BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716664.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 = 4,093,118 number of mapped reads = 3,830,672 (93.59%) number of supplementary alignments = 73,409 (1.79%) number of secondary alignments = 0 number of mapped bases = 303,877,211 bp number of sequenced bases = 303,748,558 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 258,360 duplication rate = 5.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7944 >>>>>>> ACTG content number of A's = 76,394,195 bp (25.15%) number of C's = 58,043,788 bp (19.11%) number of T's = 94,766,428 bp (31.2%) number of G's = 74,522,026 bp (24.53%) number of N's = 22,121 bp (0.01%) GC percentage = 43.64% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,923,570 number of insertions = 25,436 mapped reads with insertion percentage = 0.65% number of deletions = 66,129 mapped reads with deletion percentage = 1.7% homopolymer indels = 43.07% >>>>>>> Coverage mean coverageData = 0.0982X std coverageData = 0.7461X There is a 7.48% of reference with a coverageData >= 1X There is a 1.53% of reference with a coverageData >= 2X There is a 0.39% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 24339058 0.09764893624878872 1.4086063593586895 chr2 243199373 25734568 0.10581675307197441 0.8849539412941426 chr3 198022430 20238680 0.10220397759991129 0.3951698876446154 chr4 191154276 19689997 0.10300578889482964 0.5931887595854913 chr5 180915260 18383593 0.1016143856521556 0.40155676263336776 chr6 171115067 17184479 0.10042645163444315 0.44771631492453295 chr7 159138663 16628903 0.10449316769740613 1.0246917484927907 chr8 146364022 15634789 0.10682125830075918 0.9478895074908191 chr9 141213431 12949462 0.09170134815292463 0.6657734086015756 chr10 135534747 14585472 0.1076142636692272 0.8516757040044968 chr11 135006516 13960541 0.10340642373142937 0.6985083122666321 chr12 133851895 13436337 0.10038212010371612 0.40045234077816466 chr13 115169878 9790882 0.08501252384759841 0.36034146610486273 chr14 107349540 9087793 0.08465609633725492 0.41644001159126093 chr15 102531392 8779629 0.08562869213752604 0.3646890266019349 chr16 90354753 8813906 0.09754778478559949 0.44798744505036553 chr17 81195210 8172183 0.10064858505815799 0.485177290522151 chr18 78077248 8105947 0.1038195787843342 1.115957598599331 chr19 59128983 6109825 0.1033304597848402 0.985821081947385 chr20 63025520 6576523 0.10434698515775832 0.4513615169918112 chr21 48129895 4145389 0.08612919267744092 0.4900884433936036 chr22 51304566 3587350 0.06992262637988206 0.3401912510287887 chrMT 16571 28831 1.7398467201737975 1.8321220405832055 chrX 155270560 16993801 0.10944638185113778 0.5214240140838817 chrY 59373566 919273 0.015482866567253178 0.5384584219039421