BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716770.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 = 2,322,120 number of mapped reads = 2,192,170 (94.4%) number of supplementary alignments = 45,392 (1.95%) number of secondary alignments = 0 number of mapped bases = 170,624,499 bp number of sequenced bases = 170,560,038 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 135,285 duplication rate = 4.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6108 >>>>>>> ACTG content number of A's = 41,203,848 bp (24.16%) number of C's = 34,859,458 bp (20.44%) number of T's = 51,188,520 bp (30.01%) number of G's = 43,301,535 bp (25.39%) number of N's = 6,677 bp (0%) GC percentage = 45.83% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,091,554 number of insertions = 14,011 mapped reads with insertion percentage = 0.63% number of deletions = 31,126 mapped reads with deletion percentage = 1.4% homopolymer indels = 39.87% >>>>>>> Coverage mean coverageData = 0.0551X std coverageData = 0.4425X There is a 4.35% of reference with a coverageData >= 1X There is a 0.77% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 18804991 0.07544611493666048 0.8846289865421012 chr2 243199373 16180558 0.06653207119904869 0.4584792489428237 chr3 198022430 10914238 0.055116170425744196 0.2911521056597245 chr4 191154276 8326689 0.04356004570883887 0.37861781428382857 chr5 180915260 10190367 0.056326741038870906 0.2971953640692848 chr6 171115067 11207330 0.0654958689289471 0.3356816418319401 chr7 159138663 10882132 0.06838144668841412 0.5753797200355547 chr8 146364022 10494160 0.07169904090227856 0.46388822059207135 chr9 141213431 5259940 0.03724815665728 0.29973699424871625 chr10 135534747 6481354 0.04782060795081574 0.5530458253054572 chr11 135006516 7281807 0.05393670776601627 0.3620096865520118 chr12 133851895 6064573 0.04530808473051502 0.26089976598194936 chr13 115169878 3343698 0.029032747607842392 0.20410708847416079 chr14 107349540 3337111 0.031086402419609808 0.2273901249593166 chr15 102531392 3196169 0.031172589561643715 0.21111437675660832 chr16 90354753 6336877 0.07013330001577227 0.3515068183307232 chr17 81195210 3203732 0.039457155169621456 0.28569134791883066 chr18 78077248 5116856 0.0655358139672136 0.48327202445739315 chr19 59128983 4312154 0.072927924364943 0.6205845269520291 chr20 63025520 2742300 0.04351094604217466 0.27355019917292134 chr21 48129895 2693860 0.05597061867681199 0.3617122103906162 chr22 51304566 2747649 0.05355564259134363 0.2961713459178315 chrMT 16571 48003 2.896807676060588 2.5809063369704752 chrX 155270560 10876979 0.07005177929415596 0.3456350159261461 chrY 59373566 580972 0.009785027902821266 0.33259874875711165