BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094154.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 50,566 number of mapped reads = 4,662 (9.22%) number of supplementary alignments = 167 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,161 number of mapped paired reads (second in pair) = 2,501 number of mapped paired reads (both in pair) = 4,020 number of mapped paired reads (singletons) = 642 number of mapped bases = 542,713 bp number of sequenced bases = 537,604 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,999 duplication rate = 18.55% >>>>>>> Insert size mean insert size = 265,022.472 std insert size = 5,357,158.9633 median insert size = 149 >>>>>>> Mapping quality mean mapping quality = 9.2034 >>>>>>> ACTG content number of A's = 158,292 bp (29.44%) number of C's = 94,868 bp (17.65%) number of T's = 143,685 bp (26.73%) number of G's = 140,755 bp (26.18%) number of N's = 4 bp (0%) GC percentage = 43.83% >>>>>>> Mismatches and indels general error rate = 0.0302 number of mismatches = 15,603 number of insertions = 233 mapped reads with insertion percentage = 4.48% number of deletions = 1,487 mapped reads with deletion percentage = 31.19% homopolymer indels = 35.87% >>>>>>> Coverage mean coverageData = 0.0002X std coverageData = 0.5847X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 1765 7.081226088499896E-6 0.0031230092559839913 chr2 243199373 48576 1.997373570531368E-4 0.1894099197464615 chr3 198022430 3970 2.00482339298634E-5 0.008981213728147738 chr4 191154276 1618 8.464367284151154E-6 0.003772170809310863 chr5 180915260 1680 9.286115499599094E-6 0.0035398647934774185 chr6 171115067 3502 2.046576062176921E-5 0.007095890932805725 chr7 159138663 1072 6.736263707330506E-6 0.003240406060630896 chr8 146364022 5024 3.432537539860718E-5 0.022034235336904868 chr9 141213431 817 5.785568654584987E-6 0.0028599083097975058 chr10 135534747 2063 1.522118899886241E-5 0.008480700812172974 chr11 135006516 4082 3.0235577666488335E-5 0.011514568699965918 chr12 133851895 14161 1.0579603673149342E-4 0.061673298729600506 chr13 115169878 488 4.2372190409023445E-6 0.0024119443807103674 chr14 107349540 548 5.1048192661095705E-6 0.004021373545516933 chr15 102531392 937 9.1386645760159E-6 0.0075412402192061995 chr16 90354753 667 7.382013428778893E-6 0.002958771239594691 chr17 81195210 538 6.626006632657271E-6 0.0033952511978401993 chr18 78077248 342 4.3802773376438675E-6 0.0020929066273520933 chr19 59128983 465 7.864163670800833E-6 0.0028043005947527436 chr20 63025520 506 8.028493854552886E-6 0.0031212210705969462 chr21 48129895 696 1.4460866785601755E-5 0.004832521294461152 chr22 51304566 300 5.847432760663057E-6 0.002901769974151106 chrMT 16571 14931 0.9010319232393941 4.276416580689488 chrX 155270560 433335 0.002790838134415178 2.5988604154971284 chrY 59373566 630 1.0610782582942719E-5 0.00665550103801883