BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971281.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 12,401,029 number of mapped reads = 8,947,849 (72.15%) number of secondary alignments = 0 number of mapped bases = 353,345,711 bp number of sequenced bases = 353,309,898 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 921,621 duplication rate = 9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6475 >>>>>>> ACTG content number of A's = 101,527,566 bp (28.74%) number of C's = 72,693,935 bp (20.58%) number of T's = 103,886,566 bp (29.4%) number of G's = 75,198,829 bp (21.28%) number of N's = 3,002 bp (0%) GC percentage = 41.86% >>>>>>> Mismatches and indels general error rate = 0.0027 number of mismatches = 928,455 number of insertions = 11,120 mapped reads with insertion percentage = 0.12% number of deletions = 27,775 mapped reads with deletion percentage = 0.31% homopolymer indels = 40.84% >>>>>>> Coverage mean coverageData = 0.1141X std coverageData = 1.2834X There is a 5.92% of reference with a coverageData >= 1X There is a 2.64% of reference with a coverageData >= 2X There is a 1.31% of reference with a coverageData >= 3X There is a 0.66% of reference with a coverageData >= 4X There is a 0.34% of reference with a coverageData >= 5X There is a 0.18% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% 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 0.01% 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 29277921 0.11746378357067364 1.6313300539171103 chr2 243199373 30185307 0.12411753627341794 0.6946152533224231 chr3 198022430 24475234 0.12359829136527614 0.5958631193757831 chr4 191154276 23062911 0.12065077215432 0.6378331038222277 chr5 180915260 22314872 0.12334433258974395 0.6069010641001734 chr6 171115067 20609007 0.12043946428165792 0.6100597405390299 chr7 159138663 18593447 0.11683802445921014 1.0454277171329938 chr8 146364022 19182962 0.13106337020446185 4.644923154713177 chr9 141213431 15097580 0.10691320147868938 0.632975775720575 chr10 135534747 17516137 0.12923724275664897 0.8403475979137668 chr11 135006516 16453902 0.12187487306168245 0.6850777010509198 chr12 133851895 16606437 0.12406575939772836 0.6124273893485812 chr13 115169878 11223316 0.09745009888783593 0.5315017747652948 chr14 107349540 11030679 0.10275478590779243 0.5766444066180259 chr15 102531392 10550539 0.10290057312398529 0.5421890138153875 chr16 90354753 9845716 0.10896732792795084 0.5771339486705087 chr17 81195210 9402589 0.11580226222704516 0.5906949082542171 chr18 78077248 9629479 0.12333271531291677 0.9412459200284394 chr19 59128983 6740587 0.11399802022639219 1.3278169528254202 chr20 63025520 8143184 0.1292045507914889 0.6349923296591707 chr21 48129895 4802896 0.0997902862659476 0.5874435637151885 chr22 51304566 4443577 0.08661172574776288 0.5187248185178869 chrMT 16571 68512 4.134451753062579 5.303278909331811 chrX 155270560 11049851 0.07116513909655507 0.47257654735493543 chrY 59373566 3039069 0.05118555621200182 0.5776573070436045