BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081028.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 = 2,826,137 number of mapped reads = 2,111,606 (74.72%) number of supplementary alignments = 10,573 (0.37%) number of secondary alignments = 0 number of mapped bases = 129,437,245 bp number of sequenced bases = 129,394,940 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 71,917 duplication rate = 2.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.209 >>>>>>> ACTG content number of A's = 37,315,901 bp (28.84%) number of C's = 26,064,513 bp (20.14%) number of T's = 37,614,150 bp (29.07%) number of G's = 28,398,771 bp (21.95%) number of N's = 1,605 bp (0%) GC percentage = 42.09% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 943,298 number of insertions = 8,482 mapped reads with insertion percentage = 0.4% number of deletions = 24,735 mapped reads with deletion percentage = 1.16% homopolymer indels = 45.56% >>>>>>> Coverage mean coverageData = 0.0418X std coverageData = 0.2854X There is a 3.54% of reference with a coverageData >= 1X There is a 0.48% 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% 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 10338142 0.041476895658366285 0.38266413252983716 chr2 243199373 10533498 0.043312192256350926 0.31176651350927925 chr3 198022430 8799584 0.04443730945024763 0.24305092359591934 chr4 191154276 8396585 0.04392569800531169 0.2520304533587805 chr5 180915260 7919800 0.04377629615102673 0.24062235115378358 chr6 171115067 7916847 0.04626621804145394 0.2871194949644454 chr7 159138663 6798968 0.042723546068751374 0.3427148300253587 chr8 146364022 6310635 0.04311602615019694 0.30394030741293354 chr9 141213431 5787009 0.04098058491334298 0.28757142299691096 chr10 135534747 5975090 0.044085300133404164 0.27873410763929346 chr11 135006516 6040119 0.04473946279748453 0.2867815976409241 chr12 133851895 6119895 0.04572139228958992 0.24723039942075106 chr13 115169878 4112637 0.035709311075244866 0.21718186209949883 chr14 107349540 3995533 0.03721984276784046 0.23165422815459566 chr15 102531392 3584188 0.034956981760278845 0.2280472283050061 chr16 90354753 3672295 0.04064307496917179 0.24809095037187964 chr17 81195210 3296808 0.04060347894906608 0.24780630690184696 chr18 78077248 3484011 0.04462261528480102 0.4515941331959768 chr19 59128983 2478373 0.04191469012751327 0.3190862909470427 chr20 63025520 2568328 0.040750603882363845 0.23628118719467037 chr21 48129895 1734821 0.03604456232451785 0.22657472287065322 chr22 51304566 1472127 0.02869387882552208 0.19305079618300688 chrMT 16571 26372 1.5914549514211573 1.459581901709243 chrX 155270560 7752862 0.04993130700372305 0.2791171244821335 chrY 59373566 322718 0.005435381799368426 0.11025131338944236