BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819034.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 3,374,465 number of mapped reads = 3,037,180 (90%) number of supplementary alignments = 14,077 (0.42%) number of secondary alignments = 0 number of mapped bases = 174,078,455 bp number of sequenced bases = 174,032,470 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 122,449 duplication rate = 3.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0798 >>>>>>> ACTG content number of A's = 45,388,083 bp (26.08%) number of C's = 34,000,220 bp (19.54%) number of T's = 51,505,309 bp (29.6%) number of G's = 43,135,046 bp (24.79%) number of N's = 3,812 bp (0%) GC percentage = 44.32% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 847,375 number of insertions = 13,119 mapped reads with insertion percentage = 0.43% number of deletions = 27,191 mapped reads with deletion percentage = 0.89% homopolymer indels = 40.11% >>>>>>> Coverage mean coverageData = 0.0562X std coverageData = 0.3742X There is a 4.73% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% 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 19931935 0.07996744369194571 0.5636040168831434 chr2 243199373 14974067 0.061571157915773084 0.45489799788699276 chr3 198022430 11706173 0.05911538910011356 0.2827750065364358 chr4 191154276 11375587 0.05950997925884745 0.3214361462312465 chr5 180915260 9060023 0.05007882143275255 0.26417119305048453 chr6 171115067 9383739 0.05483876530872644 0.2980904790781003 chr7 159138663 8997128 0.05653640561250662 0.3566335066137776 chr8 146364022 11268710 0.07699098348089943 0.3699174182066352 chr9 141213431 6463558 0.04577155270733419 0.4012687176490647 chr10 135534747 8554722 0.06311829393830647 0.44030710594077316 chr11 135006516 6624594 0.04906869828416282 0.377541480277221 chr12 133851895 8085384 0.06040545036736312 0.2904416066283444 chr13 115169878 3029562 0.026305159409824155 0.1840250336787683 chr14 107349540 4156995 0.03872392000934517 0.25579530571989967 chr15 102531392 5109120 0.04982981212232055 0.2586601942722509 chr16 90354753 5259243 0.058206600376628774 0.31914455400847536 chr17 81195210 4031311 0.04964961603030524 0.27618363223144915 chr18 78077248 4410455 0.05648835112631019 0.7370123571517074 chr19 59128983 2886795 0.048821996481826856 0.4232692728115464 chr20 63025520 3845713 0.061018346219118856 0.30048116168524197 chr21 48129895 2293235 0.04764679000442448 0.29677737754359523 chr22 51304566 2146739 0.041843039857310166 0.23620094860899932 chrMT 16571 3770 0.2275058837728562 0.5086754356245143 chrX 155270560 9969238 0.06420559055109996 0.35168034984514285 chrY 59373566 510659 0.008600780354004677 0.18345457764109716