BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716302.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 = 1,299,787 number of mapped reads = 1,157,440 (89.05%) number of supplementary alignments = 4,547 (0.35%) number of secondary alignments = 0 number of mapped bases = 66,890,179 bp number of sequenced bases = 66,871,353 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,625 duplication rate = 2.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1274 >>>>>>> ACTG content number of A's = 16,624,134 bp (24.86%) number of C's = 11,969,201 bp (17.9%) number of T's = 21,993,785 bp (32.89%) number of G's = 16,282,342 bp (24.35%) number of N's = 1,891 bp (0%) GC percentage = 42.25% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 333,875 number of insertions = 5,365 mapped reads with insertion percentage = 0.46% number of deletions = 11,820 mapped reads with deletion percentage = 1.01% homopolymer indels = 41.23% >>>>>>> Coverage mean coverageData = 0.0216X std coverageData = 0.209X There is a 1.97% 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 5530813 0.022189766179158285 0.3522088135667649 chr2 243199373 5654783 0.023251634781147237 0.2768020905145486 chr3 198022430 4457722 0.02251119734264447 0.16256451976163694 chr4 191154276 4336118 0.022683866093584013 0.17319885619903364 chr5 180915260 3961654 0.021897843222290922 0.16055808576429287 chr6 171115067 3810042 0.022265964457706112 0.18573584052273537 chr7 159138663 3708548 0.023303878077698816 0.23000342205314006 chr8 146364022 3345408 0.02285676462211458 0.19618950368667357 chr9 141213431 2782836 0.01970659575575357 0.18219608997505884 chr10 135534747 3186236 0.023508628381473277 0.20704415962767467 chr11 135006516 3041376 0.022527623777803436 0.18571518855566688 chr12 133851895 2977485 0.02224462343248857 0.16189686069261963 chr13 115169878 2097936 0.01821601304466086 0.14514419930354824 chr14 107349540 2030447 0.01891435212484376 0.1524160316519469 chr15 102531392 1944582 0.018965723200168785 0.14916606280627376 chr16 90354753 1956066 0.021648733852440503 0.1659931633038595 chr17 81195210 1818233 0.022393353006907674 0.16565048324903667 chr18 78077248 1742520 0.022317897270149687 0.27681314776334903 chr19 59128983 1422637 0.024059892929327063 0.26229981492689863 chr20 63025520 1415938 0.02246610579333578 0.16348600764717572 chr21 48129895 880510 0.01829445088130776 0.1567934505987578 chr22 51304566 779313 0.015189934556702029 0.13240262998126737 chrMT 16571 11792 0.7116046104640638 0.9600423685983206 chrX 155270560 3792945 0.0244279726948882 0.1814728577099362 chrY 59373566 204239 0.0034398978158057744 0.09398650100372624