BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237802.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 = 3,062,372 number of mapped reads = 2,145,780 (70.07%) number of supplementary alignments = 9,831 (0.32%) number of secondary alignments = 0 number of mapped bases = 128,429,050 bp number of sequenced bases = 128,353,478 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 230,104 duplication rate = 8.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3029 >>>>>>> ACTG content number of A's = 35,335,294 bp (27.53%) number of C's = 25,508,606 bp (19.87%) number of T's = 39,034,367 bp (30.41%) number of G's = 28,382,087 bp (22.11%) number of N's = 93,124 bp (0.07%) GC percentage = 41.99% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 1,354,737 number of insertions = 10,906 mapped reads with insertion percentage = 0.5% number of deletions = 47,530 mapped reads with deletion percentage = 2.19% homopolymer indels = 46.83% >>>>>>> Coverage mean coverageData = 0.0415X std coverageData = 0.402X There is a 2.57% of reference with a coverageData >= 1X There is a 0.86% of reference with a coverageData >= 2X There is a 0.33% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% 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 0.01% 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 10875214 0.043631642546639836 0.4750977321335338 chr2 243199373 11170721 0.04593235937331138 0.47401088531263824 chr3 198022430 8519934 0.04302509569244252 0.3381641277861568 chr4 191154276 7681938 0.04018711043638909 0.33355297559400093 chr5 180915260 6691239 0.03698548701751306 0.29147522175604546 chr6 171115067 6833451 0.03993482935082508 0.37911492962876553 chr7 159138663 7429283 0.046684337168271924 0.5147867067686172 chr8 146364022 8235580 0.0562677896348052 0.4274436450800931 chr9 141213431 5042955 0.03571158185371192 0.34255034319078737 chr10 135534747 5705907 0.04209921902905091 0.6559359950614118 chr11 135006516 5658922 0.041915917599117954 0.4207100158698252 chr12 133851895 6275372 0.04688295223612635 0.3405309234232768 chr13 115169878 4209523 0.03655055534573024 0.30189946252454414 chr14 107349540 3360670 0.0313058630712344 0.28919613312397424 chr15 102531392 3488324 0.03402200957146861 0.2842069364736334 chr16 90354753 3370689 0.037305054666022935 0.3369258072117708 chr17 81195210 2900324 0.03572038301274176 0.3159298353729768 chr18 78077248 3122719 0.039995249320262924 0.48075576011790766 chr19 59128983 2467352 0.041728300992425325 0.388987519121227 chr20 63025520 2515477 0.03991203880586785 0.3148894782223006 chr21 48129895 1591639 0.0330696545255293 0.30944115939671357 chr22 51304566 1235606 0.02408374334557279 0.23605175578417223 chrMT 16571 337944 20.39369983706475 12.319797022884908 chrX 155270560 9064961 0.05838171125292522 0.3866121702695321 chrY 59373566 643306 0.010834889048099284 0.21490136554481992