BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716153.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 = 2,654,663 number of mapped reads = 2,398,061 (90.33%) number of supplementary alignments = 9,263 (0.35%) number of secondary alignments = 0 number of mapped bases = 138,695,277 bp number of sequenced bases = 138,660,521 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 126,819 duplication rate = 4.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5301 >>>>>>> ACTG content number of A's = 34,176,741 bp (24.65%) number of C's = 24,164,734 bp (17.43%) number of T's = 43,867,066 bp (31.64%) number of G's = 36,448,848 bp (26.29%) number of N's = 3,132 bp (0%) GC percentage = 43.71% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 643,257 number of insertions = 8,206 mapped reads with insertion percentage = 0.34% number of deletions = 20,465 mapped reads with deletion percentage = 0.85% homopolymer indels = 43.32% >>>>>>> Coverage mean coverageData = 0.0448X std coverageData = 0.3101X There is a 3.74% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 11659455 0.04677803791710513 0.4102207259552367 chr2 243199373 12508496 0.05143309312725901 0.38192231202874477 chr3 198022430 9918659 0.05008856319963349 0.2606188700633812 chr4 191154276 9059152 0.04739183548266532 0.2705595222517969 chr5 180915260 7236698 0.04000048420459391 0.23632993070000619 chr6 171115067 7570514 0.04424224080746788 0.259541464455393 chr7 159138663 7762120 0.048775827656664425 0.33459970715489357 chr8 146364022 9854863 0.06733118470876674 0.3680808733765676 chr9 141213431 5001750 0.03541978949580228 0.32333850104413064 chr10 135534747 6697660 0.049416552937528266 0.3136419235326624 chr11 135006516 5329649 0.039476976059437015 0.31420072078603817 chr12 133851895 6368974 0.04758224752813548 0.2579924731990938 chr13 115169878 2376441 0.0206342234729119 0.1660001234843473 chr14 107349540 3717073 0.03462588661302135 0.2254638880349364 chr15 102531392 3922006 0.03825175805669351 0.22797204288647968 chr16 90354753 4046849 0.04478844627022554 0.26286621014674744 chr17 81195210 3620327 0.04458793813083309 0.2569996398108399 chr18 78077248 4633902 0.059350221975036824 0.5712450657462103 chr19 59128983 2594950 0.04388626132805294 0.3462818241275987 chr20 63025520 2954283 0.046874393102984316 0.2660895305629082 chr21 48129895 1771152 0.03679941541530477 0.24452967796535025 chr22 51304566 1733247 0.033783484300403205 0.2155136861240102 chrMT 16571 46934 2.832297387001388 2.3954358769655015 chrX 155270560 7938653 0.05112786995809122 0.29816938974192286 chrY 59373566 371470 0.006256487946167828 0.12405247002964757