BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716488.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 = 577,117 number of mapped reads = 405,755 (70.31%) number of supplementary alignments = 1,740 (0.3%) number of secondary alignments = 0 number of mapped bases = 23,335,857 bp number of sequenced bases = 23,329,025 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,372 duplication rate = 1.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5969 >>>>>>> ACTG content number of A's = 5,742,480 bp (24.62%) number of C's = 4,662,775 bp (19.99%) number of T's = 7,185,268 bp (30.8%) number of G's = 5,738,203 bp (24.6%) number of N's = 299 bp (0%) GC percentage = 44.58% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 117,587 number of insertions = 1,307 mapped reads with insertion percentage = 0.32% number of deletions = 4,208 mapped reads with deletion percentage = 1.03% homopolymer indels = 41.38% >>>>>>> Coverage mean coverageData = 0.0075X std coverageData = 0.1021X There is a 0.72% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 1915811 0.007686283758546784 0.14495537074915635 chr2 243199373 1967434 0.00808979881703889 0.12141367207058328 chr3 198022430 1536536 0.007759403821072188 0.09093632362552315 chr4 191154276 1458653 0.007630763122452987 0.09266678936538486 chr5 180915260 1371745 0.007582251491665214 0.09002308341687074 chr6 171115067 1358294 0.00793789830325111 0.09770665975870953 chr7 159138663 1285524 0.008078011815393976 0.1150348326463374 chr8 146364022 1171297 0.0080026292253707 0.10115274187912575 chr9 141213431 967469 0.0068511117756214 0.09175465041627986 chr10 135534747 1112028 0.008204744721292762 0.10292950216493868 chr11 135006516 1068525 0.00791461798777179 0.09670205426139378 chr12 133851895 1056665 0.007894284948300507 0.09191651336623256 chr13 115169878 710452 0.006168731028785148 0.08084855490410124 chr14 107349540 713193 0.006643652129296502 0.08577426540750685 chr15 102531392 669703 0.006531687387995279 0.08320989230448843 chr16 90354753 683207 0.00756138418086318 0.09141064383443465 chr17 81195210 665497 0.008196259360619918 0.09466599494334209 chr18 78077248 607682 0.007783086821912576 0.11525399027630931 chr19 59128983 524023 0.008862371267234548 0.11933189225727986 chr20 63025520 512558 0.008132546942889167 0.09331895957312762 chr21 48129895 313692 0.006517612390386474 0.0860821966828046 chr22 51304566 295063 0.005751203508865078 0.07808842494912105 chrMT 16571 3419 0.20632430149055578 0.49556461394786444 chrX 155270560 1292161 0.008321996133716527 0.09711354086329346 chrY 59373566 75226 0.0012669948104515063 0.04666943020790366