BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238264.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 = 1,935,416 number of mapped reads = 1,557,287 (80.46%) number of supplementary alignments = 17,496 (0.9%) number of secondary alignments = 0 number of mapped bases = 99,870,268 bp number of sequenced bases = 99,805,235 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 192,368 duplication rate = 9.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1702 >>>>>>> ACTG content number of A's = 27,887,389 bp (27.94%) number of C's = 19,419,698 bp (19.46%) number of T's = 30,541,838 bp (30.6%) number of G's = 21,925,863 bp (21.97%) number of N's = 30,447 bp (0.03%) GC percentage = 41.43% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 1,035,106 number of insertions = 8,412 mapped reads with insertion percentage = 0.54% number of deletions = 39,629 mapped reads with deletion percentage = 2.51% homopolymer indels = 46.25% >>>>>>> Coverage mean coverageData = 0.0323X std coverageData = 0.3542X There is a 1.86% of reference with a coverageData >= 1X There is a 0.75% 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 0.06% of reference with a coverageData >= 5X There is a 0.03% 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% 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 7358015 0.0295205483159057 0.4588489701722068 chr2 243199373 8564342 0.03521531282895207 0.4416754924255896 chr3 198022430 6483442 0.032740947578514215 0.2842869554906347 chr4 191154276 6121658 0.03202469820764041 0.2908857770709943 chr5 180915260 6373737 0.03523051068218347 0.29486521467416743 chr6 171115067 6060388 0.03541703314764211 0.3450382515369244 chr7 159138663 6505535 0.04087966354222795 0.48063792632566027 chr8 146364022 5148364 0.03517506508532541 0.4495340864096293 chr9 141213431 3962227 0.028058428804835143 0.318919577467643 chr10 135534747 4158296 0.03068066375628384 0.3153825848366046 chr11 135006516 4124163 0.03054788111116059 0.30424207965511474 chr12 133851895 4582493 0.03423554817808145 0.29295634071763876 chr13 115169878 3695482 0.03208722683547516 0.29078779218366796 chr14 107349540 3528383 0.032868170650754536 0.3486873239093446 chr15 102531392 2893210 0.028217796945544247 0.326296679607648 chr16 90354753 2862633 0.03168215179560061 0.28617188574815444 chr17 81195210 2630600 0.03239846291425319 0.29376934203098726 chr18 78077248 2628796 0.033669168257569736 0.4816558125854825 chr19 59128983 1802572 0.030485422013769456 0.3699645642042529 chr20 63025520 1976234 0.03135609194497721 0.2775085597235621 chr21 48129895 1290295 0.026808597857942554 0.2610129520511917 chr22 51304566 1196316 0.023317924568351286 0.236853229521428 chrMT 16571 13830 0.8345905497555971 1.4459941653621666 chrX 155270560 5635675 0.03629583740794134 0.31772737947074653 chrY 59373566 273582 0.00460780812794704 0.1250429460365976