BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524928.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 = 1,013,039 number of mapped reads = 930,760 (91.88%) number of supplementary alignments = 3,716 (0.37%) number of secondary alignments = 0 number of mapped bases = 53,947,018 bp number of sequenced bases = 53,929,821 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,216 duplication rate = 3.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6948 >>>>>>> ACTG content number of A's = 12,711,168 bp (23.57%) number of C's = 11,000,683 bp (20.4%) number of T's = 17,365,275 bp (32.2%) number of G's = 12,852,260 bp (23.83%) number of N's = 435 bp (0%) GC percentage = 44.23% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 280,983 number of insertions = 3,799 mapped reads with insertion percentage = 0.41% number of deletions = 10,336 mapped reads with deletion percentage = 1.1% homopolymer indels = 42.53% >>>>>>> Coverage mean coverageData = 0.0174X std coverageData = 0.1898X There is a 1.56% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 5572694 0.022357793844774414 0.31845309430464 chr2 243199373 4681304 0.019248832520633183 0.23491382746556497 chr3 198022430 3598903 0.018174218950853194 0.1470236232751553 chr4 191154276 2480693 0.012977439228197019 0.15034951374611177 chr5 180915260 3318645 0.018343643316766092 0.1475980255346289 chr6 171115067 3398654 0.01986180445465974 0.16154250063866973 chr7 159138663 3308135 0.020787751622621083 0.22192158053563743 chr8 146364022 4664475 0.03186899988304503 0.2518381042373684 chr9 141213431 1954692 0.01384211109494252 0.15233386739627927 chr10 135534747 2402096 0.017723100925550846 0.20653052573547265 chr11 135006516 2746534 0.02034371437301589 0.17575636928080335 chr12 133851895 1653298 0.012351696627081746 0.12358850191727269 chr13 115169878 1283467 0.01114412051387256 0.11638004426050122 chr14 107349540 971261 0.009047649389089139 0.10521132333228489 chr15 102531392 1391697 0.0135733746792397 0.128598482851949 chr16 90354753 1597000 0.017674775780749465 0.15074574982094832 chr17 81195210 1235065 0.015211057401046195 0.13806822887614698 chr18 78077248 1358563 0.01740024187327914 0.2341193663846999 chr19 59128983 1147259 0.019402650642579122 0.23796144738099823 chr20 63025520 1054034 0.016723923896224895 0.14404238185193283 chr21 48129895 482018 0.010014939779112338 0.13090858017561133 chr22 51304566 1053692 0.020537977068161926 0.15937691407558635 chrMT 16571 27379 1.6522237644077002 1.5970974091251653 chrX 155270560 2397113 0.015438296867094446 0.14322966274960325 chrY 59373566 168347 0.002835386373794695 0.12328042514740761