BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084763.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,128,560 number of mapped reads = 1,948,558 (91.54%) number of supplementary alignments = 16,298 (0.77%) number of secondary alignments = 0 number of mapped bases = 133,596,947 bp number of sequenced bases = 133,538,466 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 72,456 duplication rate = 2.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4103 >>>>>>> ACTG content number of A's = 37,995,323 bp (28.45%) number of C's = 24,887,996 bp (18.64%) number of T's = 41,858,225 bp (31.35%) number of G's = 28,759,883 bp (21.54%) number of N's = 37,039 bp (0.03%) GC percentage = 40.17% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,130,921 number of insertions = 10,833 mapped reads with insertion percentage = 0.55% number of deletions = 35,502 mapped reads with deletion percentage = 1.8% homopolymer indels = 46.91% >>>>>>> Coverage mean coverageData = 0.0432X std coverageData = 0.3639X There is a 3.76% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.05% 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 11101235 0.04453844470060518 0.6002099445492839 chr2 243199373 12098254 0.04974623844938943 0.43881609897285556 chr3 198022430 8950706 0.045200465422023155 0.23618077962226927 chr4 191154276 7883576 0.04124195474444945 0.24603511920003918 chr5 180915260 8002477 0.04423328911005075 0.23486064532158787 chr6 171115067 6953620 0.04063709947879692 0.2336402302521543 chr7 159138663 7035036 0.04420695679716751 0.40092841707202037 chr8 146364022 6762666 0.04620442857193416 0.4789683128718053 chr9 141213431 5882564 0.04165725567563046 0.3634035806470815 chr10 135534747 6419459 0.047363935389941 0.3465649353393814 chr11 135006516 6135998 0.0454496433342521 0.3301966568028406 chr12 133851895 5403906 0.040372278629301435 0.22714266007851835 chr13 115169878 4138027 0.03592976802493444 0.2107530208357468 chr14 107349540 4368952 0.04069837653705829 0.24164764870463512 chr15 102531392 3987613 0.0388916303798938 0.22094613899827806 chr16 90354753 3694593 0.04088985778091829 0.2610311403900978 chr17 81195210 3418058 0.04209679364090566 0.24933528328265425 chr18 78077248 3748079 0.04800475293391488 0.8158368559413268 chr19 59128983 2511326 0.04247199719298402 0.4625944991677437 chr20 63025520 2921229 0.04634993888190054 0.2576776012357628 chr21 48129895 1784807 0.0370831268175424 0.2333640443675824 chr22 51304566 1525549 0.029735150668655886 0.18981304219751308 chrMT 16571 12942 0.7810029569730251 1.03007756377165 chrX 155270560 8510618 0.054811536713720875 0.2945413938779093 chrY 59373566 345657 0.005821732182971796 0.14087374769397057