BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054571.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 14,204,440 number of mapped reads = 10,656,965 (75.03%) number of supplementary alignments = 312 (0%) number of secondary alignments = 0 number of mapped bases = 501,273,052 bp number of sequenced bases = 501,167,835 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,822,223 duplication rate = 24.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8723 >>>>>>> ACTG content number of A's = 152,770,684 bp (30.48%) number of C's = 97,851,221 bp (19.52%) number of T's = 147,977,873 bp (29.53%) number of G's = 102,478,171 bp (20.45%) number of N's = 89,886 bp (0.02%) GC percentage = 39.97% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 2,733,974 number of insertions = 22,645 mapped reads with insertion percentage = 0.21% number of deletions = 71,882 mapped reads with deletion percentage = 0.67% homopolymer indels = 47.93% >>>>>>> Coverage mean coverageData = 0.1619X std coverageData = 1.474X There is a 4.85% of reference with a coverageData >= 1X There is a 2.36% of reference with a coverageData >= 2X There is a 1.56% of reference with a coverageData >= 3X There is a 1.15% of reference with a coverageData >= 4X There is a 0.89% of reference with a coverageData >= 5X There is a 0.7% of reference with a coverageData >= 6X There is a 0.57% of reference with a coverageData >= 7X There is a 0.47% of reference with a coverageData >= 8X There is a 0.4% of reference with a coverageData >= 9X There is a 0.34% of reference with a coverageData >= 10X There is a 0.29% of reference with a coverageData >= 11X There is a 0.25% of reference with a coverageData >= 12X There is a 0.22% of reference with a coverageData >= 13X There is a 0.19% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.13% of reference with a coverageData >= 17X There is a 0.12% of reference with a coverageData >= 18X There is a 0.11% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.08% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 41186888 0.165242870147152 1.571563569417097 chr2 243199373 54196897 0.22284965759348402 1.7900344707235931 chr3 198022430 32734183 0.1653054302989818 1.414654451095137 chr4 191154276 24632838 0.12886365147280304 1.2472648469058476 chr5 180915260 25693170 0.14201770486359194 1.3020762066336748 chr6 171115067 31712416 0.18532801673157162 1.6199347423969976 chr7 159138663 25971418 0.16319992584077447 1.5551445336034089 chr8 146364022 30484788 0.20828061147431437 1.7380882082519231 chr9 141213431 26042029 0.18441609141272122 1.5622325752810577 chr10 135534747 17375645 0.12820066724291743 1.283450283109338 chr11 135006516 23959223 0.17746716017766134 1.5448323640506207 chr12 133851895 27156784 0.2028868100821434 1.623064126423879 chr13 115169878 12522761 0.10873295359399443 1.1161492006311184 chr14 107349540 9820226 0.09147897606268271 1.125619839545968 chr15 102531392 11838230 0.11545956578839776 1.1310720610701752 chr16 90354753 11949237 0.1322480179874987 1.3183801752627018 chr17 81195210 11559536 0.1423672159971013 1.2724443428152434 chr18 78077248 15852768 0.20303953336060204 1.7078665265674444 chr19 59128983 10688136 0.18075967922533015 1.582434446111454 chr20 63025520 10612507 0.16838428306501874 1.4955226060104965 chr21 48129895 4855583 0.10088496972619616 1.0893986983577868 chr22 51304566 6244737 0.12171893238508245 1.1777703237862125 chrMT 16571 34534 2.0840021724699778 5.6856706147794265 chrX 155270560 33023787 0.21268543760001896 1.7064477716438997 chrY 59373566 1124731 0.018943295405231344 0.40657915624271973