BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8751169.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP188831/SRP188831.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 = 4,446,748 number of mapped reads = 4,233,450 (95.2%) number of supplementary alignments = 212,615 (4.78%) number of secondary alignments = 0 number of mapped bases = 415,706,445 bp number of sequenced bases = 415,563,116 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 141,266 duplication rate = 1.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.9911 >>>>>>> ACTG content number of A's = 122,698,854 bp (29.53%) number of C's = 84,841,793 bp (20.42%) number of T's = 123,454,964 bp (29.71%) number of G's = 84,565,247 bp (20.35%) number of N's = 2,258 bp (0%) GC percentage = 40.77% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 1,735,980 number of insertions = 377,940 mapped reads with insertion percentage = 8.49% number of deletions = 66,028 mapped reads with deletion percentage = 1.53% homopolymer indels = 54.04% >>>>>>> Coverage mean coverageData = 0.1343X std coverageData = 1.4567X There is a 10.98% of reference with a coverageData >= 1X There is a 1.66% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% 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 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 47297680 0.18975952721899136 4.061400180204724 chr2 243199373 31713262 0.13040026217501802 0.6509005003527376 chr3 198022430 27955224 0.14117200763570067 0.5163310577307152 chr4 191154276 19880692 0.1040033862491258 0.5201325344317045 chr5 180915260 34711004 0.19186332872086082 0.5020454149668642 chr6 171115067 23514418 0.13741874641582555 0.9323058016464537 chr7 159138663 24107240 0.15148575176856927 0.9246947098142467 chr8 146364022 21068039 0.14394274434464502 0.5833237117491141 chr9 141213431 18177374 0.1287226991885779 0.7502347755434572 chr10 135534747 21463461 0.15836131674780046 2.280850806710593 chr11 135006516 19072697 0.14127241828831433 0.7521820773480284 chr12 133851895 18661264 0.13941725666267182 0.4310436079877433 chr13 115169878 12350663 0.10723865662165588 0.36416209356405316 chr14 107349540 9190858 0.08561618428919211 0.4626214737561852 chr15 102531392 10008264 0.09761170510588602 0.35014886537885204 chr16 90354753 11914579 0.13186444104384856 1.0323799999718726 chr17 81195210 11049749 0.13608868060073986 0.6767402235046184 chr18 78077248 8972568 0.11491911190312445 1.6024638799694402 chr19 59128983 7480610 0.12651342236006324 2.828487869960066 chr20 63025520 7248035 0.11500158983218227 0.4056769744169355 chr21 48129895 5280898 0.10972178518153841 0.4676904144626069 chr22 51304566 4367922 0.08513710066273633 0.32975046827141696 chrMT 16571 554784 33.479210669241446 13.367894185894746 chrX 155270560 18484522 0.11904717803555291 0.467693136524558 chrY 59373566 1180638 0.019884909725651313 0.8294595047099432