BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708538.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 21,168,003 number of mapped reads = 20,678,312 (97.69%) number of supplementary alignments = 565 (0%) number of secondary alignments = 0 number of mapped bases = 1,031,307,414 bp number of sequenced bases = 1,031,212,359 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 218,907 duplication rate = 1.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6734 >>>>>>> ACTG content number of A's = 321,055,435 bp (31.13%) number of C's = 193,107,635 bp (18.73%) number of T's = 319,450,802 bp (30.98%) number of G's = 197,561,823 bp (19.16%) number of N's = 36,664 bp (0%) GC percentage = 37.88% >>>>>>> Mismatches and indels general error rate = 0.0021 number of mismatches = 2,033,959 number of insertions = 62,376 mapped reads with insertion percentage = 0.3% number of deletions = 56,828 mapped reads with deletion percentage = 0.27% homopolymer indels = 49.24% >>>>>>> Coverage mean coverageData = 0.3331X std coverageData = 0.6637X There is a 25.14% of reference with a coverageData >= 1X There is a 6.21% of reference with a coverageData >= 2X There is a 1.48% of reference with a coverageData >= 3X There is a 0.36% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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 81201521 0.3257826226238369 0.6731415741125136 chr2 243199373 93650958 0.38507894508428686 0.7013495394250525 chr3 198022430 81933669 0.4137595372403015 0.7248808966169112 chr4 191154276 86106598 0.45045603897450875 0.7532757051317279 chr5 180915260 69880267 0.38625966101477566 0.7033578784285955 chr6 171115067 72864949 0.4258242729729931 0.7374449297810852 chr7 159138663 56943868 0.3578254770181147 0.6824390223339646 chr8 146364022 57785421 0.39480618399513506 0.7103062282418933 chr9 141213431 43935916 0.3111312832559107 0.6504477688708996 chr10 135534747 44122297 0.32554232753317497 0.6433965867604541 chr11 135006516 49384501 0.36579346288737646 0.699340425117392 chr12 133851895 48167094 0.3598536576564717 0.6826443435886073 chr13 115169878 40881596 0.35496778072474816 0.68277107504679 chr14 107349540 33989419 0.3166237973632677 0.6548912161386511 chr15 102531392 27175087 0.26504162744615817 0.5976673460294407 chr16 90354753 19220094 0.2127181289511134 0.5292106667105696 chr17 81195210 16114477 0.1984658577765856 0.5067337247246643 chr18 78077248 30279860 0.38781925305564047 0.7026282106100545 chr19 59128983 8129462 0.1374869241366793 0.4127030173866326 chr20 63025520 16161174 0.2564226998841104 0.5838771865794234 chr21 48129895 12243821 0.254391184522634 0.5926016479150208 chr22 51304566 5337311 0.10403189065082434 0.3634170767873724 chrMT 16571 1169 0.07054492788606602 0.29769222588815564 chrX 155270560 30663607 0.19748500295226604 0.4902045342961504 chrY 59373566 5133278 0.08645729650127466 0.33850380372473454