BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085028.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 = 2,579,793 number of mapped reads = 2,344,592 (90.88%) number of supplementary alignments = 16,131 (0.63%) number of secondary alignments = 0 number of mapped bases = 156,596,153 bp number of sequenced bases = 156,539,844 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 77,963 duplication rate = 2.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2223 >>>>>>> ACTG content number of A's = 44,017,899 bp (28.12%) number of C's = 30,369,314 bp (19.4%) number of T's = 47,750,179 bp (30.5%) number of G's = 34,395,044 bp (21.97%) number of N's = 7,408 bp (0%) GC percentage = 41.37% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,330,383 number of insertions = 10,908 mapped reads with insertion percentage = 0.46% number of deletions = 32,997 mapped reads with deletion percentage = 1.39% homopolymer indels = 46.16% >>>>>>> Coverage mean coverageData = 0.0506X std coverageData = 0.3727X There is a 4.31% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% 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 15504447 0.06220424622332235 0.5266154662883246 chr2 243199373 16535767 0.06799263828694163 0.47232807027662654 chr3 198022430 9260529 0.04676505080762821 0.24888462714549414 chr4 191154276 9618931 0.050320250225529876 0.25819834923146934 chr5 180915260 7906973 0.04370539555369735 0.23655063211120594 chr6 171115067 10498692 0.06135457376175998 0.3351144130089591 chr7 159138663 13292364 0.08352693022185313 0.4438422414075318 chr8 146364022 9223089 0.06301472775871109 0.6941526159474095 chr9 141213431 4676753 0.03311832994129291 0.3012022674212885 chr10 135534747 9074780 0.06695537639510257 0.46223213918835415 chr11 135006516 7363541 0.05454211558203605 0.4023861850569189 chr12 133851895 6641764 0.04962024631776786 0.25830283229681233 chr13 115169878 3277333 0.02845651186675738 0.1902224428695417 chr14 107349540 5140233 0.047883139508562406 0.25984719804498435 chr15 102531392 2824409 0.02754677318727907 0.1956050782445446 chr16 90354753 3861972 0.04274232258705859 0.24462855407844455 chr17 81195210 2597708 0.031993365125849174 0.24033547493435292 chr18 78077248 4305096 0.05513893112626101 0.5303858943095386 chr19 59128983 2435477 0.04118922525692688 0.39401785385289 chr20 63025520 3405704 0.05403690441586202 0.2664537506681067 chr21 48129895 1685189 0.0350133529275308 0.21820735095280944 chr22 51304566 1026007 0.019998356481565404 0.15722589710955473 chrMT 16571 123325 7.442218333232756 5.255754955696633 chrX 155270560 6022702 0.03878843484560112 0.26214757226907165 chrY 59373566 293368 0.004941054071099587 0.09330256195466374