BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472552.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 = 20,571,068 number of mapped reads = 20,324,904 (98.8%) number of supplementary alignments = 105,105 (0.51%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,188,284 number of mapped paired reads (second in pair) = 10,136,620 number of mapped paired reads (both in pair) = 20,209,064 number of mapped paired reads (singletons) = 115,840 number of mapped bases = 1,995,969,164 bp number of sequenced bases = 1,995,730,802 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,173,965 duplication rate = 46.61% >>>>>>> Insert size mean insert size = 39,558.468 std insert size = 1,965,611.0821 median insert size = 230 >>>>>>> Mapping quality mean mapping quality = 55.0164 >>>>>>> ACTG content number of A's = 551,916,556 bp (27.65%) number of C's = 448,795,943 bp (22.49%) number of T's = 548,446,079 bp (27.48%) number of G's = 446,262,518 bp (22.36%) number of N's = 309,706 bp (0.02%) GC percentage = 44.85% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 11,687,344 number of insertions = 105,598 mapped reads with insertion percentage = 0.51% number of deletions = 99,006 mapped reads with deletion percentage = 0.48% homopolymer indels = 45% >>>>>>> Coverage mean coverageData = 0.6448X std coverageData = 22.4783X There is a 6.1% of reference with a coverageData >= 1X There is a 2.78% of reference with a coverageData >= 2X There is a 1.19% of reference with a coverageData >= 3X There is a 0.82% of reference with a coverageData >= 4X There is a 0.57% of reference with a coverageData >= 5X There is a 0.5% of reference with a coverageData >= 6X There is a 0.44% of reference with a coverageData >= 7X There is a 0.41% of reference with a coverageData >= 8X There is a 0.38% of reference with a coverageData >= 9X There is a 0.37% of reference with a coverageData >= 10X There is a 0.35% of reference with a coverageData >= 11X There is a 0.34% of reference with a coverageData >= 12X There is a 0.33% of reference with a coverageData >= 13X There is a 0.32% of reference with a coverageData >= 14X There is a 0.31% of reference with a coverageData >= 15X There is a 0.31% of reference with a coverageData >= 16X There is a 0.3% of reference with a coverageData >= 17X There is a 0.29% of reference with a coverageData >= 18X There is a 0.28% of reference with a coverageData >= 19X There is a 0.28% of reference with a coverageData >= 20X There is a 0.27% of reference with a coverageData >= 21X There is a 0.27% of reference with a coverageData >= 22X There is a 0.26% of reference with a coverageData >= 23X There is a 0.26% of reference with a coverageData >= 24X There is a 0.25% of reference with a coverageData >= 25X There is a 0.25% of reference with a coverageData >= 26X There is a 0.24% of reference with a coverageData >= 27X There is a 0.24% of reference with a coverageData >= 28X There is a 0.24% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.23% of reference with a coverageData >= 32X There is a 0.22% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.22% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.21% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.2% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.19% of reference with a coverageData >= 46X There is a 0.19% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.18% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 190561423 0.7645374051043989 30.82458094903841 chr2 243199373 147346824 0.6058684370045642 21.433985646437943 chr3 198022430 225035938 1.1364164049496817 26.884693087647936 chr4 191154276 73402177 0.383994428667659 16.438468834021386 chr5 180915260 133674219 0.7388775219956569 24.347965289542337 chr6 171115067 138783927 0.8110561473818083 21.892372387953156 chr7 159138663 71637455 0.4501574516809909 16.425460340873173 chr8 146364022 74232388 0.5071764699114376 18.109892227597356 chr9 141213431 119844599 0.8486770567878915 21.283581515919085 chr10 135534747 47618494 0.3513379045153639 13.23447220706606 chr11 135006516 84264511 0.6241514372535916 19.203384847817205 chr12 133851895 114156275 0.8528551276767505 28.27387389048317 chr13 115169878 40161942 0.34871915033199913 11.301115450246378 chr14 107349540 82012687 0.7639780012098795 43.048553281177206 chr15 102531392 74117890 0.7228799741644003 26.165271224282694 chr16 90354753 69645340 0.7707988532711721 24.676340429039122 chr17 81195210 76065779 0.9368259408405989 21.672155258060187 chr18 78077248 40131254 0.5139942176240638 20.96020299353849 chr19 59128983 29813308 0.5042080294193458 11.520372167697058 chr20 63025520 40005386 0.6347490032609013 18.6926027611705 chr21 48129895 15067391 0.31305680180686035 14.982218597799562 chr22 51304566 23588522 0.45977432106140415 15.016055079169654 chrMT 16571 1920 0.11586506547583127 0.44918872110542857 chrX 155270560 81726470 0.5263487811211603 14.41607820457838 chrY 59373566 3073045 0.05175779740095112 1.73815968003006