BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240030.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,972,037 number of mapped reads = 1,521,688 (77.16%) number of supplementary alignments = 12,256 (0.62%) number of secondary alignments = 0 number of mapped bases = 99,719,818 bp number of sequenced bases = 99,670,296 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 228,824 duplication rate = 11.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6562 >>>>>>> ACTG content number of A's = 27,630,186 bp (27.72%) number of C's = 17,957,610 bp (18.02%) number of T's = 32,418,788 bp (32.53%) number of G's = 21,654,252 bp (21.73%) number of N's = 9,460 bp (0.01%) GC percentage = 39.74% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 852,692 number of insertions = 7,169 mapped reads with insertion percentage = 0.47% number of deletions = 28,090 mapped reads with deletion percentage = 1.82% homopolymer indels = 48.88% >>>>>>> Coverage mean coverageData = 0.0322X std coverageData = 0.3894X There is a 1.55% of reference with a coverageData >= 1X There is a 0.75% of reference with a coverageData >= 2X There is a 0.4% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% 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% 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 8183796 0.032833603251082775 0.5639080330977378 chr2 243199373 10814415 0.044467281582999806 0.45077269900281186 chr3 198022430 6190687 0.03126255444900863 0.3183725248926952 chr4 191154276 6530243 0.034162160201951224 0.33852791614676964 chr5 180915260 5297436 0.029281311040317993 0.30448250982746317 chr6 171115067 5358427 0.03131475850691745 0.3410512798355249 chr7 159138663 5844674 0.03672692663001699 0.5225542446337638 chr8 146364022 5486559 0.03748570806560645 0.544443837908792 chr9 141213431 3591364 0.025432170117019533 0.32396759350355575 chr10 135534747 4611009 0.03402086256153929 0.3691170596020475 chr11 135006516 4596270 0.03404480121537245 0.37072430883897733 chr12 133851895 5055919 0.037772487270352054 0.3538778910220805 chr13 115169878 2594121 0.022524301015583257 0.2715567526921256 chr14 107349540 3196364 0.02977529293558221 0.31343866102232587 chr15 102531392 2747698 0.026798602324642193 0.2932439070844473 chr16 90354753 2941139 0.03255101588291653 0.3187057182681682 chr17 81195210 2408428 0.029662193126909826 0.3170257337956079 chr18 78077248 2360720 0.03023569683193752 0.4733756886035235 chr19 59128983 1652308 0.02794413020768512 0.4092524179843254 chr20 63025520 1974999 0.031336496708000185 0.3159108033105254 chr21 48129895 1660135 0.03449280327746404 0.33751237928309874 chr22 51304566 850748 0.01658230575422858 0.21931665540104694 chrMT 16571 21153 1.2765071510470098 2.1417134868841283 chrX 155270560 5497203 0.03540402636533287 0.34796462536516926 chrY 59373566 254003 0.004278048584786031 0.11215413666343894