BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716801.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 = 865,518 number of mapped reads = 780,210 (90.14%) number of supplementary alignments = 3,835 (0.44%) number of secondary alignments = 0 number of mapped bases = 45,778,515 bp number of sequenced bases = 45,765,410 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,656 duplication rate = 1.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.067 >>>>>>> ACTG content number of A's = 11,788,959 bp (25.76%) number of C's = 8,898,378 bp (19.44%) number of T's = 13,638,984 bp (29.8%) number of G's = 11,438,493 bp (24.99%) number of N's = 596 bp (0%) GC percentage = 44.44% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 225,292 number of insertions = 3,264 mapped reads with insertion percentage = 0.42% number of deletions = 8,243 mapped reads with deletion percentage = 1.05% homopolymer indels = 41.37% >>>>>>> Coverage mean coverageData = 0.0148X std coverageData = 0.1567X There is a 1.38% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% 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 3476350 0.01394720697606607 0.24304384893963937 chr2 243199373 3613129 0.014856654256259124 0.173970071537258 chr3 198022430 2855337 0.014419260484784476 0.12633302811045277 chr4 191154276 2715504 0.014205823991088747 0.13126096729501496 chr5 180915260 3161664 0.01747593873507409 0.1396608064117989 chr6 171115067 2475894 0.014469175879176087 0.1368493106742517 chr7 159138663 3379532 0.02123639809641985 0.2253913711945007 chr8 146364022 2277545 0.01556082546023503 0.14859400179410545 chr9 141213431 1787243 0.012656324454010328 0.13345450365438014 chr10 135534747 2326665 0.017166557296189145 0.158056489286797 chr11 135006516 1953535 0.01446993121428302 0.14343641520573544 chr12 133851895 1977468 0.014773552514889685 0.1289483757326434 chr13 115169878 1338919 0.011625600575872799 0.11335930839139514 chr14 107349540 1278328 0.01190809015110824 0.11664549672092947 chr15 102531392 1259126 0.012280395061836282 0.11749643075406202 chr16 90354753 1278871 0.01415388739981393 0.1285251303693975 chr17 81195210 1224509 0.015081049731874577 0.13293432343871253 chr18 78077248 1122214 0.014373124421598465 0.19055877342436217 chr19 59128983 939330 0.0158861179804158 0.18229470598287068 chr20 63025520 930903 0.014770254969732895 0.1297671636999217 chr21 48129895 583697 0.01212753528757958 0.1209938169825423 chr22 51304566 537295 0.010472654617134857 0.10757809146816431 chrMT 16571 7387 0.4457787701406071 0.8151169728932174 chrX 155270560 3135946 0.020196655438094638 0.15563883550955238 chrY 59373566 142124 0.0023937251806637316 0.07313650612565831