BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695982.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 10,858,678 number of mapped reads = 9,762,598 (89.91%) number of supplementary alignments = 160,423 (1.48%) number of secondary alignments = 0 number of mapped bases = 1,286,819,482 bp number of sequenced bases = 1,277,581,970 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,829,317 duplication rate = 15.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.0574 >>>>>>> ACTG content number of A's = 363,099,542 bp (28.42%) number of C's = 273,107,095 bp (21.38%) number of T's = 360,097,187 bp (28.19%) number of G's = 281,278,146 bp (22.02%) number of N's = 0 bp (0%) GC percentage = 43.39% >>>>>>> Mismatches and indels general error rate = 0.0177 number of mismatches = 14,245,739 number of insertions = 7,634,889 mapped reads with insertion percentage = 47.45% number of deletions = 8,325,872 mapped reads with deletion percentage = 50.44% homopolymer indels = 36.43% >>>>>>> Coverage mean coverageData = 0.4157X std coverageData = 1.196X There is a 20.29% of reference with a coverageData >= 1X There is a 9.63% of reference with a coverageData >= 2X There is a 4.84% of reference with a coverageData >= 3X There is a 2.58% of reference with a coverageData >= 4X There is a 1.44% of reference with a coverageData >= 5X There is a 0.85% of reference with a coverageData >= 6X There is a 0.52% of reference with a coverageData >= 7X There is a 0.33% of reference with a coverageData >= 8X There is a 0.21% of reference with a coverageData >= 9X There is a 0.14% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 139872183 0.5611708506034173 1.765690463851764 chr2 243199373 99820971 0.41044912973521525 1.114739752022435 chr3 198022430 88944503 0.44916377907290606 1.1346963746718486 chr4 191154276 48096547 0.25161114889211267 0.8563219989146517 chr5 180915260 107440358 0.593871174825164 1.360740993346812 chr6 171115067 64763498 0.37847922532736405 1.0893813776860481 chr7 159138663 81440717 0.5117594647631293 1.2492692380368111 chr8 146364022 53283091 0.36404500417459146 1.0195702094145178 chr9 141213431 51922854 0.36769062002324693 1.0484835385258158 chr10 135534747 51357972 0.3789284529376072 1.1922400513024038 chr11 135006516 71394494 0.5288225792005476 1.2792725099204019 chr12 133851895 63783198 0.4765206947574407 1.1794587502162002 chr13 115169878 24159221 0.20977030990690118 0.7505693536806691 chr14 107349540 28239852 0.2630644900760637 0.8580365467836155 chr15 102531392 48458093 0.4726171375884568 1.213789003298415 chr16 90354753 50615098 0.5601819087480655 1.342502908251466 chr17 81195210 38763867 0.47741568745249874 1.2559987903816807 chr18 78077248 23295934 0.29837032678200953 1.1247593149642536 chr19 59128983 22247780 0.3762584585633749 1.4357639268084652 chr20 63025520 38417754 0.6095586993966888 1.4163297964231403 chr21 48129895 10513142 0.21843268097717644 0.8449036254069301 chr22 51304566 13593486 0.26495665122671536 0.9157178703898455 chrMT 16571 181908 10.97749079717579 6.446292463463915 chrX 155270560 64746540 0.41699173365511144 1.0971531588203975 chrY 59373566 1466421 0.024698213342954675 0.48686446653785964