BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013282.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 = 1,939,836 number of mapped reads = 1,730,216 (89.19%) number of supplementary alignments = 9,623 (0.5%) number of secondary alignments = 0 number of mapped bases = 115,969,285 bp number of sequenced bases = 115,922,116 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 67,752 duplication rate = 3.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1263 >>>>>>> ACTG content number of A's = 31,985,717 bp (27.59%) number of C's = 21,145,109 bp (18.24%) number of T's = 36,967,780 bp (31.89%) number of G's = 25,821,916 bp (22.28%) number of N's = 1,594 bp (0%) GC percentage = 40.52% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 800,058 number of insertions = 7,969 mapped reads with insertion percentage = 0.46% number of deletions = 27,444 mapped reads with deletion percentage = 1.57% homopolymer indels = 48.34% >>>>>>> Coverage mean coverageData = 0.0375X std coverageData = 0.3089X There is a 3.17% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 10608975 0.04256348472648339 0.4736282484490446 chr2 243199373 17931905 0.07373335210037733 0.42506320081342985 chr3 198022430 6741140 0.03404230520754644 0.2099769323714376 chr4 191154276 7875922 0.04120191378821157 0.24923668287173234 chr5 180915260 3621304 0.020016575716166784 0.16325536066952276 chr6 171115067 3049801 0.017823100288415866 0.17397876304638873 chr7 159138663 6559675 0.04121986999476048 0.46876780005491736 chr8 146364022 6993492 0.04778149646639254 0.34462673777354064 chr9 141213431 3895096 0.027583042012483926 0.27576711595084424 chr10 135534747 5170738 0.038150644867474465 0.32256967457757635 chr11 135006516 4876854 0.0361231009027742 0.32052143727130955 chr12 133851895 7607911 0.056838276365082464 0.2746202539355242 chr13 115169878 1554692 0.013499119969546204 0.13282664016317777 chr14 107349540 4215564 0.03926951154145607 0.23318857567846238 chr15 102531392 4192452 0.04088944778980471 0.2373486202726375 chr16 90354753 3663037 0.040540612180080884 0.2359729722415207 chr17 81195210 1671818 0.020590106239025678 0.19473838718109254 chr18 78077248 2223860 0.028482817427171615 0.4648569990523199 chr19 59128983 1807521 0.03056912039227869 0.3343630233396262 chr20 63025520 2202271 0.03494252804260877 0.21703224538515467 chr21 48129895 2422613 0.05033489061216526 0.26961755591445197 chr22 51304566 720985 0.014053037696488847 0.13171300417248552 chrMT 16571 12303 0.7424416148693501 0.9877398595163144 chrX 155270560 6101262 0.0392943903854021 0.25200093780084565 chrY 59373566 248094 0.004178526181162843 0.10223083051651836