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Diffstat (limited to 'test/check.chk')
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diff --git a/test/check.chk b/test/check.chk new file mode 100644 index 0000000..1012e5c --- /dev/null +++ b/test/check.chk @@ -0,0 +1,80 @@ +# +# Definition of sets: +# ID [2]id [3]tab-separated file names +# SN, Summary numbers: +# SN [2]id [3]key [4]value +SN 0 number of samples: 2 +SN 0 number of records: 18 +SN 0 number of SNPs: 5 +SN 0 number of MNPs: 1 +SN 0 number of indels: 9 +SN 0 number of others: 2 +SN 0 number of multiallelic sites: 6 +SN 0 number of multiallelic SNP sites: 1 +# TSTV, transitions/transversions: +# TSTV [2]id [3]ts [4]tv [5]ts/tv [6]ts (1st ALT) [7]tv (1st ALT) [8]ts/tv (1st ALT) +TSTV 0 3 2 1.50 3 1 3.00 +# SiS, Singleton stats: +# SiS [2]id [3]allele count [4]number of SNPs [5]number of transitions [6]number of transversions [7]number of indels [8]repeat-consistent [9]repeat-inconsistent [10]not applicable +SiS 0 1 3 1 2 0 0 0 0 +# AF, Stats by non-reference allele frequency: +# AF [2]id [3]allele frequency [4]number of SNPs [5]number of transitions [6]number of transversions [7]number of indels [8]repeat-consistent [9]repeat-inconsistent [10]not applicable +AF 0 0.000000 3 1 2 2 0 0 2 +AF 0 49.000000 0 0 0 12 0 0 12 +AF 0 74.000000 1 1 0 0 0 0 0 +AF 0 99.000000 1 1 0 0 0 0 0 +# QUAL, Stats by quality: +# QUAL [2]id [3]Quality [4]number of SNPs [5]number of transitions (1st ALT) [6]number of transversions (1st ALT) [7]number of indels +QUAL 0 12 1 0 1 1 +QUAL 0 45 0 0 0 1 +QUAL 0 59 2 1 0 3 +QUAL 0 60 1 1 0 0 +QUAL 0 61 0 0 0 1 +QUAL 0 79 0 0 0 1 +QUAL 0 82 0 0 0 1 +QUAL 0 90 1 1 0 0 +QUAL 0 342 0 0 0 1 +# IDD, InDel distribution: +# IDD [2]id [3]length (deletions negative) [4]count +IDD 0 -10 1 +IDD 0 -8 1 +IDD 0 -4 3 +IDD 0 -3 4 +IDD 0 -2 1 +IDD 0 -1 2 +IDD 0 1 1 +IDD 0 2 1 +# ST, Substitution types: +# ST [2]id [3]type [4]count +ST 0 A>C 0 +ST 0 A>G 0 +ST 0 A>T 0 +ST 0 C>A 0 +ST 0 C>G 0 +ST 0 C>T 0 +ST 0 G>A 3 +ST 0 G>C 1 +ST 0 G>T 1 +ST 0 T>A 0 +ST 0 T>C 0 +ST 0 T>G 0 +# DP, Depth distribution +# DP [2]id [3]bin [4]number of genotypes [5]fraction of genotypes (%) [6]number of sites [7]fraction of sites (%) +DP 0 10 2 5.555556 0 0.000000 +DP 0 21 2 5.555556 0 0.000000 +DP 0 22 2 5.555556 0 0.000000 +DP 0 26 4 11.111111 0 0.000000 +DP 0 30 2 5.555556 0 0.000000 +DP 0 31 16 44.444444 0 0.000000 +DP 0 32 4 11.111111 0 0.000000 +DP 0 35 4 11.111111 0 0.000000 +# PSC, Per-sample counts +# PSC [2]id [3]sample [4]nRefHom [5]nNonRefHom [6]nHets [7]nTransitions [8]nTransversions [9]nIndels [10]average depth [11]nSingletons +PSC 0 A 0 2 3 3 2 9 28.7 1 +PSC 0 B 1 1 3 2 2 9 28.7 0 +# HWE +# HWE [2]id [3]1st ALT allele frequency [4]Number of observations [5]25th percentile [6]median [7]75th percentile +HWE 0 0.000000 2 0.490000 0.490000 0.990000 +HWE 0 49.000000 14 0.990000 0.990000 0.990000 +HWE 0 74.000000 1 0.490000 0.490000 0.490000 +HWE 0 99.000000 1 0.000000 0.000000 0.000000 |