BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617659.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,126,397 (94.14%) number of supplementary alignments = 184,479 (0.58%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,283,873 number of mapped paired reads (second in pair) = 14,842,524 number of mapped paired reads (both in pair) = 29,312,920 number of mapped paired reads (singletons) = 813,477 number of mapped bases = 2,907,535,577 bp number of sequenced bases = 2,905,764,319 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,946,659 duplication rate = 10.76% >>>>>>> Insert size mean insert size = 51,013.7814 std insert size = 2,128,170.3849 median insert size = 223 >>>>>>> Mapping quality mean mapping quality = 52.5131 >>>>>>> ACTG content number of A's = 865,728,673 bp (29.79%) number of C's = 577,965,723 bp (19.89%) number of T's = 864,660,351 bp (29.76%) number of G's = 594,312,710 bp (20.45%) number of N's = 3,096,862 bp (0.11%) GC percentage = 40.34% >>>>>>> Mismatches and indels general error rate = 0.0141 number of mismatches = 40,167,194 number of insertions = 458,140 mapped reads with insertion percentage = 1.49% number of deletions = 1,065,604 mapped reads with deletion percentage = 3.46% homopolymer indels = 47.57% >>>>>>> Coverage mean coverageData = 0.9392X std coverageData = 10.5454X There is a 33.16% of reference with a coverageData >= 1X There is a 19.13% of reference with a coverageData >= 2X There is a 11.65% of reference with a coverageData >= 3X There is a 7.42% of reference with a coverageData >= 4X There is a 4.87% of reference with a coverageData >= 5X There is a 3.29% of reference with a coverageData >= 6X There is a 2.28% of reference with a coverageData >= 7X There is a 1.61% of reference with a coverageData >= 8X There is a 1.17% of reference with a coverageData >= 9X There is a 0.86% of reference with a coverageData >= 10X There is a 0.65% of reference with a coverageData >= 11X There is a 0.5% of reference with a coverageData >= 12X There is a 0.39% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.24% of reference with a coverageData >= 15X There is a 0.2% of reference with a coverageData >= 16X There is a 0.16% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 178170109 0.7148231297686516 10.15957982559397 chr2 243199373 300807832 1.2368774980353259 12.138417880848433 chr3 198022430 243292808 1.2286123748708668 2.4821198445798673 chr4 191154276 162808608 0.8517131366708218 8.25921546606046 chr5 180915260 192416166 1.0635706794440667 2.325109910213736 chr6 171115067 140877158 0.8232890327536149 5.710576568647551 chr7 159138663 227503846 1.4295950569849893 13.21692475474498 chr8 146364022 129107435 0.8820981634407395 4.068342529076152 chr9 141213431 119324630 0.8449949070354363 20.411142930496872 chr10 135534747 123028992 0.9077302663943438 21.314921423106636 chr11 135006516 159790122 1.1835734061902612 11.968501349955902 chr12 133851895 124171260 0.927676518886789 2.211523594916057 chr13 115169878 124652746 1.0823380919097614 2.325845637381495 chr14 107349540 83180386 0.7748555419985964 2.449918659363041 chr15 102531392 62257829 0.607207488219803 1.7808310125568474 chr16 90354753 80553583 0.8915256843212221 16.590264939180603 chr17 81195210 71781075 0.8840555372662994 12.664142546633938 chr18 78077248 53710798 0.6879186879127707 18.24643158603029 chr19 59128983 30888278 0.5223881154864443 6.1892381039852955 chr20 63025520 78542056 1.246194493912942 3.0279919147818855 chr21 48129895 42436772 0.8817133716996474 4.321300577999652 chr22 51304566 18730451 0.3650835093313137 1.2769488941096696 chrMT 16571 3081439 185.95371432019795 131.52647411245619 chrX 155270560 144601137 0.9312849583333763 4.3724254774841285 chrY 59373566 11820061 0.19907951966368334 17.382689545168912