BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524610.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,190,699 number of mapped reads = 2,040,472 (93.14%) number of supplementary alignments = 4,447 (0.2%) number of secondary alignments = 0 number of mapped bases = 119,167,436 bp number of sequenced bases = 119,130,359 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 114,152 duplication rate = 4.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4407 >>>>>>> ACTG content number of A's = 30,483,042 bp (25.59%) number of C's = 23,004,984 bp (19.31%) number of T's = 37,471,793 bp (31.45%) number of G's = 28,169,761 bp (23.65%) number of N's = 779 bp (0%) GC percentage = 42.96% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 559,958 number of insertions = 7,186 mapped reads with insertion percentage = 0.35% number of deletions = 21,963 mapped reads with deletion percentage = 1.07% homopolymer indels = 43.86% >>>>>>> Coverage mean coverageData = 0.0385X std coverageData = 0.3243X There is a 3.27% of reference with a coverageData >= 1X There is a 0.42% of reference with a coverageData >= 2X There is a 0.07% 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 13140871 0.05272151759252788 0.5644030915264961 chr2 243199373 10128980 0.04164887382337125 0.37876216058226797 chr3 198022430 7520061 0.0379758040541165 0.2239825755905907 chr4 191154276 5407757 0.028290013245636212 0.23029201221276002 chr5 180915260 7340378 0.04057357018971202 0.23201966410319202 chr6 171115067 7723706 0.04513749803224517 0.2658318945964674 chr7 159138663 7256943 0.04560138223606918 0.443705184241177 chr8 146364022 10586633 0.07233084234320918 0.4237218658485928 chr9 141213431 4337042 0.030712673499165954 0.29206234446301665 chr10 135534747 5045657 0.03722777451305531 0.32247400617613065 chr11 135006516 6064720 0.04492168363192189 0.31857982415751834 chr12 133851895 3956353 0.02955769135730204 0.2041976432073164 chr13 115169878 2893487 0.02512364387500697 0.18226824651412313 chr14 107349540 2165844 0.02017562441348142 0.17369762212275092 chr15 102531392 3012355 0.029379831300837114 0.20786814142396345 chr16 90354753 3491488 0.038641995955652715 0.23810013562235874 chr17 81195210 2578547 0.03175737829854741 0.21381305601706493 chr18 78077248 3105977 0.03978082065597394 0.4764460156177494 chr19 59128983 2357169 0.03986486627040414 0.3945339567862147 chr20 63025520 2206420 0.03500835851889838 0.2210711483186805 chr21 48129895 1020219 0.021197199786120457 0.1888849636217726 chr22 51304566 2101367 0.040958674126587484 0.2313272022977065 chrMT 16571 47809 2.885100476736467 2.5626966892447007 chrX 155270560 5403292 0.03479920469147532 0.25196765049725617 chrY 59373566 274361 0.004620928444823409 0.1249574513382201