BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716399.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 = 1,937,019 number of mapped reads = 1,755,131 (90.61%) number of supplementary alignments = 26,196 (1.35%) number of secondary alignments = 0 number of mapped bases = 138,777,293 bp number of sequenced bases = 138,720,123 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 83,475 duplication rate = 3.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.397 >>>>>>> ACTG content number of A's = 35,170,195 bp (25.35%) number of C's = 26,364,550 bp (19.01%) number of T's = 43,747,802 bp (31.54%) number of G's = 33,429,366 bp (24.1%) number of N's = 8,210 bp (0.01%) GC percentage = 43.1% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,128,914 number of insertions = 13,091 mapped reads with insertion percentage = 0.74% number of deletions = 32,459 mapped reads with deletion percentage = 1.82% homopolymer indels = 43.78% >>>>>>> Coverage mean coverageData = 0.0448X std coverageData = 0.4538X There is a 3.79% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.08% 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 0.01% 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 11410347 0.045778610116281315 0.6987462690671101 chr2 243199373 12184473 0.05010075827785954 0.6904214223414287 chr3 198022430 9365154 0.047293400045641296 0.2531161949415249 chr4 191154276 9191441 0.04808388905723459 0.2856530793158263 chr5 180915260 8383693 0.04634044137570264 0.25218007173581036 chr6 171115067 7977373 0.046619933240595345 0.30176662876150306 chr7 159138663 7822355 0.04915433404137623 0.6096069648724337 chr8 146364022 7180383 0.049058388133116484 0.6147049273213119 chr9 141213431 5940024 0.04206415748088438 0.48580431620372244 chr10 135534747 6702777 0.04945430709366359 0.46295268484183844 chr11 135006516 6230335 0.04614840220008344 0.4013669784842933 chr12 133851895 5814117 0.04343694200220326 0.2454062880411311 chr13 115169878 4272100 0.037093900542292835 0.21857894613631168 chr14 107349540 4082142 0.038026637095976375 0.2973691063897184 chr15 102531392 4105599 0.04004236088007076 0.23643236314002886 chr16 90354753 3903402 0.04320084854860928 0.2742192853485549 chr17 81195210 3626732 0.044666822094554595 0.2668533962243656 chr18 78077248 3698361 0.047367973317912024 0.8767827983875023 chr19 59128983 2991436 0.05059170390263604 0.5288519804682408 chr20 63025520 2513477 0.039880305628577126 0.25210035464353825 chr21 48129895 1825004 0.03791830420573326 0.2504936025954652 chr22 51304566 1445505 0.02817497764234084 0.19285786996024074 chrMT 16571 2568 0.15496952507392434 0.41920280469915033 chrX 155270560 7720850 0.04972513784969926 0.32612278838988423 chrY 59373566 387645 0.006528915578356873 0.19651970677049907