BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081925.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,838,242 number of mapped reads = 2,607,072 (91.86%) number of supplementary alignments = 17,336 (0.61%) number of secondary alignments = 0 number of mapped bases = 176,401,751 bp number of sequenced bases = 176,338,179 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 135,012 duplication rate = 3.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.992 >>>>>>> ACTG content number of A's = 49,298,954 bp (27.96%) number of C's = 32,695,005 bp (18.54%) number of T's = 55,300,132 bp (31.36%) number of G's = 39,021,795 bp (22.13%) number of N's = 22,293 bp (0.01%) GC percentage = 40.67% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,354,141 number of insertions = 12,965 mapped reads with insertion percentage = 0.49% number of deletions = 35,289 mapped reads with deletion percentage = 1.34% homopolymer indels = 47.33% >>>>>>> Coverage mean coverageData = 0.057X std coverageData = 0.6117X There is a 4.86% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% 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 16201941 0.06500261036460968 1.1918066546526818 chr2 243199373 15718792 0.06463335742234828 0.8497316818407213 chr3 198022430 11053616 0.05582001998460477 0.2672810096850328 chr4 191154276 8984777 0.04700275185055238 0.29158562303379115 chr5 180915260 8836027 0.04884069480927148 0.2538779969312487 chr6 171115067 15309707 0.08947024518887048 0.5093637290077172 chr7 159138663 11626605 0.07305958703448451 0.8940084004977382 chr8 146364022 10139296 0.069274510644426 0.7673091037467825 chr9 141213431 8608262 0.060959229862490916 0.619858227473459 chr10 135534747 7194643 0.05308338384989939 0.6120569166788239 chr11 135006516 7903840 0.05854413723260587 0.4175888138820026 chr12 133851895 7477845 0.05586656057428249 0.2837334002216256 chr13 115169878 4700844 0.04081661005145807 0.22424601882383152 chr14 107349540 4433120 0.04129612479010157 0.2760216357965272 chr15 102531392 3946845 0.038494015569397515 0.2256476861740468 chr16 90354753 3829145 0.04237901021100683 0.29720157327827834 chr17 81195210 4622236 0.05692744682845207 0.3313013125661745 chr18 78077248 5058469 0.0647880032861814 0.9842484700424965 chr19 59128983 3721497 0.06293862689977266 0.84508107576315 chr20 63025520 4456087 0.0707028993969427 0.3197321390321432 chr21 48129895 1902820 0.039535095599107374 0.28322336348019395 chr22 51304566 1372736 0.026756604860471874 0.1813018238274124 chrMT 16571 129693 7.826504133727596 4.938896086856711 chrX 155270560 8742788 0.05630679763118005 0.34939906099383816 chrY 59373566 430120 0.007244301277103686 0.20594736182879195