BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819141.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 4,971,334 number of mapped reads = 4,338,277 (87.27%) number of supplementary alignments = 28,220 (0.57%) number of secondary alignments = 0 number of mapped bases = 247,214,092 bp number of sequenced bases = 247,145,280 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 208,344 duplication rate = 2.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.2798 >>>>>>> ACTG content number of A's = 64,071,571 bp (25.92%) number of C's = 44,978,560 bp (18.2%) number of T's = 76,342,776 bp (30.89%) number of G's = 61,748,940 bp (24.98%) number of N's = 3,433 bp (0%) GC percentage = 43.18% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 1,286,840 number of insertions = 18,981 mapped reads with insertion percentage = 0.44% number of deletions = 41,096 mapped reads with deletion percentage = 0.94% homopolymer indels = 40.8% >>>>>>> Coverage mean coverageData = 0.0799X std coverageData = 0.9782X There is a 6.79% of reference with a coverageData >= 1X There is a 0.71% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 23729185 0.09520210984750165 2.383450964316804 chr2 243199373 19916629 0.08189424485070528 1.0219805819926455 chr3 198022430 13950903 0.07045112515789247 0.32540309486505836 chr4 191154276 14054319 0.07352343507084298 0.45890908214737103 chr5 180915260 13587419 0.07510377510443288 0.3471424931834773 chr6 171115067 11167445 0.0652627801618428 0.5323024296378885 chr7 159138663 13011503 0.08176204798201679 1.390347793936064 chr8 146364022 20834137 0.14234466035649115 0.7940055801477555 chr9 141213431 10325449 0.07311945419695949 0.6736081597814352 chr10 135534747 12822509 0.09460680219515959 0.8495591869515154 chr11 135006516 8918035 0.06605633019964754 0.7720786709067018 chr12 133851895 11453787 0.08557060025186793 0.3629216591926409 chr13 115169878 5707769 0.049559564524328144 0.2701781153096976 chr14 107349540 6038467 0.0562505158382607 0.33561085024569126 chr15 102531392 6424984 0.06266357916997753 0.3622239101928456 chr16 90354753 7544943 0.08350355404103645 0.44175123907199837 chr17 81195210 8309060 0.10233436184228109 0.4659432522222727 chr18 78077248 5925195 0.07588888122696127 1.5927363238839918 chr19 59128983 5489121 0.09283300204909663 1.5746954338646708 chr20 63025520 6474460 0.10272759352084679 0.40234902948989626 chr21 48129895 3247054 0.06746438985582662 0.4090488024360628 chr22 51304566 2066176 0.04027275077231917 0.23019447617042582 chrMT 16571 137315 8.28646430511134 5.463383624418879 chrX 155270560 15104630 0.09727941987199634 0.5571538422982723 chrY 59373566 973598 0.01639783603363153 0.4957822888946509