BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084256.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 = 2,909,774 number of mapped reads = 1,823,138 (62.66%) number of supplementary alignments = 11,441 (0.39%) number of secondary alignments = 0 number of mapped bases = 115,281,772 bp number of sequenced bases = 115,243,768 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 69,042 duplication rate = 3.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6533 >>>>>>> ACTG content number of A's = 32,363,476 bp (28.08%) number of C's = 22,414,631 bp (19.45%) number of T's = 34,811,552 bp (30.21%) number of G's = 25,652,821 bp (22.26%) number of N's = 1,288 bp (0%) GC percentage = 41.71% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 952,034 number of insertions = 8,459 mapped reads with insertion percentage = 0.46% number of deletions = 23,906 mapped reads with deletion percentage = 1.3% homopolymer indels = 45.87% >>>>>>> Coverage mean coverageData = 0.0372X std coverageData = 0.269X There is a 3.24% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.06% 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 9138869 0.03666538106639261 0.3570861084977143 chr2 243199373 9618563 0.03955011430066475 0.35437817443492303 chr3 198022430 7974583 0.040271109691967726 0.2245688751203328 chr4 191154276 7487971 0.03917239601796823 0.22548171166075123 chr5 180915260 7049950 0.03896824402761823 0.2210392991190846 chr6 171115067 6965706 0.040707730313427046 0.2719030572840752 chr7 159138663 6265587 0.03937187156084125 0.31989239243950135 chr8 146364022 5650657 0.038606871571211676 0.2786640319376116 chr9 141213431 4697874 0.03326789786730697 0.2488880915010108 chr10 135534747 5449443 0.040206981018675605 0.26744054952584617 chr11 135006516 5232705 0.038758907014532544 0.24491393927787714 chr12 133851895 5285507 0.039487726341117545 0.22401670587797345 chr13 115169878 3756720 0.03261894572815298 0.2057763441163028 chr14 107349540 3436905 0.03201601981713196 0.20832766132969432 chr15 102531392 3196761 0.031178363403083418 0.201692471247026 chr16 90354753 3216169 0.03559490666749983 0.22316595589305882 chr17 81195210 2925844 0.036034687267881935 0.22283200501667724 chr18 78077248 3225037 0.041305720713926804 0.42584448090350924 chr19 59128983 2131607 0.036050121139408066 0.3088042390003032 chr20 63025520 2392761 0.03796495451366367 0.22138189925559507 chr21 48129895 1535575 0.031904806773420134 0.20666450528320335 chr22 51304566 1288187 0.025108622885534202 0.17736775600991872 chrMT 16571 58846 3.551143564057691 3.0871673555733588 chrX 155270560 7045719 0.04537704378730907 0.2516761711140555 chrY 59373566 254226 0.004281804464970152 0.0864702026683544