BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716347.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 = 392,535 number of mapped reads = 361,759 (92.16%) number of supplementary alignments = 7,148 (1.82%) number of secondary alignments = 0 number of mapped bases = 28,530,337 bp number of sequenced bases = 28,518,054 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,605 duplication rate = 1.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.3259 >>>>>>> ACTG content number of A's = 7,585,406 bp (26.6%) number of C's = 5,650,378 bp (19.81%) number of T's = 8,696,400 bp (30.49%) number of G's = 6,583,984 bp (23.09%) number of N's = 1,886 bp (0.01%) GC percentage = 42.9% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 187,573 number of insertions = 2,423 mapped reads with insertion percentage = 0.66% number of deletions = 6,540 mapped reads with deletion percentage = 1.79% homopolymer indels = 44.42% >>>>>>> Coverage mean coverageData = 0.0092X std coverageData = 0.1258X There is a 0.88% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% 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 2770087 0.011113661377798532 0.23118302302367488 chr2 243199373 2330067 0.00958089229942217 0.13017228228326733 chr3 198022430 1824449 0.009213345175089508 0.09866434469487687 chr4 191154276 1822276 0.009533011963593218 0.1060344210139593 chr5 180915260 1679974 0.009285971785906838 0.09901972170377198 chr6 171115067 1547540 0.009043855851688385 0.10061519006276862 chr7 159138663 1511921 0.009500651642398177 0.1321895750429247 chr8 146364022 1422140 0.009716458871292837 0.13131072197475963 chr9 141213431 1152107 0.008158621965640081 0.10828377957962526 chr10 135534747 1326476 0.009786981046270002 0.12270887912530748 chr11 135006516 1630777 0.012079246604660178 0.13796723969372002 chr12 133851895 1241148 0.009272547093935428 0.09897227306373438 chr13 115169878 1019081 0.008848502904552873 0.09670841265195075 chr14 107349540 837043 0.007797359914164513 0.09267768104238187 chr15 102531392 780582 0.007613102531564187 0.08941986801812149 chr16 90354753 618742 0.006847918670089221 0.08711543745097403 chr17 81195210 857504 0.010561017084628515 0.11020427744192356 chr18 78077248 755426 0.009675366631774726 0.15815121382561292 chr19 59128983 512945 0.008675018137890178 0.14914254121925682 chr20 63025520 554799 0.008802767513857878 0.09773942989136168 chr21 48129895 361672 0.00751449800586517 0.09144667737937896 chr22 51304566 300474 0.005856671704424905 0.07846763783932562 chrMT 16571 8961 0.5407639852754813 0.7759438288531959 chrX 155270560 1577771 0.01016143047336211 0.10864692352242705 chrY 59373566 86375 0.0014547719771455195 0.05581367416231035