BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716427.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,537,164 number of mapped reads = 1,420,513 (92.41%) number of supplementary alignments = 5,448 (0.35%) number of secondary alignments = 0 number of mapped bases = 83,134,553 bp number of sequenced bases = 83,108,537 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,867 duplication rate = 3.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.907 >>>>>>> ACTG content number of A's = 20,446,728 bp (24.6%) number of C's = 14,991,917 bp (18.04%) number of T's = 25,948,506 bp (31.22%) number of G's = 21,719,815 bp (26.13%) number of N's = 1,571 bp (0%) GC percentage = 44.17% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 416,648 number of insertions = 6,236 mapped reads with insertion percentage = 0.44% number of deletions = 15,980 mapped reads with deletion percentage = 1.12% homopolymer indels = 42.27% >>>>>>> Coverage mean coverageData = 0.0269X std coverageData = 0.266X There is a 2.41% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 6992299 0.02805328617415962 0.39689352093243885 chr2 243199373 6533174 0.026863449191540472 0.3808497656142275 chr3 198022430 4699386 0.02373158434627835 0.16763788102529367 chr4 191154276 5067307 0.0265089910936651 0.22525189703526682 chr5 180915260 4611887 0.025491973424464028 0.17364635757641383 chr6 171115067 4379413 0.02559338038888183 0.19717528753868044 chr7 159138663 4694257 0.029497903975729645 0.3131766082525953 chr8 146364022 4363621 0.02981348107528775 0.34802918061006444 chr9 141213431 2705121 0.01915625858562986 0.1820527641912672 chr10 135534747 3680721 0.02715702859577404 0.30076539481122183 chr11 135006516 2930038 0.02170293765672762 0.19587424287772878 chr12 133851895 4105167 0.030669472404555795 0.19126909267553857 chr13 115169878 2447247 0.021249019643834303 0.1609257960767205 chr14 107349540 2775155 0.02585157793875968 0.1779728603813783 chr15 102531392 3072449 0.029965934725630177 0.18737457835905993 chr16 90354753 2897310 0.032065939021492317 0.20425073491394596 chr17 81195210 3668913 0.04518632318335035 0.24287937390971437 chr18 78077248 1539217 0.019714027318175967 0.3058349558611903 chr19 59128983 2221108 0.037563778155967946 0.33429839786574894 chr20 63025520 2809066 0.044570294699670866 0.24050156986904137 chr21 48129895 1066425 0.022157226812981826 0.20894170065371717 chr22 51304566 787476 0.015349043202119671 0.13417526963293983 chrMT 16571 298494 18.013034819866032 10.898579263389227 chrX 155270560 4450555 0.028663225018316415 0.19594121094957193 chrY 59373566 338747 0.005705350424800154 0.26790525173408364