BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524584.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 = 1,408,316 number of mapped reads = 1,290,176 (91.61%) number of supplementary alignments = 5,079 (0.36%) number of secondary alignments = 0 number of mapped bases = 74,914,416 bp number of sequenced bases = 74,890,629 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 44,397 duplication rate = 2.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5695 >>>>>>> ACTG content number of A's = 18,454,932 bp (24.64%) number of C's = 14,723,825 bp (19.66%) number of T's = 23,299,093 bp (31.11%) number of G's = 18,411,627 bp (24.58%) number of N's = 1,152 bp (0%) GC percentage = 44.25% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 379,157 number of insertions = 4,178 mapped reads with insertion percentage = 0.32% number of deletions = 14,198 mapped reads with deletion percentage = 1.09% homopolymer indels = 44.75% >>>>>>> Coverage mean coverageData = 0.0242X std coverageData = 0.2388X There is a 2.2% of reference with a coverageData >= 1X There is a 0.16% 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 7428398 0.02980292674977929 0.4466898180417764 chr2 243199373 5838185 0.024005756791157518 0.2677702794761283 chr3 198022430 4077401 0.020590601781828453 0.1561938957998713 chr4 191154276 3890027 0.020350196089780382 0.17062284547640555 chr5 180915260 4084293 0.022575724126311952 0.16264809967252675 chr6 171115067 3252599 0.01900825600588404 0.19078026870026565 chr7 159138663 3800508 0.023881738908413476 0.2805307462451231 chr8 146364022 6799955 0.0464591974658909 0.2715097019078063 chr9 141213431 3176229 0.022492400174031604 0.20725339192054706 chr10 135534747 3948029 0.029129275609301872 0.2477463661199416 chr11 135006516 2600802 0.019264270177892746 0.21302170234502799 chr12 133851895 3512832 0.026244170842706412 0.17493799252576897 chr13 115169878 1659551 0.014409592410960095 0.13014238900614764 chr14 107349540 1789436 0.016669247022390594 0.14224036345578406 chr15 102531392 1993480 0.019442630799355577 0.1516357818558332 chr16 90354753 2377455 0.026312450879036768 0.18596936387129617 chr17 81195210 2701511 0.033271802610030814 0.20430513073693282 chr18 78077248 1783031 0.02283675520940492 0.35009920767452246 chr19 59128983 1579652 0.026715358862167474 0.30207687717509896 chr20 63025520 2182335 0.03462621173137485 0.20242031468341268 chr21 48129895 1037322 0.02155255065484768 0.16836693416789217 chr22 51304566 641574 0.0125052027532988 0.12077478413563747 chrMT 16571 6017 0.36310421821253996 0.6518057674604207 chrX 155270560 4503238 0.029002523079713245 0.20118457917099247 chrY 59373566 250556 0.004219992445796502 0.12456315113234953