BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819116.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,197,048 number of mapped reads = 1,032,039 (86.22%) number of supplementary alignments = 5,239 (0.44%) number of secondary alignments = 0 number of mapped bases = 58,569,038 bp number of sequenced bases = 58,545,620 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 110,737 duplication rate = 8.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3448 >>>>>>> ACTG content number of A's = 13,660,007 bp (23.33%) number of C's = 10,848,320 bp (18.53%) number of T's = 18,956,815 bp (32.38%) number of G's = 15,079,619 bp (25.76%) number of N's = 859 bp (0%) GC percentage = 44.29% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 336,548 number of insertions = 3,428 mapped reads with insertion percentage = 0.33% number of deletions = 13,687 mapped reads with deletion percentage = 1.31% homopolymer indels = 43.16% >>>>>>> Coverage mean coverageData = 0.0189X std coverageData = 0.2311X There is a 1.4% of reference with a coverageData >= 1X There is a 0.32% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.03% 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% 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 5540417 0.022228297677942394 0.34738343425606616 chr2 243199373 4562872 0.018761857580940393 0.28309899918888287 chr3 198022430 3080127 0.015554434919316969 0.1624995844946757 chr4 191154276 3497316 0.018295776967081814 0.2226612684717674 chr5 180915260 3094374 0.017103996644616933 0.16919981200624257 chr6 171115067 2600464 0.015197165542412462 0.17900850786508202 chr7 159138663 2734234 0.017181456400698805 0.23921326174297755 chr8 146364022 5136460 0.035093733622597496 0.2770948818620066 chr9 141213431 2839316 0.020106557711213745 0.20395611642233613 chr10 135534747 2969159 0.02190699481661334 0.2939442115550819 chr11 135006516 1985646 0.014707778993422807 0.1887257968965527 chr12 133851895 2459055 0.018371461980422468 0.17627917896810616 chr13 115169878 1382472 0.01200376369244743 0.14179677785265563 chr14 107349540 1467882 0.01367385458754644 0.15440141111890507 chr15 102531392 1442218 0.014066111576832976 0.15398730241047887 chr16 90354753 1804167 0.01996759373577171 0.1927177011083709 chr17 81195210 2139502 0.026350101194393117 0.2580598395238529 chr18 78077248 1220981 0.015638115216355986 0.2963706462165171 chr19 59128983 1784319 0.030176723993375634 0.28661579946572396 chr20 63025520 1609299 0.02553408524039151 0.21376388682581282 chr21 48129895 892949 0.01855289732088549 0.22252311868277275 chr22 51304566 459234 0.008951133121367794 0.1221759483242835 chrMT 16571 17820 1.075372638947559 1.388399942425578 chrX 155270560 3557136 0.022909275267636055 0.20785297669827604 chrY 59373566 291619 0.004911596517547893 0.21659919772598663