BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231889.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 4,981,439 number of mapped reads = 4,673,321 (93.81%) number of supplementary alignments = 27,454 (0.55%) number of secondary alignments = 0 number of mapped bases = 315,710,717 bp number of sequenced bases = 315,588,883 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 447,946 duplication rate = 3.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.7222 >>>>>>> ACTG content number of A's = 81,803,194 bp (25.92%) number of C's = 58,501,313 bp (18.54%) number of T's = 89,543,407 bp (28.37%) number of G's = 85,674,510 bp (27.15%) number of N's = 66,459 bp (0.02%) GC percentage = 45.68% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 2,185,819 number of insertions = 23,277 mapped reads with insertion percentage = 0.49% number of deletions = 74,169 mapped reads with deletion percentage = 1.57% homopolymer indels = 45.59% >>>>>>> Coverage mean coverageData = 0.102X std coverageData = 32.5438X There is a 7.39% of reference with a coverageData >= 1X There is a 1.46% of reference with a coverageData >= 2X There is a 0.37% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 34108017 0.1368422548483841 2.194590785499896 chr2 243199373 42318241 0.17400637377465608 116.04721731409097 chr3 198022430 23673462 0.11954939650018435 0.43540402587574895 chr4 191154276 11070873 0.05791590557984693 0.35210171501561366 chr5 180915260 17889380 0.09888264815251074 0.41233303050541453 chr6 171115067 17775688 0.10388148929047844 0.6178285741943766 chr7 159138663 22673208 0.14247454121189895 2.631445589055651 chr8 146364022 17963632 0.1227325660673632 0.9005944055964594 chr9 141213431 8360495 0.05920467296060528 0.8949844307280559 chr10 135534747 9724632 0.07175010257701665 0.5860783370350697 chr11 135006516 9467486 0.07012614117084541 0.8866615813848413 chr12 133851895 7223265 0.053964607673279485 0.3093487290404867 chr13 115169878 15274563 0.13262637128086566 0.4648995782060745 chr14 107349540 10587333 0.09862485670641905 0.6001844996561624 chr15 102531392 6181446 0.060288326135277674 0.3160639751983671 chr16 90354753 9485055 0.10497571721545185 0.5337566282870986 chr17 81195210 6892408 0.08488687941074356 0.49751953282786066 chr18 78077248 8494839 0.10880044081471724 1.992241905210231 chr19 59128983 7361539 0.12449967218276019 1.437535293092598 chr20 63025520 8437784 0.13387884780641238 0.5175102432222394 chr21 48129895 5709221 0.11862109817609201 0.4932637821450898 chr22 51304566 2884869 0.056230258336070905 0.292899079103073 chrMT 16571 8704 0.5252549634904351 1.220596057848941 chrX 155270560 11386250 0.07333167343506715 0.5574392783659107 chrY 59373566 758327 0.012772131625040005 0.23648761489749912