BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549056.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 3,176,977 number of mapped reads = 2,785,281 (87.67%) number of secondary alignments = 0 number of mapped bases = 110,070,100 bp number of sequenced bases = 110,058,860 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 84,088 duplication rate = 2.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 36.7706 >>>>>>> ACTG content number of A's = 30,544,654 bp (27.75%) number of C's = 24,103,430 bp (21.9%) number of T's = 31,212,584 bp (28.36%) number of G's = 24,197,278 bp (21.99%) number of N's = 914 bp (0%) GC percentage = 43.89% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 336,946 number of insertions = 3,711 mapped reads with insertion percentage = 0.13% number of deletions = 8,607 mapped reads with deletion percentage = 0.31% homopolymer indels = 39.4% >>>>>>> Coverage mean coverageData = 0.0356X std coverageData = 0.3452X There is a 3.2% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.03% 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% 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 8972727 0.03599881502401553 0.5435863843598168 chr2 243199373 9374109 0.03854495545923961 0.33503768331129974 chr3 198022430 7392530 0.037331781051267776 0.20868692945388742 chr4 191154276 7171503 0.03751683273880831 0.22550171901649066 chr5 180915260 6748479 0.03730187823846369 0.21187313422267132 chr6 171115067 6352859 0.037126239736679646 0.21564613773539018 chr7 159138663 6193238 0.03891724288270538 0.4244474758194998 chr8 146364022 5636652 0.03851118548791998 0.7276498621405462 chr9 141213431 4698675 0.03327357013229145 0.3453958167451522 chr10 135534747 5247823 0.038719392009489643 0.28848358563771564 chr11 135006516 5043224 0.037355411793605575 0.2647073500899704 chr12 133851895 5135164 0.038364522220623025 0.21912912973480675 chr13 115169878 3447375 0.02993295694903836 0.1849134723824287 chr14 107349540 3403536 0.03170517544835311 0.22344156106276744 chr15 102531392 3187831 0.031091268125960875 0.19141577565424844 chr16 90354753 3231800 0.03576790254741773 0.2272407097614048 chr17 81195210 3151207 0.038810257403115285 0.21968280512747865 chr18 78077248 2921952 0.03742386002129583 0.5876909378225642 chr19 59128983 2601482 0.04399673168740278 0.5397096665029372 chr20 63025520 2342657 0.03716997495617648 0.21745772945111042 chr21 48129895 1411180 0.029320238492105584 0.22487342863959564 chr22 51304566 1364478 0.026595644528013353 0.21515191201847828 chrMT 16571 3693 0.22285921187616922 0.5566122587568055 chrX 155270560 4023332 0.025911750430989623 0.21812170079272522 chrY 59373566 1012594 0.01705462663300365 0.1971674121926104