BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524342.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 = 2,030,921 number of mapped reads = 1,868,833 (92.02%) number of supplementary alignments = 8,032 (0.4%) number of secondary alignments = 0 number of mapped bases = 109,224,723 bp number of sequenced bases = 109,195,084 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 84,597 duplication rate = 3.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5628 >>>>>>> ACTG content number of A's = 26,651,320 bp (24.41%) number of C's = 20,814,636 bp (19.06%) number of T's = 34,704,339 bp (31.78%) number of G's = 27,009,548 bp (24.74%) number of N's = 15,241 bp (0.01%) GC percentage = 43.8% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 549,926 number of insertions = 6,793 mapped reads with insertion percentage = 0.36% number of deletions = 18,410 mapped reads with deletion percentage = 0.98% homopolymer indels = 42.42% >>>>>>> Coverage mean coverageData = 0.0353X std coverageData = 0.3333X There is a 3.09% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 9342253 0.037481362985250094 0.6097548339735037 chr2 243199373 7041845 0.028955029419422063 0.4276207332524544 chr3 198022430 7499720 0.03787308336737409 0.21574104414177428 chr4 191154276 5607303 0.029333913513920035 0.23410399554128336 chr5 180915260 6324357 0.03495756521589168 0.20832348257055328 chr6 171115067 6816584 0.03983625825305027 0.23909421919402354 chr7 159138663 4916647 0.030895364503596465 0.3702740673520803 chr8 146364022 11252843 0.07688257569199622 0.41590003453406793 chr9 141213431 4502513 0.03188445297388178 0.2566304457047386 chr10 135534747 5499006 0.04057266584191875 0.3313810904516325 chr11 135006516 5186519 0.03841680500813753 0.26730977075220685 chr12 133851895 4263586 0.03185301186808002 0.20244931461237456 chr13 115169878 2729103 0.023696326221687932 0.1706407628511308 chr14 107349540 2275024 0.02119267581398113 0.17035431665307302 chr15 102531392 3329610 0.03247405438521697 0.1985609077026472 chr16 90354753 3482236 0.038539599571480204 0.23171524718487455 chr17 81195210 3406324 0.041952277726727966 0.24802945089407624 chr18 78077248 2531065 0.03241744637310987 0.4437515147112197 chr19 59128983 2025462 0.03425497779997332 0.399493313339529 chr20 63025520 2513789 0.039885256004234475 0.23096460112462489 chr21 48129895 1884986 0.03916455666483378 0.24237892199434666 chr22 51304566 825149 0.016083344316761203 0.14137740017779463 chrMT 16571 501490 30.263110252851366 17.78525646542738 chrX 155270560 5128482 0.03302932635781052 0.2217726917759494 chrY 59373566 338827 0.0057066978257630675 0.18836659000489248