BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082977.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 = 3,014,928 number of mapped reads = 2,307,841 (76.55%) number of supplementary alignments = 14,259 (0.47%) number of secondary alignments = 0 number of mapped bases = 157,241,298 bp number of sequenced bases = 157,176,623 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,461 duplication rate = 2.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.851 >>>>>>> ACTG content number of A's = 44,930,596 bp (28.59%) number of C's = 28,582,535 bp (18.18%) number of T's = 50,144,463 bp (31.9%) number of G's = 33,503,861 bp (21.32%) number of N's = 15,168 bp (0.01%) GC percentage = 39.5% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 1,522,688 number of insertions = 14,274 mapped reads with insertion percentage = 0.61% number of deletions = 37,166 mapped reads with deletion percentage = 1.59% homopolymer indels = 47.9% >>>>>>> Coverage mean coverageData = 0.0508X std coverageData = 0.4057X There is a 4.32% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.03% 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 14797567 0.05936822520494342 0.7105799280376296 chr2 243199373 15901854 0.06538608140243848 0.5004967263164614 chr3 198022430 11176194 0.05643903066940447 0.2681960446094578 chr4 191154276 10216964 0.05344878604755878 0.2702243554126811 chr5 180915260 8098548 0.044764316730385265 0.24000736150273796 chr6 171115067 11575248 0.0676459893505462 0.4871012683661822 chr7 159138663 10565305 0.0663905602876656 0.39190057922796784 chr8 146364022 11703413 0.0799609961524561 0.5796419333948265 chr9 141213431 4875048 0.034522551895223054 0.37038979066543537 chr10 135534747 5795921 0.04276335868321649 0.31329273844469935 chr11 135006516 6292208 0.04660669859816248 0.33254945591389146 chr12 133851895 5042428 0.037671696766041304 0.2275359637719725 chr13 115169878 3593595 0.031202559752646433 0.19668888242216562 chr14 107349540 3320686 0.030933397572080887 0.23670749227000207 chr15 102531392 2918582 0.0284652528661661 0.1900895521738775 chr16 90354753 5816426 0.06437321565142234 0.3265736890946121 chr17 81195210 3488459 0.04296385217797946 0.2643226805854255 chr18 78077248 5076300 0.0650163796756771 0.7599574932365414 chr19 59128983 2124376 0.03592782916628213 0.5100525036499353 chr20 63025520 2848191 0.04519107498042063 0.25620930262543506 chr21 48129895 3390785 0.07045070428680553 0.3109651959432067 chr22 51304566 1850663 0.03607209151715658 0.21356878847576785 chrMT 16571 171627 10.357069579385675 7.196624490306634 chrX 155270560 6328337 0.04075683761300275 0.25790760306060395 chrY 59373566 272573 0.0045908140333022944 0.09782830227551921