BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008681.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 = 1,742,651 number of mapped reads = 1,515,327 (86.96%) number of supplementary alignments = 9,412 (0.54%) number of secondary alignments = 0 number of mapped bases = 96,803,814 bp number of sequenced bases = 96,761,290 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 56,535 duplication rate = 3.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7285 >>>>>>> ACTG content number of A's = 26,474,990 bp (27.36%) number of C's = 17,454,241 bp (18.04%) number of T's = 30,706,618 bp (31.73%) number of G's = 22,107,069 bp (22.85%) number of N's = 18,372 bp (0.02%) GC percentage = 40.89% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 674,945 number of insertions = 7,411 mapped reads with insertion percentage = 0.49% number of deletions = 26,292 mapped reads with deletion percentage = 1.71% homopolymer indels = 48.02% >>>>>>> Coverage mean coverageData = 0.0313X std coverageData = 0.2715X There is a 2.74% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 3823535 0.015340122261922067 0.46141189365268426 chr2 243199373 8618446 0.035437780507764714 0.2582974419143051 chr3 198022430 10459899 0.05282178892562828 0.25511935502876376 chr4 191154276 6780120 0.03546936088418969 0.210559551355967 chr5 180915260 1714592 0.009477321039695601 0.11063481248656956 chr6 171115067 1392212 0.008136115798616377 0.1181498592973172 chr7 159138663 3905476 0.02454133977486037 0.37053996528638267 chr8 146364022 8901373 0.06081667392277591 0.3238613079265328 chr9 141213431 1509042 0.010686249808631872 0.16760860784713005 chr10 135534747 7578659 0.055916723701856325 0.31887518767672063 chr11 135006516 6409780 0.04747756026827624 0.3581296483065775 chr12 133851895 7195212 0.053755025283728705 0.25785802818402626 chr13 115169878 5634187 0.048920664828697655 0.2434924013124612 chr14 107349540 3270808 0.030468765865228672 0.19967324511420348 chr15 102531392 3241217 0.031611947685251364 0.19785392805330673 chr16 90354753 3432508 0.037989235607782584 0.22556380459854378 chr17 81195210 1378142 0.016973193369411815 0.16554755199631413 chr18 78077248 1158751 0.01484108405050342 0.34107405928179035 chr19 59128983 3092483 0.052300628948750906 0.3623934857390599 chr20 63025520 1330438 0.021109512464157376 0.1655943379469431 chr21 48129895 402173 0.008355991634720998 0.10880618807316052 chr22 51304566 1370375 0.026710585564645454 0.1792218340405787 chrMT 16571 158949 9.591998068915576 5.259728291603038 chrX 155270560 3844351 0.024759046402614893 0.18949700832174685 chrY 59373566 201086 0.003386793375354952 0.10379780733240407