .. variant type
#GS 2 .. number of mismatches
#GS 3 .. number of matches
#GS 4 .. discordance
GS hom_RR 0 3 0.00%
GS het_RA 1 3 25.00%
GS hom_AA 0 4 0.00%
GS het_AA 0 0 0.00%
SN Non-reference Discordance Rate (NDR): 12.50
SN Summary: NDR 12.50, RR 0.00, RA 25.00, AA 0.00
#GC Genotype Comparison. Use `grep ^GC | cut -f 2-` to extract this part.
#GC The columns are:
#GC 1 .. Sample
#GC 2-6 .. Gtype mismatches: total hom_RR hom_AA het_RA het_AA
#GC 7-9 .. Gtype lost: total het_RA het_AA
#GC 10-14 .. Gtype gained: total hom_RR hom_AA het_RA het_AA
#GC 15-17 .. Phase lost: total het_RA het_AA
#GC 18 .. Phase gained
#GC 19-23 .. Matching sites: total hom_RR hom_AA het_RA het_AA
#GC 24 .. Phased matches: het_RA
#GC 25 .. Misphased matches: het_RA
GC A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 4 2 0 2 1
GC B 1 0 0 1 0 0 0 0 1 1 0 0 0 0 0 0 0 4 3 0 1 0 0 0
#AF Number of matching and mismatching genotypes vs non-ref allele frequency. Use `^AF | cut -f 2-` to extract this part.
#AF The columns are:
#AF 1 .. Non-ref allele count
#AF 2 .. Hom(RR) matches
#AF 3 .. Het(RA) matches
#AF 4 .. Hom(AA) matches
#AF 5 .. Het(AA) matches
#AF 6 .. Hom(RR) mismatches
#AF 7 .. Het(RA) mismatches
#AF 8 .. Hom(AA) mismatches
#AF 9 .. Het(AA) mismatches
AF 0.25 1 1 0 0 0 0 0 0
AF 0.50 2 2 2 0 0 0 0 0
AF 0.75 0 0 1 0 0 1 0 0
AF 1.00 0 0 1 0 0 0 0 0
#DP Counts by depth. Use `grep ^DP | cut -f 2-` to extract this part.
#DP The columns are:
#DP 1 .. depth
#DP 2 .. RR matches
#DP 3 .. RA matches
#DP 4 .. AA matches
#DP 5 .. RR -> RA mismatches
#DP 6 .. RR -> AA mismatches
#DP 7 .. RA -> RR mismatches
#DP 8 .. RA -> AA mismatches
#DP 9 .. AA -> RR mismatches
#DP 10 .. AA -> RA mismatches
DP 1 3 3 4 0 0 1 0 0 0
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