BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472697.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 13,563,114 number of mapped reads = 13,458,345 (99.23%) number of supplementary alignments = 91,466 (0.67%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,756,645 number of mapped paired reads (second in pair) = 6,701,700 number of mapped paired reads (both in pair) = 13,396,714 number of mapped paired reads (singletons) = 61,631 number of mapped bases = 1,324,515,135 bp number of sequenced bases = 1,324,318,633 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,760,754 duplication rate = 47.63% >>>>>>> Insert size mean insert size = 24,118.7979 std insert size = 1,553,915.6544 median insert size = 211 >>>>>>> Mapping quality mean mapping quality = 54.3035 >>>>>>> ACTG content number of A's = 359,330,740 bp (27.13%) number of C's = 301,938,796 bp (22.8%) number of T's = 364,641,778 bp (27.53%) number of G's = 298,097,048 bp (22.51%) number of N's = 310,271 bp (0.02%) GC percentage = 45.31% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 5,486,434 number of insertions = 90,539 mapped reads with insertion percentage = 0.67% number of deletions = 85,032 mapped reads with deletion percentage = 0.62% homopolymer indels = 47.3% >>>>>>> Coverage mean coverageData = 0.4279X std coverageData = 30.0823X There is a 2.68% of reference with a coverageData >= 1X There is a 1.29% of reference with a coverageData >= 2X There is a 0.64% of reference with a coverageData >= 3X There is a 0.48% of reference with a coverageData >= 4X There is a 0.36% of reference with a coverageData >= 5X There is a 0.31% of reference with a coverageData >= 6X There is a 0.28% of reference with a coverageData >= 7X There is a 0.26% of reference with a coverageData >= 8X There is a 0.24% of reference with a coverageData >= 9X There is a 0.23% of reference with a coverageData >= 10X There is a 0.22% of reference with a coverageData >= 11X There is a 0.21% of reference with a coverageData >= 12X There is a 0.2% of reference with a coverageData >= 13X There is a 0.19% of reference with a coverageData >= 14X There is a 0.19% of reference with a coverageData >= 15X There is a 0.18% of reference with a coverageData >= 16X There is a 0.17% of reference with a coverageData >= 17X There is a 0.17% of reference with a coverageData >= 18X There is a 0.16% of reference with a coverageData >= 19X There is a 0.16% of reference with a coverageData >= 20X There is a 0.16% of reference with a coverageData >= 21X There is a 0.15% of reference with a coverageData >= 22X There is a 0.15% of reference with a coverageData >= 23X There is a 0.15% of reference with a coverageData >= 24X There is a 0.14% of reference with a coverageData >= 25X There is a 0.14% of reference with a coverageData >= 26X There is a 0.14% of reference with a coverageData >= 27X There is a 0.13% of reference with a coverageData >= 28X There is a 0.13% of reference with a coverageData >= 29X There is a 0.13% of reference with a coverageData >= 30X There is a 0.13% of reference with a coverageData >= 31X There is a 0.12% of reference with a coverageData >= 32X There is a 0.12% of reference with a coverageData >= 33X There is a 0.12% of reference with a coverageData >= 34X There is a 0.12% of reference with a coverageData >= 35X There is a 0.12% of reference with a coverageData >= 36X There is a 0.11% of reference with a coverageData >= 37X There is a 0.11% of reference with a coverageData >= 38X There is a 0.11% of reference with a coverageData >= 39X There is a 0.11% of reference with a coverageData >= 40X There is a 0.11% of reference with a coverageData >= 41X There is a 0.11% of reference with a coverageData >= 42X There is a 0.11% of reference with a coverageData >= 43X There is a 0.1% of reference with a coverageData >= 44X There is a 0.1% of reference with a coverageData >= 45X There is a 0.1% of reference with a coverageData >= 46X There is a 0.1% of reference with a coverageData >= 47X There is a 0.1% of reference with a coverageData >= 48X There is a 0.1% of reference with a coverageData >= 49X There is a 0.1% of reference with a coverageData >= 50X There is a 0.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 118864407 0.4768871047266117 19.199599571279773 chr2 243199373 135875196 0.5586987923690083 47.81506936264362 chr3 198022430 137095693 0.6923240614712182 55.610262138479015 chr4 191154276 46892313 0.24531134736426194 16.692230377255814 chr5 180915260 97393632 0.5383384021889586 32.6000838159962 chr6 171115067 80226517 0.4688454290235003 21.05478738809676 chr7 159138663 120762058 0.7588480116865126 52.90121069511398 chr8 146364022 66113572 0.45170644463432413 24.686725244176156 chr9 141213431 54872439 0.38857804538436574 17.74378658963245 chr10 135534747 26119032 0.19271096584553332 18.021227830755013 chr11 135006516 32947242 0.24404186535707653 16.25539660616842 chr12 133851895 39612059 0.2959394710101041 16.67668461882136 chr13 115169878 38820923 0.337075315821729 21.443881654058735 chr14 107349540 21248032 0.19793314438049758 9.792353208628418 chr15 102531392 18619745 0.1816004312123257 9.166704155778422 chr16 90354753 48602944 0.5379124217184236 24.385233630610077 chr17 81195210 75289041 0.9272596376067012 34.63634935456813 chr18 78077248 15501451 0.19853992548507857 16.377856096710886 chr19 59128983 48601204 0.8219523072128604 50.1004850327057 chr20 63025520 22665352 0.3596218166863201 17.033240951408303 chr21 48129895 9532754 0.19806305415791994 10.997712591303852 chr22 51304566 12880769 0.2510647687771104 28.812154407821968 chrMT 16571 4577 0.27620541910566654 0.7088291441262254 chrX 155270560 52797579 0.3400359926569467 19.40005471704398 chrY 59373566 3176604 0.05350199110493043 10.215894482874317