BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818881.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 = 1,614,322 number of mapped reads = 1,575,344 (97.59%) number of supplementary alignments = 23,321 (1.44%) number of secondary alignments = 0 number of mapped bases = 145,814,073 bp number of sequenced bases = 145,719,534 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 258,778 duplication rate = 13.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2041 >>>>>>> ACTG content number of A's = 42,918,688 bp (29.45%) number of C's = 30,790,974 bp (21.13%) number of T's = 40,376,762 bp (27.71%) number of G's = 31,630,981 bp (21.71%) number of N's = 2,129 bp (0%) GC percentage = 42.84% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 882,292 number of insertions = 24,773 mapped reads with insertion percentage = 1.52% number of deletions = 47,791 mapped reads with deletion percentage = 2.96% homopolymer indels = 40.02% >>>>>>> Coverage mean coverageData = 0.0471X std coverageData = 0.6163X There is a 3.53% of reference with a coverageData >= 1X There is a 0.73% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.03% 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% 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 13433559 0.053895789491332904 0.9712375907902332 chr2 243199373 10779390 0.044323263941967485 0.8612710538538035 chr3 198022430 9013058 0.04551533884318054 0.26845231932564045 chr4 191154276 7119933 0.03724705064928812 0.3405195537824305 chr5 180915260 7694314 0.04252993362748947 0.27274993957361765 chr6 171115067 6971638 0.04074239704444028 0.2879290095312681 chr7 159138663 12734266 0.0800199383351612 1.3692074949006077 chr8 146364022 13787561 0.0942004791314084 0.5181304190193844 chr9 141213431 5182868 0.03670237287839852 0.4892342685472922 chr10 135534747 6292797 0.04642940013013785 0.8122510496266322 chr11 135006516 6157475 0.045608724544821226 0.3443625938863136 chr12 133851895 5484924 0.04097755956312759 0.25508333656108173 chr13 115169878 4573478 0.039710713247434366 0.24775615493926592 chr14 107349540 4747476 0.0442244652375781 0.29267815846734835 chr15 102531392 3017209 0.02942717289939846 0.21139642894192182 chr16 90354753 3568476 0.039494059598613476 0.6385559275857072 chr17 81195210 3798805 0.04678607272522603 0.3751455824372789 chr18 78077248 2526390 0.03235756977500027 0.5683640996950436 chr19 59128983 3086180 0.05219403147860669 0.8896516176455658 chr20 63025520 5809305 0.0921738527504414 0.4109899469893393 chr21 48129895 1755256 0.03646914251527039 0.2963146941325609 chr22 51304566 1704508 0.03322331973337422 0.2562687870365973 chrMT 16571 227344 13.719389294550721 9.249393199117561 chrX 155270560 5776624 0.037203601249328914 0.31079138893267505 chrY 59373566 571239 0.009621099733170818 0.7235329827248875