BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472471.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 = 17,928,038 number of mapped reads = 17,731,679 (98.9%) number of supplementary alignments = 64,372 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,889,688 number of mapped paired reads (second in pair) = 8,841,991 number of mapped paired reads (both in pair) = 17,633,136 number of mapped paired reads (singletons) = 98,543 number of mapped bases = 1,740,353,760 bp number of sequenced bases = 1,740,133,522 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,102,214 duplication rate = 46.2% >>>>>>> Insert size mean insert size = 30,402.0644 std insert size = 1,723,761.9053 median insert size = 228 >>>>>>> Mapping quality mean mapping quality = 55.0691 >>>>>>> ACTG content number of A's = 479,760,259 bp (27.57%) number of C's = 392,754,853 bp (22.57%) number of T's = 476,641,117 bp (27.39%) number of G's = 390,706,513 bp (22.45%) number of N's = 270,780 bp (0.02%) GC percentage = 45.02% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 10,236,071 number of insertions = 94,604 mapped reads with insertion percentage = 0.53% number of deletions = 87,469 mapped reads with deletion percentage = 0.49% homopolymer indels = 44.2% >>>>>>> Coverage mean coverageData = 0.5622X std coverageData = 18.597X There is a 5.74% of reference with a coverageData >= 1X There is a 2.61% of reference with a coverageData >= 2X There is a 1.1% of reference with a coverageData >= 3X There is a 0.76% of reference with a coverageData >= 4X There is a 0.53% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.41% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.34% 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 0.29% 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 0.19% 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 0.18% 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 0.16% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 208022518 0.8345917741966228 24.915286757892567 chr2 243199373 147320014 0.6057581982335127 19.391594752208167 chr3 198022430 169903239 0.8579999700033981 19.13889465021134 chr4 191154276 76814616 0.40184618208592937 15.429067424076598 chr5 180915260 86616863 0.478770353589852 15.344578047396322 chr6 171115067 104555088 0.6110221024546015 18.84943381489275 chr7 159138663 62173160 0.3906854489534074 15.989339298363468 chr8 146364022 82404999 0.5630140376984174 16.6862144239328 chr9 141213431 119286553 0.8447252655450316 22.601120096249723 chr10 135534747 52001766 0.383678482094337 23.630164992689956 chr11 135006516 97872961 0.7249499053808632 24.074700561093298 chr12 133851895 93952854 0.7019165025642707 23.084554655708267 chr13 115169878 36148610 0.3138720872831002 10.94922065800232 chr14 107349540 39546405 0.3683891426083428 12.716929883515592 chr15 102531392 35988386 0.3509987068155673 9.907522123139264 chr16 90354753 51740581 0.5726381765439611 19.155495643747585 chr17 81195210 54947302 0.6767308317818256 17.592563278584226 chr18 78077248 32715859 0.4190191104071701 13.601749947203588 chr19 59128983 41352637 0.6993632378219663 20.1176007069302 chr20 63025520 27601366 0.4379395203720652 12.112864843508865 chr21 48129895 7870478 0.16352576709340422 6.340250256894919 chr22 51304566 16992779 0.3312137753976907 8.778650239248003 chrMT 16571 1428 0.08617464244764951 0.3616174223322986 chrX 155270560 91389857 0.588584577784739 21.354263464290252 chrY 59373566 3133441 0.05277501775790257 2.031108840103284