BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174013.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 4,658,992 number of mapped reads = 4,552,798 (97.72%) number of supplementary alignments = 464,043 (9.96%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,274,892 number of mapped paired reads (second in pair) = 2,277,906 number of mapped paired reads (both in pair) = 4,477,418 number of mapped paired reads (singletons) = 75,380 number of mapped bases = 539,241,935 bp number of sequenced bases = 538,937,861 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,507,273 duplication rate = 64.74% >>>>>>> Insert size mean insert size = 844,543.4081 std insert size = 8,760,314.3759 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 52.6924 >>>>>>> ACTG content number of A's = 161,929,927 bp (30.05%) number of C's = 105,795,493 bp (19.63%) number of T's = 161,626,169 bp (29.99%) number of G's = 109,579,861 bp (20.33%) number of N's = 6,411 bp (0%) GC percentage = 39.96% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 5,358,961 number of insertions = 56,595 mapped reads with insertion percentage = 1.21% number of deletions = 122,548 mapped reads with deletion percentage = 2.63% homopolymer indels = 43.04% >>>>>>> Coverage mean coverageData = 0.1742X std coverageData = 2.6554X There is a 3.77% of reference with a coverageData >= 1X There is a 2.95% of reference with a coverageData >= 2X There is a 2.25% of reference with a coverageData >= 3X There is a 1.83% of reference with a coverageData >= 4X There is a 1.38% of reference with a coverageData >= 5X There is a 1.1% of reference with a coverageData >= 6X There is a 0.8% of reference with a coverageData >= 7X There is a 0.65% of reference with a coverageData >= 8X There is a 0.47% of reference with a coverageData >= 9X There is a 0.39% of reference with a coverageData >= 10X There is a 0.28% of reference with a coverageData >= 11X There is a 0.24% of reference with a coverageData >= 12X There is a 0.18% of reference with a coverageData >= 13X There is a 0.15% of reference with a coverageData >= 14X There is a 0.11% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% 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 49387108 0.1981423669151059 2.1535956184460328 chr2 243199373 54801646 0.2253362964056655 7.698894967983232 chr3 198022430 39275216 0.19833720856773648 1.268848261136207 chr4 191154276 32804110 0.171610652329849 1.3707972131935846 chr5 180915260 30412892 0.16810573082668648 1.163904456234438 chr6 171115067 33742412 0.19719135545205962 1.335965597570394 chr7 159138663 36934431 0.23208961482854734 2.5363236724208296 chr8 146364022 26981319 0.18434392982177 1.382326335381996 chr9 141213431 22801660 0.1614694851511681 1.387964436076937 chr10 135534747 24459633 0.1804676183886631 2.713606786481491 chr11 135006516 20526396 0.15204003931188032 1.131900771110434 chr12 133851895 18771244 0.14023891107406436 1.060318898406517 chr13 115169878 20814827 0.18073151905222995 1.209604286896984 chr14 107349540 11017911 0.10263584734503753 0.9036857028884699 chr15 102531392 9774094 0.09532781921072524 0.859229076048199 chr16 90354753 21640407 0.23950491016228 2.308206449170484 chr17 81195210 14097319 0.17362254497525162 1.3229210528081123 chr18 78077248 9215195 0.11802663690195637 1.846581242736971 chr19 59128983 11240334 0.1900985511622955 2.4343157117959056 chr20 63025520 16222668 0.2573983998862683 1.4364277763586344 chr21 48129895 8782126 0.18246717554650804 1.2400420698121781 chr22 51304566 4077310 0.07947265356459696 0.7532188435577979 chrMT 16571 1175145 70.91575644197695 60.446384923489916 chrX 155270560 19537880 0.12583119427147038 1.0123724789597914 chrY 59373566 748652 0.012609180321087671 0.5302034937653674