BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472480.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 = 16,526,178 number of mapped reads = 16,336,611 (98.85%) number of supplementary alignments = 80,121 (0.48%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,183,941 number of mapped paired reads (second in pair) = 8,152,670 number of mapped paired reads (both in pair) = 16,249,564 number of mapped paired reads (singletons) = 87,047 number of mapped bases = 1,597,977,411 bp number of sequenced bases = 1,597,785,150 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,202,912 duplication rate = 44.71% >>>>>>> Insert size mean insert size = 33,396.1154 std insert size = 1,757,929.3421 median insert size = 206 >>>>>>> Mapping quality mean mapping quality = 54.6481 >>>>>>> ACTG content number of A's = 450,081,800 bp (28.17%) number of C's = 351,004,611 bp (21.97%) number of T's = 446,556,427 bp (27.95%) number of G's = 349,888,107 bp (21.9%) number of N's = 254,205 bp (0.02%) GC percentage = 43.87% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 8,413,490 number of insertions = 88,184 mapped reads with insertion percentage = 0.54% number of deletions = 78,786 mapped reads with deletion percentage = 0.48% homopolymer indels = 43.01% >>>>>>> Coverage mean coverageData = 0.5162X std coverageData = 25.6831X There is a 5.05% of reference with a coverageData >= 1X There is a 2.63% of reference with a coverageData >= 2X There is a 1.21% of reference with a coverageData >= 3X There is a 0.81% of reference with a coverageData >= 4X There is a 0.52% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.33% of reference with a coverageData >= 7X There is a 0.29% of reference with a coverageData >= 8X There is a 0.26% of reference with a coverageData >= 9X There is a 0.24% of reference with a coverageData >= 10X There is a 0.22% of reference with a coverageData >= 11X There is a 0.21% of reference with a coverageData >= 12X There is a 0.2% of reference with a coverageData >= 13X There is a 0.19% of reference with a coverageData >= 14X There is a 0.19% of reference with a coverageData >= 15X There is a 0.18% of reference with a coverageData >= 16X There is a 0.18% of reference with a coverageData >= 17X There is a 0.17% of reference with a coverageData >= 18X There is a 0.17% of reference with a coverageData >= 19X There is a 0.16% of reference with a coverageData >= 20X There is a 0.16% of reference with a coverageData >= 21X There is a 0.15% of reference with a coverageData >= 22X There is a 0.15% of reference with a coverageData >= 23X There is a 0.15% of reference with a coverageData >= 24X There is a 0.14% of reference with a coverageData >= 25X There is a 0.14% of reference with a coverageData >= 26X There is a 0.14% of reference with a coverageData >= 27X There is a 0.14% of reference with a coverageData >= 28X There is a 0.13% of reference with a coverageData >= 29X There is a 0.13% of reference with a coverageData >= 30X There is a 0.13% of reference with a coverageData >= 31X There is a 0.13% of reference with a coverageData >= 32X There is a 0.13% of reference with a coverageData >= 33X There is a 0.12% of reference with a coverageData >= 34X There is a 0.12% of reference with a coverageData >= 35X There is a 0.12% of reference with a coverageData >= 36X There is a 0.12% of reference with a coverageData >= 37X There is a 0.12% of reference with a coverageData >= 38X There is a 0.12% of reference with a coverageData >= 39X There is a 0.11% of reference with a coverageData >= 40X There is a 0.11% of reference with a coverageData >= 41X There is a 0.11% of reference with a coverageData >= 42X There is a 0.11% of reference with a coverageData >= 43X There is a 0.11% of reference with a coverageData >= 44X There is a 0.11% of reference with a coverageData >= 45X There is a 0.11% of reference with a coverageData >= 46X There is a 0.1% of reference with a coverageData >= 47X There is a 0.1% of reference with a coverageData >= 48X There is a 0.1% of reference with a coverageData >= 49X There is a 0.1% of reference with a coverageData >= 50X There is a 0.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 139945820 0.5614662841702609 23.30518608310275 chr2 243199373 84589644 0.3478201565922623 16.077547398389818 chr3 198022430 178477800 0.901300928384729 30.394623306863537 chr4 191154276 74618641 0.39035820993091463 19.58842322359807 chr5 180915260 90585682 0.5007078009892587 19.281444913671194 chr6 171115067 113182218 0.6614392290773553 29.606612085948328 chr7 159138663 71662730 0.4503162754358443 22.271818399243784 chr8 146364022 64742379 0.4423380699390729 20.893164418584668 chr9 141213431 120586391 0.8539300415411619 26.350627324264373 chr10 135534747 37236773 0.27473967985493786 16.57991896500138 chr11 135006516 58770801 0.4353182553055439 18.038362122145408 chr12 133851895 90460569 0.675825837206115 35.19566631762733 chr13 115169878 56596351 0.4914162625057222 30.495056090840315 chr14 107349540 50969735 0.47480161535857535 39.363487295914524 chr15 102531392 32227544 0.3143187990659485 18.413836155744523 chr16 90354753 78697617 0.8709848058574184 47.27774228028002 chr17 81195210 32663557 0.40228428499661495 16.577677422142955 chr18 78077248 35787141 0.4583555634542857 33.6533495307651 chr19 59128983 21950802 0.37123591318998334 11.873423266438873 chr20 63025520 59048451 0.936897482162781 42.21039428221618 chr21 48129895 10014798 0.20807853414182598 14.445694514312635 chr22 51304566 13454014 0.2622381407533981 14.688524545685116 chrMT 16571 4108 0.24790296300766398 0.8197889753730375 chrX 155270560 79431019 0.5115652252429566 27.742001237895934 chrY 59373566 2272826 0.038280099261681536 1.0862147267712599