BamQC report ----------------------------------- >>>>>>> Input bam file = SRR536758.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP014781/SRP014781.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 = 25,194,632 number of mapped reads = 24,622,441 (97.73%) number of supplementary alignments = 597 (0%) number of secondary alignments = 0 number of mapped bases = 1,228,360,559 bp number of sequenced bases = 1,228,253,107 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 282,691 duplication rate = 1.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.666 >>>>>>> ACTG content number of A's = 379,172,012 bp (30.87%) number of C's = 233,344,032 bp (19%) number of T's = 379,086,464 bp (30.86%) number of G's = 236,607,532 bp (19.26%) number of N's = 43,067 bp (0%) GC percentage = 38.26% >>>>>>> Mismatches and indels general error rate = 0.002 number of mismatches = 2,306,357 number of insertions = 70,620 mapped reads with insertion percentage = 0.29% number of deletions = 64,490 mapped reads with deletion percentage = 0.26% homopolymer indels = 49.37% >>>>>>> Coverage mean coverageData = 0.3968X std coverageData = 0.7361X There is a 28.76% of reference with a coverageData >= 1X There is a 7.99% of reference with a coverageData >= 2X There is a 2.13% of reference with a coverageData >= 3X There is a 0.57% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.05% 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% 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 97778405 0.3922895140951324 0.7533745923587295 chr2 243199373 111292303 0.4576175572623701 0.7743982960052095 chr3 198022430 94249535 0.4759538351286771 0.788144650619616 chr4 191154276 100271790 0.5245594924593787 0.8253419376799497 chr5 180915260 87795479 0.4852850942479921 0.7962359111624557 chr6 171115067 80654388 0.4713459160203584 0.7869147086121129 chr7 159138663 69525591 0.4368868613656758 0.7693155866323657 chr8 146364022 66780559 0.4562634866647761 0.7738172550129282 chr9 141213431 52131795 0.3691702314066712 0.7182865608987882 chr10 135534747 53511974 0.3948210712342275 0.7167152239032998 chr11 135006516 57434881 0.42542302921141967 0.7723832491135731 chr12 133851895 57787350 0.4317260506472471 0.7660166110086454 chr13 115169878 47237269 0.4101529828832501 0.7474187311948732 chr14 107349540 39395735 0.3669855967710714 0.7202150204844796 chr15 102531392 33496319 0.3266933018913856 0.6861284563384153 chr16 90354753 21648271 0.23959194487532937 0.5672525350158025 chr17 81195210 20208057 0.24888237865263235 0.5812282572686457 chr18 78077248 35777418 0.4582310329380462 0.7699372885645082 chr19 59128983 9727720 0.16451695101875843 0.457792884195639 chr20 63025520 19783293 0.31389337208165835 0.6542295309746999 chr21 48129895 14583536 0.30300369448136133 0.6709001020942078 chr22 51304566 6628367 0.12919643448499302 0.41279786465169177 chrMT 16571 1384 0.08351940136382838 0.3052859546749684 chrX 155270560 44483002 0.2864870326995665 0.5955472441054245 chrY 59373566 6176138 0.1040216786035725 0.37745678289597656