BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716688.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 = 2,856,345 number of mapped reads = 2,517,120 (88.12%) number of supplementary alignments = 8,833 (0.31%) number of secondary alignments = 0 number of mapped bases = 142,583,272 bp number of sequenced bases = 142,539,150 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 85,579 duplication rate = 2.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.5736 >>>>>>> ACTG content number of A's = 35,461,265 bp (24.88%) number of C's = 29,223,772 bp (20.5%) number of T's = 43,360,289 bp (30.42%) number of G's = 34,492,744 bp (24.2%) number of N's = 1,080 bp (0%) GC percentage = 44.7% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 753,669 number of insertions = 10,034 mapped reads with insertion percentage = 0.4% number of deletions = 27,394 mapped reads with deletion percentage = 1.08% homopolymer indels = 40.86% >>>>>>> Coverage mean coverageData = 0.0461X std coverageData = 0.3492X There is a 3.98% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 12021701 0.048231378328240954 0.41281975014984 chr2 243199373 11026505 0.04533936442344364 0.580859443610014 chr3 198022430 8012872 0.04046446657583184 0.23588677497071864 chr4 191154276 8506769 0.04450211200088456 0.27157678114782063 chr5 180915260 7948032 0.04393234711101761 0.23603801966743934 chr6 171115067 7572291 0.04425262563231793 0.2950901982732659 chr7 159138663 8084476 0.05080145734289599 0.5221454200701688 chr8 146364022 7299279 0.04987071891205613 0.3134878109438675 chr9 141213431 4745903 0.03360801424051513 0.2519144188328548 chr10 135534747 6334509 0.04673715884827675 0.4431109410089208 chr11 135006516 5062927 0.037501352897663105 0.2876454963039724 chr12 133851895 7185232 0.05368046526349141 0.26444343823176525 chr13 115169878 4194498 0.03642009588653033 0.21450251974679532 chr14 107349540 4830626 0.04499903772293761 0.2581421622950841 chr15 102531392 5245287 0.05115786392522594 0.26845202165043963 chr16 90354753 5142319 0.056912545596798876 0.30050114790584875 chr17 81195210 6773915 0.08342751992389699 0.35580695674733687 chr18 78077248 2565813 0.032862492796877266 0.4061706703510742 chr19 59128983 4112481 0.06955101866034125 0.4350539742867498 chr20 63025520 4693732 0.07447351485556962 0.33446686690894667 chr21 48129895 1766115 0.03669476112507621 0.2391883655145995 chr22 51304566 1474476 0.02873966422403807 0.19669568905548654 chrMT 16571 61969 3.7396053346207228 3.1093337978027455 chrX 155270560 7488971 0.04823175108017901 0.27424344033739 chrY 59373566 432574 0.007285632801641053 0.19955037326137448