BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094106.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 = 398,986 number of mapped reads = 383,158 (96.03%) number of supplementary alignments = 28,992 (7.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 192,583 number of mapped paired reads (second in pair) = 190,575 number of mapped paired reads (both in pair) = 380,160 number of mapped paired reads (singletons) = 2,998 number of mapped bases = 47,660,290 bp number of sequenced bases = 46,801,971 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 367,252 duplication rate = 52.33% >>>>>>> Insert size mean insert size = 1,903,414.0273 std insert size = 12,288,719.4767 median insert size = 147 >>>>>>> Mapping quality mean mapping quality = 40.4775 >>>>>>> ACTG content number of A's = 13,450,146 bp (28.74%) number of C's = 10,060,242 bp (21.5%) number of T's = 12,643,330 bp (27.01%) number of G's = 10,647,756 bp (22.75%) number of N's = 497 bp (0%) GC percentage = 44.25% >>>>>>> Mismatches and indels general error rate = 0.0342 number of mismatches = 1,542,101 number of insertions = 29,984 mapped reads with insertion percentage = 7.72% number of deletions = 121,962 mapped reads with deletion percentage = 30.72% homopolymer indels = 28.65% >>>>>>> Coverage mean coverageData = 0.0154X std coverageData = 3.1424X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% 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 1028583 0.004126701854837104 1.7953092675961764 chr2 243199373 2147934 0.008831988230495972 3.0730647439062886 chr3 198022430 796009 0.004019792101329127 1.1060729587312224 chr4 191154276 2377894 0.012439658948565713 3.9695809703851888 chr5 180915260 832899 0.004603807329464634 1.9607543184925595 chr6 171115067 963083 0.005628277023670861 1.7145438045511325 chr7 159138663 934604 0.005872890863736865 1.5249924401428219 chr8 146364022 928880 0.006346368371866687 1.9963105154287344 chr9 141213431 878845 0.006223522746926247 2.3136214924102885 chr10 135534747 1005283 0.007417160707873679 2.0436559986829788 chr11 135006516 1569141 0.01162270567740597 2.988235887744732 chr12 133851895 1574506 0.01176304601440271 2.9877447319043253 chr13 115169878 1139021 0.009889921043417273 2.6887764523729922 chr14 107349540 141917 0.0013220084594680146 0.49604470160006764 chr15 102531392 519558 0.005067306605961226 1.4629082665425415 chr16 90354753 305724 0.0033835962121439257 1.3193401496753991 chr17 81195210 260938 0.0032137117448184445 0.9980527633240505 chr18 78077248 272831 0.003494372650019632 1.0307348192022379 chr19 59128983 83358 0.0014097654952056253 0.470204980531054 chr20 63025520 208532 0.0033086914633945106 1.1899346040260383 chr21 48129895 131669 0.002735700960910054 0.6484143413607584 chr22 51304566 62671 0.0012215481951450482 0.428827185974795 chrMT 16571 52272 3.1544264075795065 16.056268080541063 chrX 155270560 28764834 0.18525620053151093 10.298869797212339 chrY 59373566 679304 0.011441185796386224 2.3572130136518945