BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524627.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 = 1,418,023 number of mapped reads = 1,321,263 (93.18%) number of supplementary alignments = 2,731 (0.19%) number of secondary alignments = 0 number of mapped bases = 76,677,660 bp number of sequenced bases = 76,653,102 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,846 duplication rate = 3.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3646 >>>>>>> ACTG content number of A's = 19,566,250 bp (25.53%) number of C's = 12,714,026 bp (16.59%) number of T's = 24,831,559 bp (32.39%) number of G's = 19,540,807 bp (25.49%) number of N's = 460 bp (0%) GC percentage = 42.08% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 355,899 number of insertions = 5,268 mapped reads with insertion percentage = 0.4% number of deletions = 14,505 mapped reads with deletion percentage = 1.09% homopolymer indels = 43.7% >>>>>>> Coverage mean coverageData = 0.0248X std coverageData = 0.2238X There is a 2.21% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.03% 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 7963854 0.0319511902038551 0.3617488549103618 chr2 243199373 6793902 0.027935524323905225 0.2638692075344375 chr3 198022430 5155482 0.026034838578639804 0.17846927797669893 chr4 191154276 3450825 0.018052565039141474 0.16762631405526002 chr5 180915260 4737117 0.02618417595066331 0.17716652402722377 chr6 171115067 5053683 0.029533828251371925 0.20089848657686177 chr7 159138663 4700260 0.02953562579572508 0.2955619151396413 chr8 146364022 6793147 0.04641268330273132 0.30558695685296466 chr9 141213431 2825395 0.020007976436745595 0.196767775647152 chr10 135534747 3308918 0.024413798477817647 0.22943032910089572 chr11 135006516 3929612 0.029106832147272062 0.21264577588124028 chr12 133851895 2361528 0.017642843233560496 0.148826425043891 chr13 115169878 1821797 0.015818346182497476 0.13860032529779445 chr14 107349540 1439821 0.013412456168885306 0.13040348583163577 chr15 102531392 1995493 0.019462263810872675 0.16256216947994329 chr16 90354753 2344843 0.025951518012561 0.18387893143092623 chr17 81195210 1797317 0.0221357516040663 0.16689753875613444 chr18 78077248 1988562 0.02546916100321569 0.27167485262173063 chr19 59128983 1531222 0.025896301987808585 0.2738048904500911 chr20 63025520 1105760 0.01754463906049486 0.14971453386068503 chr21 48129895 659214 0.013696560110924821 0.1411307720094761 chr22 51304566 1254871 0.024459245986020037 0.17263466053685236 chrMT 16571 5564 0.33576730432683605 0.6420547109728051 chrX 155270560 3481143 0.022419852159997363 0.18135267305552252 chrY 59373566 178330 0.003003525171454246 0.09577589387660436