BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063574.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 = 2,702,176 number of mapped reads = 2,485,049 (91.96%) number of supplementary alignments = 18,143 (0.67%) number of secondary alignments = 0 number of mapped bases = 167,318,814 bp number of sequenced bases = 167,247,795 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 205,662 duplication rate = 6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.9722 >>>>>>> ACTG content number of A's = 47,213,943 bp (28.23%) number of C's = 31,452,796 bp (18.81%) number of T's = 52,484,800 bp (31.38%) number of G's = 36,091,499 bp (21.58%) number of N's = 4,757 bp (0%) GC percentage = 40.39% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 1,243,128 number of insertions = 12,479 mapped reads with insertion percentage = 0.5% number of deletions = 39,544 mapped reads with deletion percentage = 1.57% homopolymer indels = 48.22% >>>>>>> Coverage mean coverageData = 0.054X std coverageData = 0.996X There is a 3.47% of reference with a coverageData >= 1X There is a 1.12% of reference with a coverageData >= 2X There is a 0.39% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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% 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 36257335 0.14546537478837415 2.944798218845506 chr2 243199373 16602995 0.06826906992066957 0.88674245465251 chr3 198022430 8283758 0.041832422721001856 0.32187647818869614 chr4 191154276 2214226 0.01158345000872489 0.2923287078401669 chr5 180915260 4199969 0.02321511739805697 0.22443927452007462 chr6 171115067 3225570 0.01885029796937753 0.20430541376472386 chr7 159138663 5087539 0.031969220452731845 0.341215489148701 chr8 146364022 2229443 0.015232179121177743 0.40990495079280764 chr9 141213431 12287604 0.08701441437252523 0.6718690441331813 chr10 135534747 7930987 0.05851626372977256 0.9263918833534792 chr11 135006516 11354429 0.08410282211860055 0.7090586207335191 chr12 133851895 1341940 0.010025558472668616 0.19934116909383742 chr13 115169878 1799135 0.015621575981872622 0.17347849082282973 chr14 107349540 866437 0.008071175712536821 0.22580931812211644 chr15 102531392 5483311 0.05347933830840802 0.32751980985551765 chr16 90354753 1088907 0.012051463413330342 0.2634974081269128 chr17 81195210 4110160 0.050620720113908196 0.44039846442411174 chr18 78077248 9810141 0.12564660322044138 0.9624536147257339 chr19 59128983 10983538 0.18575557100314072 1.639552716675456 chr20 63025520 569816 0.009041036075545272 0.16804835688545716 chr21 48129895 3580018 0.07438241866100061 0.48460130511791877 chr22 51304566 235753 0.004595166052081992 0.0894643560215314 chrMT 16571 130497 7.875022629895601 5.679552127035244 chrX 155270560 17227243 0.11094983492041247 0.6674248713492055 chrY 59373566 418063 0.007041231109480606 0.28467345565792074