BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472501.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 = 19,758,460 number of mapped reads = 19,496,947 (98.68%) number of supplementary alignments = 85,355 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,776,455 number of mapped paired reads (second in pair) = 9,720,492 number of mapped paired reads (both in pair) = 19,375,644 number of mapped paired reads (singletons) = 121,303 number of mapped bases = 1,918,470,011 bp number of sequenced bases = 1,918,238,540 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,655,139 duplication rate = 45.91% >>>>>>> Insert size mean insert size = 24,762.2847 std insert size = 1,556,743.3004 median insert size = 232 >>>>>>> Mapping quality mean mapping quality = 54.9355 >>>>>>> ACTG content number of A's = 526,322,614 bp (27.44%) number of C's = 435,407,414 bp (22.7%) number of T's = 523,355,703 bp (27.28%) number of G's = 432,856,433 bp (22.57%) number of N's = 296,376 bp (0.02%) GC percentage = 45.26% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 11,644,792 number of insertions = 102,617 mapped reads with insertion percentage = 0.52% number of deletions = 97,870 mapped reads with deletion percentage = 0.5% homopolymer indels = 44.72% >>>>>>> Coverage mean coverageData = 0.6197X std coverageData = 22.6811X There is a 5.99% of reference with a coverageData >= 1X There is a 2.7% of reference with a coverageData >= 2X There is a 1.17% of reference with a coverageData >= 3X There is a 0.8% of reference with a coverageData >= 4X There is a 0.55% of reference with a coverageData >= 5X There is a 0.47% of reference with a coverageData >= 6X There is a 0.42% of reference with a coverageData >= 7X There is a 0.39% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.35% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.25% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.2% 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 0.19% of reference with a coverageData >= 38X There is a 0.19% 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 0.18% 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 0.17% of reference with a coverageData >= 46X There is a 0.17% 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 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 199161663 0.7990417925578609 30.264790765886396 chr2 243199373 103421420 0.4252536456991606 18.07966656358831 chr3 198022430 214574999 1.0835893640937544 27.913550815905534 chr4 191154276 66513896 0.3479592368626899 15.977797257545115 chr5 180915260 99162215 0.5481141557655225 15.938324024419138 chr6 171115067 138797260 0.8111340657102978 28.020748015574075 chr7 159138663 77989237 0.4900709578036357 15.528836975321905 chr8 146364022 78254162 0.5346543565193911 20.281970159536506 chr9 141213431 115026806 0.8145599549946492 23.259495108894576 chr10 135534747 50720488 0.3742249801078686 18.76343630528807 chr11 135006516 96616409 0.71564256202271 23.23472476629691 chr12 133851895 95166686 0.7109849733543182 21.27943853845394 chr13 115169878 62391767 0.5417368506720134 26.988518910164203 chr14 107349540 57730381 0.5377794911836604 18.484404111830077 chr15 102531392 51065184 0.49804438429939585 19.66093671512535 chr16 90354753 77772914 0.8607506679809085 32.37194271418549 chr17 81195210 74656797 0.9194729221095678 26.52786863210567 chr18 78077248 21799861 0.2792088804154573 9.048446960015088 chr19 59128983 48872905 0.8265473634139793 22.348071828947884 chr20 63025520 45622085 0.7238668558387142 23.140149570764454 chr21 48129895 11822361 0.24563446481651371 9.624492330608733 chr22 51304566 12574514 0.24509541704338753 7.020288279131521 chrMT 16571 3576 0.21579868444873573 0.7297361643883882 chrX 155270560 116659734 0.7513319588723065 31.72214965261618 chrY 59373566 2092691 0.03524617335600156 0.8056354651514435