BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504416.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 2,103,881 number of mapped reads = 1,852,908 (88.07%) number of secondary alignments = 0 number of mapped bases = 59,286,408 bp number of sequenced bases = 59,286,408 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 245,719 duplication rate = 3.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 8.4088 >>>>>>> ACTG content number of A's = 16,882,417 bp (28.48%) number of C's = 12,131,731 bp (20.46%) number of T's = 18,541,202 bp (31.27%) number of G's = 11,730,918 bp (19.79%) number of N's = 140 bp (0%) GC percentage = 40.25% >>>>>>> Mismatches and indels general error rate = 0.0006 number of mismatches = 35,856 >>>>>>> Coverage mean coverageData = 0.0192X std coverageData = 1.0601X There is a 1.35% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 4103370 0.016462827589103578 0.18685448020071033 chr2 243199373 4444160 0.01827373132248988 0.2550044454777493 chr3 198022430 3388682 0.017112616989903618 0.1698066046392843 chr4 191154276 3747024 0.019602093546680587 0.2238721863736203 chr5 180915260 3679646 0.02033905818668917 0.2128133477815013 chr6 171115067 9590268 0.05604572506756521 4.390216685180886 chr7 159138663 2673304 0.01679858275546779 0.18092646328340045 chr8 146364022 2717538 0.01856698089370624 0.1776221317716884 chr9 141213431 2037264 0.01442684301042158 0.18252162877422898 chr10 135534747 2188820 0.016149511829612224 0.1662520921121601 chr11 135006516 2634966 0.019517324630464503 0.2500830231425149 chr12 133851895 2336344 0.01745469498209196 0.180617957380481 chr13 115169878 2697734 0.023423954655921404 0.8013050630574476 chr14 107349540 1484566 0.013829272114254052 0.1470070124306964 chr15 102531392 1299054 0.012669817259478931 0.15548885194562836 chr16 90354753 1133944 0.012549909798325718 0.1921817634433794 chr17 81195210 1067410 0.013146218847146278 0.15495520597716392 chr18 78077248 1380552 0.017681873213564084 0.20247331064081925 chr19 59128983 629336 0.010643443672961533 0.1470104405467706 chr20 63025520 892800 0.01416569034257869 0.16948932485150217 chr21 48129895 513950 0.01067839437422417 0.1753804489287992 chr22 51304566 339904 0.006625219283601385 0.10052648147576441 chrMT 16571 96 0.005793253273791563 0.07589263133069815 chrX 155270560 4165162 0.02682518823916137 0.23743038932431648 chrY 59373566 140514 0.0023666087362851002 0.0702021772747082