BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004075.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 = 2,111,548 number of mapped reads = 1,919,541 (90.91%) number of supplementary alignments = 12,177 (0.58%) number of secondary alignments = 0 number of mapped bases = 129,035,393 bp number of sequenced bases = 128,977,079 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 69,829 duplication rate = 2.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9922 >>>>>>> ACTG content number of A's = 36,738,916 bp (28.48%) number of C's = 23,910,132 bp (18.54%) number of T's = 40,455,413 bp (31.37%) number of G's = 27,849,418 bp (21.59%) number of N's = 23,200 bp (0.02%) GC percentage = 40.13% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,132,408 number of insertions = 9,547 mapped reads with insertion percentage = 0.49% number of deletions = 33,523 mapped reads with deletion percentage = 1.73% homopolymer indels = 46.38% >>>>>>> Coverage mean coverageData = 0.0417X std coverageData = 0.3574X There is a 3.58% 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 9645104 0.03869640910543609 0.5919271864933714 chr2 243199373 10510269 0.04321667802984015 0.38625808621508234 chr3 198022430 10299105 0.05200979000207199 0.2562241913859367 chr4 191154276 9639557 0.05042815259858482 0.2692104664897484 chr5 180915260 8249639 0.04559946463333165 0.2417358771361778 chr6 171115067 8168804 0.04773865997434346 0.2645248495937276 chr7 159138663 5482146 0.034448863001946925 0.4481516815964507 chr8 146364022 7238848 0.04945783739121353 0.6307140045524309 chr9 141213431 3962382 0.028059526434139257 0.2844092763479295 chr10 135534747 6611485 0.04878073812319139 0.3282597367017725 chr11 135006516 4776021 0.03537622584083275 0.31891425218644087 chr12 133851895 6366022 0.047560193301708575 0.2502609327460538 chr13 115169878 5207011 0.045211569990549094 0.24705068328414603 chr14 107349540 3369309 0.03138633849758462 0.21332544778490778 chr15 102531392 4481426 0.04370784315500174 0.24249331293458906 chr16 90354753 3614097 0.03999896939566643 0.2486476526315108 chr17 81195210 2422495 0.029835442263158134 0.215021012910657 chr18 78077248 3944073 0.050515010467582055 0.5809880022332569 chr19 59128983 1764835 0.02984720707947911 0.4161349127406781 chr20 63025520 2336519 0.03707258583507125 0.22942731879709038 chr21 48129895 1506098 0.03129235997709947 0.21680395110672795 chr22 51304566 1075198 0.020957160031331325 0.16037808707012216 chrMT 16571 22950 1.3849496107657957 1.533764673246855 chrX 155270560 8014465 0.05161612735859264 0.27905963460163385 chrY 59373566 327535 0.005516512179847847 0.11798175310705644