BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525258.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 = 620,143 number of mapped reads = 564,253 (90.99%) number of supplementary alignments = 1,707 (0.28%) number of secondary alignments = 0 number of mapped bases = 32,353,423 bp number of sequenced bases = 32,343,177 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,484 duplication rate = 1.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9326 >>>>>>> ACTG content number of A's = 8,252,765 bp (25.52%) number of C's = 5,766,853 bp (17.83%) number of T's = 10,710,476 bp (33.12%) number of G's = 7,612,405 bp (23.54%) number of N's = 678 bp (0%) GC percentage = 41.37% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 163,841 number of insertions = 2,374 mapped reads with insertion percentage = 0.42% number of deletions = 6,582 mapped reads with deletion percentage = 1.16% homopolymer indels = 44.43% >>>>>>> Coverage mean coverageData = 0.0105X std coverageData = 0.1321X There is a 0.99% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 3308926 0.013275497516212808 0.19844002243692277 chr2 243199373 2305152 0.009478445489248855 0.16212111951552774 chr3 198022430 2236189 0.011292604580198314 0.11023809121037294 chr4 191154276 1857664 0.009718139917518768 0.10424430076959228 chr5 180915260 1428896 0.00789815076959235 0.09205083598338379 chr6 171115067 1906324 0.011140596987873662 0.11506149987223127 chr7 159138663 2297243 0.014435480081920759 0.21125018046924085 chr8 146364022 2204390 0.015061010006953758 0.1452539794554957 chr9 141213431 1054020 0.007464020897558958 0.09932768779491641 chr10 135534747 1898520 0.014007625660746613 0.14185053968683894 chr11 135006516 1406231 0.010416023179207142 0.11559750070552409 chr12 133851895 1406349 0.010506754499067794 0.10667193527244512 chr13 115169878 984593 0.008549049604793364 0.09626917263849644 chr14 107349540 1321442 0.012309712738405773 0.11584367732660045 chr15 102531392 841806 0.008210226971267493 0.09450762616346724 chr16 90354753 804417 0.008902874207403344 0.10025669770817545 chr17 81195210 553083 0.006811768822323386 0.08642843215170017 chr18 78077248 671247 0.008597216438776121 0.14445479668112393 chr19 59128983 606500 0.010257237131915495 0.1467937679094193 chr20 63025520 550470 0.008734081051612108 0.09778119880150303 chr21 48129895 438348 0.00910760349674563 0.10089184055978467 chr22 51304566 329932 0.006430850618636946 0.0828526135455836 chrMT 16571 62281 3.7584334077605455 2.7570938620184777 chrX 155270560 1789024 0.011521978152200907 0.11507363637499834 chrY 59373566 90376 0.001522158867803224 0.049134837200608246