BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524753.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 = 1,277,810 number of mapped reads = 1,152,631 (90.2%) number of supplementary alignments = 3,424 (0.27%) number of secondary alignments = 0 number of mapped bases = 65,321,647 bp number of sequenced bases = 65,301,740 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,813 duplication rate = 2.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4442 >>>>>>> ACTG content number of A's = 16,019,310 bp (24.53%) number of C's = 11,964,252 bp (18.32%) number of T's = 21,264,810 bp (32.56%) number of G's = 16,044,812 bp (24.57%) number of N's = 8,556 bp (0.01%) GC percentage = 42.89% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 332,642 number of insertions = 4,223 mapped reads with insertion percentage = 0.36% number of deletions = 12,510 mapped reads with deletion percentage = 1.08% homopolymer indels = 43.01% >>>>>>> Coverage mean coverageData = 0.0211X std coverageData = 0.1946X There is a 1.92% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 5186893 0.020809950158559486 0.22488267415291466 chr2 243199373 5518661 0.02269192116708294 0.30735415057457716 chr3 198022430 4273808 0.02158244396859487 0.16090401604625013 chr4 191154276 4140732 0.021661728351815682 0.17416360865732328 chr5 180915260 3871086 0.021397233157667297 0.1572957002689357 chr6 171115067 3732594 0.02181335673964935 0.1721595913955897 chr7 159138663 3622718 0.022764537113146414 0.23334770149859632 chr8 146364022 3223702 0.022025235135995375 0.17777354037349086 chr9 141213431 2777218 0.019666812004588998 0.1750170832735943 chr10 135534747 3186256 0.023508775945108747 0.223130486310751 chr11 135006516 2960306 0.021927134242913135 0.18197922835132435 chr12 133851895 2946813 0.02201547464083344 0.16130303110331778 chr13 115169878 1999802 0.01736393260744793 0.1428201624397043 chr14 107349540 1961458 0.018271694503767786 0.14886900763064215 chr15 102531392 1906041 0.018589828566845167 0.1475016074286051 chr16 90354753 2015523 0.02230677339132342 0.17413374014463193 chr17 81195210 1884179 0.023205543775303986 0.1695009101969258 chr18 78077248 1730559 0.022164702833788404 0.2502092558403812 chr19 59128983 1461595 0.024718757635320734 0.21214516315881285 chr20 63025520 1420484 0.02253823530531759 0.16856654726778894 chr21 48129895 863212 0.017935048476627677 0.15524821000275235 chr22 51304566 820142 0.015985750663985734 0.13696557129144363 chrMT 16571 25716 1.5518677207169151 1.4192163738105983 chrX 155270560 3583488 0.02307899192222917 0.17395303547931926 chrY 59373566 208661 0.0035143754040308107 0.1009236580115934