BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617676.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 428,796,288 number of mapped reads = 425,599,389 (99.25%) number of supplementary alignments = 2,038,134 (0.48%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 212,870,124 number of mapped paired reads (second in pair) = 212,729,265 number of mapped paired reads (both in pair) = 423,767,070 number of mapped paired reads (singletons) = 1,832,319 number of mapped bases = 41,681,240,809 bp number of sequenced bases = 41,655,000,159 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 206,302,589 duplication rate = 21.65% >>>>>>> Insert size mean insert size = 25,032.721 std insert size = 1,413,187.4706 median insert size = 224 >>>>>>> Mapping quality mean mapping quality = 52.902 >>>>>>> ACTG content number of A's = 12,399,298,489 bp (29.77%) number of C's = 8,312,179,962 bp (19.95%) number of T's = 12,433,485,150 bp (29.85%) number of G's = 8,505,153,738 bp (20.42%) number of N's = 4,882,820 bp (0.01%) GC percentage = 40.37% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 431,983,396 number of insertions = 6,606,518 mapped reads with insertion percentage = 1.52% number of deletions = 15,594,806 mapped reads with deletion percentage = 3.59% homopolymer indels = 47.91% >>>>>>> Coverage mean coverageData = 13.4643X std coverageData = 156.3015X There is a 62.3% of reference with a coverageData >= 1X There is a 56.39% of reference with a coverageData >= 2X There is a 51.93% of reference with a coverageData >= 3X There is a 48.26% of reference with a coverageData >= 4X There is a 45.07% of reference with a coverageData >= 5X There is a 42.26% of reference with a coverageData >= 6X There is a 39.73% of reference with a coverageData >= 7X There is a 37.44% of reference with a coverageData >= 8X There is a 35.35% of reference with a coverageData >= 9X There is a 33.44% of reference with a coverageData >= 10X There is a 31.67% of reference with a coverageData >= 11X There is a 30.03% of reference with a coverageData >= 12X There is a 28.51% of reference with a coverageData >= 13X There is a 27.1% of reference with a coverageData >= 14X There is a 25.78% of reference with a coverageData >= 15X There is a 24.54% of reference with a coverageData >= 16X There is a 23.38% of reference with a coverageData >= 17X There is a 22.29% of reference with a coverageData >= 18X There is a 21.27% of reference with a coverageData >= 19X There is a 20.3% of reference with a coverageData >= 20X There is a 19.4% of reference with a coverageData >= 21X There is a 18.54% of reference with a coverageData >= 22X There is a 17.73% of reference with a coverageData >= 23X There is a 16.96% of reference with a coverageData >= 24X There is a 16.23% of reference with a coverageData >= 25X There is a 15.55% of reference with a coverageData >= 26X There is a 14.9% of reference with a coverageData >= 27X There is a 14.28% of reference with a coverageData >= 28X There is a 13.69% of reference with a coverageData >= 29X There is a 13.14% of reference with a coverageData >= 30X There is a 12.61% of reference with a coverageData >= 31X There is a 12.1% of reference with a coverageData >= 32X There is a 11.63% of reference with a coverageData >= 33X There is a 11.17% of reference with a coverageData >= 34X There is a 10.74% of reference with a coverageData >= 35X There is a 10.32% of reference with a coverageData >= 36X There is a 9.93% of reference with a coverageData >= 37X There is a 9.56% of reference with a coverageData >= 38X There is a 9.2% of reference with a coverageData >= 39X There is a 8.85% of reference with a coverageData >= 40X There is a 8.53% of reference with a coverageData >= 41X There is a 8.22% of reference with a coverageData >= 42X There is a 7.92% of reference with a coverageData >= 43X There is a 7.63% of reference with a coverageData >= 44X There is a 7.36% of reference with a coverageData >= 45X There is a 7.1% of reference with a coverageData >= 46X There is a 6.85% of reference with a coverageData >= 47X There is a 6.61% of reference with a coverageData >= 48X There is a 6.38% of reference with a coverageData >= 49X There is a 6.16% of reference with a coverageData >= 50X There is a 5.95% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2551761152 10.237732374596572 148.54070994402701 chr2 243199373 4311327687 17.72754441681887 179.82329439439596 chr3 198022430 3488630669 17.617351069775278 31.256837224050543 chr4 191154276 2335138231 12.215987420548206 126.48809746128018 chr5 180915260 2755998153 15.233641169904628 29.63652163130157 chr6 171115067 2018988937 11.799013216060045 81.80306281123173 chr7 159138663 3259624677 20.482921092531736 192.170220305611 chr8 146364022 1851820580 12.65215696245352 57.52442348295055 chr9 141213431 1718718294 12.171068161356407 312.7013426749795 chr10 135534747 1770367240 13.062091302682699 313.6400921615557 chr11 135006516 2294393726 16.994688804501852 179.03577993611847 chr12 133851895 1776482873 13.27200390401645 27.147483788798485 chr13 115169878 1791433009 15.554700934909386 28.81232164878941 chr14 107349540 1188770806 11.073832323827377 32.48954065400702 chr15 102531392 887696556 8.65780263667931 19.26878272006954 chr16 90354753 1152673832 12.75720195925941 238.73064005290112 chr17 81195210 1027721731 12.657418227011174 189.19000709542615 chr18 78077248 775727762 9.935388117163146 273.30185956288744 chr19 59128983 439186277 7.427597342575637 88.1422138518092 chr20 63025520 1124281870 17.83851795272772 40.5891562691249 chr21 48129895 608876271 12.650687706673784 62.395588104683114 chr22 51304566 265874383 5.182275257917589 15.63982769524423 chrMT 16571 43943834 2651.851668577636 1834.017131547113 chrX 155270560 2070057406 13.331937528917265 61.98658772079767 chrY 59373566 171744853 2.8926147538451707 261.99853639464163