BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068943.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,229,054 number of mapped reads = 1,910,859 (85.73%) number of supplementary alignments = 12,567 (0.56%) number of secondary alignments = 0 number of mapped bases = 125,459,005 bp number of sequenced bases = 125,405,150 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 66,231 duplication rate = 2.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2907 >>>>>>> ACTG content number of A's = 33,812,164 bp (26.96%) number of C's = 21,789,371 bp (17.38%) number of T's = 41,109,543 bp (32.78%) number of G's = 28,388,706 bp (22.64%) number of N's = 305,366 bp (0.24%) GC percentage = 40.01% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 1,204,426 number of insertions = 12,138 mapped reads with insertion percentage = 0.63% number of deletions = 32,486 mapped reads with deletion percentage = 1.68% homopolymer indels = 48.49% >>>>>>> Coverage mean coverageData = 0.0405X std coverageData = 0.4635X There is a 3.64% of reference with a coverageData >= 1X There is a 0.27% 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 9754126 0.039133808216269196 0.7782056302347458 chr2 243199373 11124754 0.04574334983996854 0.49705256804033315 chr3 198022430 9331918 0.04712556047312418 0.23262284925854912 chr4 191154276 6370192 0.03332487315115044 0.22560384177930157 chr5 180915260 6473850 0.03578388025421404 0.20776721030814446 chr6 171115067 9272094 0.054186309613518724 0.36304657463486534 chr7 159138663 8285239 0.05206301752076427 0.8541050849344457 chr8 146364022 6581218 0.04496472500598542 0.7388707933712898 chr9 141213431 6046178 0.04281588484313507 0.4968265255912438 chr10 135534747 6557352 0.048381335009243055 0.37709625774577 chr11 135006516 5947922 0.044056555018425925 0.4613964352544508 chr12 133851895 5396293 0.04031540233330279 0.2264754904160614 chr13 115169878 3036405 0.026364575987481726 0.17317744314490816 chr14 107349540 4224897 0.039356451830161544 0.24647144229343199 chr15 102531392 2776786 0.027082300804030828 0.17695017869391413 chr16 90354753 3448226 0.038163194359017286 0.25521359511289243 chr17 81195210 2983868 0.036749310704412244 0.25505412455284143 chr18 78077248 3414888 0.043737299757286525 0.8514212925079272 chr19 59128983 2262068 0.038256501046195907 0.5097481158444003 chr20 63025520 1838533 0.029171246821922295 0.1997055164806178 chr21 48129895 1929769 0.04009501786779298 0.2406510596014041 chr22 51304566 1072254 0.020899777224506685 0.15333835337831977 chrMT 16571 65568 3.956791985999638 2.9387042177750913 chrX 155270560 6949171 0.044755238855324536 0.28954025994836224 chrY 59373566 315436 0.005312734626719238 0.12839879032031415