BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046538.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 5,924,328 number of mapped reads = 5,792,441 (97.77%) number of supplementary alignments = 37,259 (0.63%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,945,985 number of mapped paired reads (second in pair) = 2,846,456 number of mapped paired reads (both in pair) = 5,678,388 number of mapped paired reads (singletons) = 114,053 number of mapped bases = 549,735,508 bp number of sequenced bases = 549,522,861 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,924,955 duplication rate = 29.2% >>>>>>> Insert size mean insert size = 37,018.1268 std insert size = 1,959,207.6815 median insert size = 127 >>>>>>> Mapping quality mean mapping quality = 52.0063 >>>>>>> ACTG content number of A's = 156,983,422 bp (28.57%) number of C's = 118,368,626 bp (21.54%) number of T's = 155,809,689 bp (28.35%) number of G's = 118,309,985 bp (21.53%) number of N's = 51,139 bp (0.01%) GC percentage = 43.07% >>>>>>> Mismatches and indels general error rate = 0.0044 number of mismatches = 2,285,632 number of insertions = 57,729 mapped reads with insertion percentage = 0.98% number of deletions = 69,993 mapped reads with deletion percentage = 1.17% homopolymer indels = 47.87% >>>>>>> Coverage mean coverageData = 0.1776X std coverageData = 26.9436X There is a 2.45% of reference with a coverageData >= 1X There is a 1.57% of reference with a coverageData >= 2X There is a 0.58% of reference with a coverageData >= 3X There is a 0.4% of reference with a coverageData >= 4X There is a 0.2% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 56033190 0.22480662144468638 22.885409914472877 chr2 243199373 54559428 0.22434033166689127 36.12776452613976 chr3 198022430 30177115 0.1523924082741536 14.510595916418806 chr4 191154276 20768799 0.1086494083972257 10.719018030130966 chr5 180915260 35194788 0.19453742044756203 25.52177520187078 chr6 171115067 43413962 0.25371209421318813 25.278885635139513 chr7 159138663 52534258 0.33011624585535193 57.648106261419784 chr8 146364022 16229064 0.11088151157802974 7.618318304013672 chr9 141213431 12722836 0.0900965008066407 8.263293112766037 chr10 135534747 46263239 0.34133858677583245 58.84996957970112 chr11 135006516 11306467 0.08374756519159415 2.6195503471829147 chr12 133851895 18954152 0.1416054064830386 36.46980926045932 chr13 115169878 15670853 0.13606728835815907 20.710690830718526 chr14 107349540 8997235 0.08381251563816669 2.0933420424327904 chr15 102531392 19041739 0.18571618534155862 16.49213397644654 chr16 90354753 26355293 0.2916868468446812 28.79066574072016 chr17 81195210 20054771 0.2469945086662132 20.814746294276674 chr18 78077248 15011768 0.19226814961510938 18.90303446670597 chr19 59128983 27152720 0.45921168642457455 38.45155011553719 chr20 63025520 5908567 0.09374880207255727 5.375563573130651 chr21 48129895 1272222 0.02643309319498827 2.619851541105482 chr22 51304566 5262427 0.1025722934679927 12.228919031033168 chrMT 16571 78825 4.756804055277292 3.1460625720508144 chrX 155270560 6608417 0.0425606567014378 0.9912869792013939 chrY 59373566 163373 0.002751611718925557 0.15067258536714145