BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524980.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 = 978,367 number of mapped reads = 905,835 (92.59%) number of supplementary alignments = 2,253 (0.23%) number of secondary alignments = 0 number of mapped bases = 52,949,407 bp number of sequenced bases = 52,931,627 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,780 duplication rate = 1.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8033 >>>>>>> ACTG content number of A's = 12,814,087 bp (24.21%) number of C's = 10,708,922 bp (20.23%) number of T's = 16,933,694 bp (31.99%) number of G's = 12,474,320 bp (23.57%) number of N's = 604 bp (0%) GC percentage = 43.8% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 259,127 number of insertions = 3,577 mapped reads with insertion percentage = 0.39% number of deletions = 10,435 mapped reads with deletion percentage = 1.14% homopolymer indels = 42.81% >>>>>>> Coverage mean coverageData = 0.0171X std coverageData = 0.1755X There is a 1.59% of reference with a coverageData >= 1X There is a 0.09% of reference with a coverageData >= 2X There is a 0.01% 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 4364104 0.017508899205510905 0.2942706334805645 chr2 243199373 4544765 0.018687404263990435 0.19405174079735987 chr3 198022430 3610685 0.018233717261221367 0.14274854815438134 chr4 191154276 3548705 0.018564612177443523 0.15279804852471995 chr5 180915260 3305455 0.018270736255194837 0.14281669347439951 chr6 171115067 3141917 0.018361428102646273 0.16315580884157518 chr7 159138663 2962721 0.018617229428401067 0.20158202249902238 chr8 146364022 2811884 0.019211579195329846 0.18485338955521005 chr9 141213431 2247020 0.01591222579954169 0.15414428451824222 chr10 135534747 2615364 0.01929663099603528 0.18253618726410742 chr11 135006516 2480532 0.018373424287165516 0.1717778255775543 chr12 133851895 2457314 0.018358455067072454 0.14397610916406978 chr13 115169878 1736677 0.015079264041592542 0.13048797136575763 chr14 107349540 1626371 0.015150237252996147 0.13420311648428018 chr15 102531392 1551558 0.015132516683280766 0.13427029113193018 chr16 90354753 1587107 0.017565285137794578 0.14517653525136118 chr17 81195210 1468652 0.018087914299378005 0.15231175334428193 chr18 78077248 1460199 0.01870197832792467 0.22871833992068996 chr19 59128983 1083642 0.018326748491513882 0.20820804436128976 chr20 63025520 1159607 0.018399007259281636 0.1482453319262361 chr21 48129895 705268 0.014653429017453706 0.1344189739579917 chr22 51304566 623291 0.012148840709421458 0.11539077530454366 chrMT 16571 7170 0.4326836038863074 0.685534147343287 chrX 155270560 1706825 0.01099258610260696 0.12097375446339005 chrY 59373566 142574 0.0024013043110801195 0.0810021993710566