BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472704.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 15,885,402 number of mapped reads = 15,722,737 (98.98%) number of supplementary alignments = 57,113 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,894,472 number of mapped paired reads (second in pair) = 7,828,265 number of mapped paired reads (both in pair) = 15,622,742 number of mapped paired reads (singletons) = 99,995 number of mapped bases = 1,550,598,687 bp number of sequenced bases = 1,550,374,661 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,596,421 duplication rate = 47.16% >>>>>>> Insert size mean insert size = 23,302.0842 std insert size = 1,480,756.5192 median insert size = 244 >>>>>>> Mapping quality mean mapping quality = 55.0771 >>>>>>> ACTG content number of A's = 431,040,314 bp (27.8%) number of C's = 346,886,757 bp (22.37%) number of T's = 428,989,400 bp (27.67%) number of G's = 343,158,482 bp (22.13%) number of N's = 299,708 bp (0.02%) GC percentage = 44.51% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 9,803,656 number of insertions = 94,640 mapped reads with insertion percentage = 0.6% number of deletions = 87,514 mapped reads with deletion percentage = 0.55% homopolymer indels = 45.24% >>>>>>> Coverage mean coverageData = 0.5009X std coverageData = 15.5471X There is a 4.6% of reference with a coverageData >= 1X There is a 1.95% of reference with a coverageData >= 2X There is a 0.88% of reference with a coverageData >= 3X There is a 0.65% of reference with a coverageData >= 4X There is a 0.5% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.41% of reference with a coverageData >= 7X There is a 0.39% of reference with a coverageData >= 8X There is a 0.37% of reference with a coverageData >= 9X There is a 0.36% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.31% of reference with a coverageData >= 15X There is a 0.3% of reference with a coverageData >= 16X There is a 0.29% of reference with a coverageData >= 17X There is a 0.28% of reference with a coverageData >= 18X There is a 0.28% of reference with a coverageData >= 19X There is a 0.27% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.26% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.24% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.21% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 154331404 0.6191816228213128 17.290091386491827 chr2 243199373 95625640 0.3931985466097398 11.114956228667648 chr3 198022430 179174203 0.9048177168616707 18.84602755970419 chr4 191154276 48513835 0.25379413955667934 8.837299800171806 chr5 180915260 83299002 0.46043104379365235 14.862865547962617 chr6 171115067 84474155 0.493668713579734 12.971567963492392 chr7 159138663 69727181 0.43815361826937055 12.21039785178275 chr8 146364022 75915516 0.5186760719106229 21.115083838117595 chr9 141213431 104289400 0.7385232357961757 21.707634292728347 chr10 135534747 31936924 0.2356364305604968 7.27518690448934 chr11 135006516 80561339 0.5967218574842713 20.601288238413474 chr12 133851895 95980644 0.7170660079186776 19.622484438544042 chr13 115169878 36529390 0.3171783337306305 13.48107990425507 chr14 107349540 32545793 0.303175896235792 8.955618989882844 chr15 102531392 38650135 0.37695903904240374 11.867012665130328 chr16 90354753 57808364 0.6397932823744203 18.78050520537182 chr17 81195210 60691134 0.7474718520957087 16.979367171955424 chr18 78077248 33766769 0.43247898542735524 16.788097896578485 chr19 59128983 40803932 0.6900834401295216 22.296650174492292 chr20 63025520 28677372 0.4550120649540059 11.080962194444785 chr21 48129895 5071993 0.10538134354957558 3.6685786446153834 chr22 51304566 13306757 0.25936788939994154 8.99117006772149 chrMT 16571 3621 0.21851427192082554 0.779490660216462 chrX 155270560 98666633 0.6354497143566687 18.79153764117753 chrY 59373566 247551 0.004169380697127068 0.37855586658077794