BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472397.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 = 20,121,624 number of mapped reads = 19,947,393 (99.13%) number of supplementary alignments = 93,056 (0.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,010,420 number of mapped paired reads (second in pair) = 9,936,973 number of mapped paired reads (both in pair) = 19,835,698 number of mapped paired reads (singletons) = 111,695 number of mapped bases = 1,957,850,968 bp number of sequenced bases = 1,957,631,888 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,715,102 duplication rate = 46.75% >>>>>>> Insert size mean insert size = 26,376.9882 std insert size = 1,601,703.5922 median insert size = 231 >>>>>>> Mapping quality mean mapping quality = 54.8182 >>>>>>> ACTG content number of A's = 534,843,356 bp (27.32%) number of C's = 445,326,311 bp (22.75%) number of T's = 536,610,106 bp (27.41%) number of G's = 440,617,682 bp (22.51%) number of N's = 234,433 bp (0.01%) GC percentage = 45.26% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 10,844,142 number of insertions = 116,751 mapped reads with insertion percentage = 0.58% number of deletions = 95,181 mapped reads with deletion percentage = 0.47% homopolymer indels = 46.58% >>>>>>> Coverage mean coverageData = 0.6324X std coverageData = 19.8508X There is a 5.38% of reference with a coverageData >= 1X There is a 2.26% of reference with a coverageData >= 2X There is a 0.96% of reference with a coverageData >= 3X There is a 0.71% of reference with a coverageData >= 4X There is a 0.55% of reference with a coverageData >= 5X There is a 0.5% of reference with a coverageData >= 6X There is a 0.46% of reference with a coverageData >= 7X There is a 0.44% of reference with a coverageData >= 8X There is a 0.42% of reference with a coverageData >= 9X There is a 0.4% of reference with a coverageData >= 10X There is a 0.39% of reference with a coverageData >= 11X There is a 0.38% of reference with a coverageData >= 12X There is a 0.37% of reference with a coverageData >= 13X There is a 0.36% of reference with a coverageData >= 14X There is a 0.35% of reference with a coverageData >= 15X There is a 0.34% of reference with a coverageData >= 16X There is a 0.33% of reference with a coverageData >= 17X There is a 0.32% of reference with a coverageData >= 18X There is a 0.32% of reference with a coverageData >= 19X There is a 0.31% of reference with a coverageData >= 20X There is a 0.3% of reference with a coverageData >= 21X There is a 0.3% of reference with a coverageData >= 22X There is a 0.29% of reference with a coverageData >= 23X There is a 0.29% of reference with a coverageData >= 24X There is a 0.28% of reference with a coverageData >= 25X There is a 0.28% of reference with a coverageData >= 26X There is a 0.27% of reference with a coverageData >= 27X There is a 0.27% of reference with a coverageData >= 28X There is a 0.26% of reference with a coverageData >= 29X There is a 0.26% of reference with a coverageData >= 30X There is a 0.25% of reference with a coverageData >= 31X There is a 0.25% of reference with a coverageData >= 32X There is a 0.25% of reference with a coverageData >= 33X There is a 0.24% of reference with a coverageData >= 34X There is a 0.24% of reference with a coverageData >= 35X There is a 0.24% of reference with a coverageData >= 36X There is a 0.23% of reference with a coverageData >= 37X There is a 0.23% of reference with a coverageData >= 38X There is a 0.23% of reference with a coverageData >= 39X There is a 0.22% of reference with a coverageData >= 40X There is a 0.22% of reference with a coverageData >= 41X There is a 0.22% of reference with a coverageData >= 42X There is a 0.22% of reference with a coverageData >= 43X There is a 0.21% of reference with a coverageData >= 44X There is a 0.21% of reference with a coverageData >= 45X There is a 0.21% of reference with a coverageData >= 46X There is a 0.2% of reference with a coverageData >= 47X There is a 0.2% of reference with a coverageData >= 48X There is a 0.2% of reference with a coverageData >= 49X There is a 0.2% of reference with a coverageData >= 50X There is a 0.2% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 189412760 0.7599289391539771 20.613644741158854 chr2 243199373 197701428 0.8129191517282407 24.01325234006384 chr3 198022430 134000693 0.6766945188986925 15.331818529379012 chr4 191154276 60855836 0.318359794368398 15.66520040008476 chr5 180915260 63103359 0.34880064290872975 9.985146569936884 chr6 171115067 148120758 0.8656207813657929 19.292463193689223 chr7 159138663 182546566 1.1470912382869523 34.98823938815918 chr8 146364022 90454390 0.6180097319271535 16.375106552588072 chr9 141213431 59929639 0.42439050291186536 12.139890697668045 chr10 135534747 45736437 0.33745174586115545 9.957025957756619 chr11 135006516 48581798 0.3598478017164742 10.733201344415564 chr12 133851895 115598049 0.863626540363885 29.597323122372174 chr13 115169878 73362369 0.6369926778944751 19.53279368386237 chr14 107349540 45317190 0.42214610328092694 14.235167199640172 chr15 102531392 21488346 0.20957821386059014 6.454468802727039 chr16 90354753 112846332 1.248925244696314 36.893869800333405 chr17 81195210 79948784 0.9846490205518281 21.357175410122466 chr18 78077248 28894117 0.37007089440447494 11.831891756545529 chr19 59128983 48920472 0.8273518250770523 15.610467663017621 chr20 63025520 70579978 1.1198634775246599 32.96642403035745 chr21 48129895 15752230 0.3272857752962062 15.638767566411218 chr22 51304566 21251746 0.4142271859389669 14.081771593833649 chrMT 16571 14111 0.8515478848590912 1.1038854195691445 chrX 155270560 103097864 0.663988485647247 18.19228559383894 chrY 59373566 335716 0.005654300770817774 0.3917389943521832