BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083674.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,569,872 number of mapped reads = 2,089,139 (81.29%) number of supplementary alignments = 15,537 (0.6%) number of secondary alignments = 0 number of mapped bases = 122,802,796 bp number of sequenced bases = 122,765,362 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 77,145 duplication rate = 3.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4848 >>>>>>> ACTG content number of A's = 36,713,606 bp (29.91%) number of C's = 24,420,870 bp (19.89%) number of T's = 35,466,278 bp (28.89%) number of G's = 26,147,583 bp (21.3%) number of N's = 17,025 bp (0.01%) GC percentage = 41.19% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 995,387 number of insertions = 8,851 mapped reads with insertion percentage = 0.42% number of deletions = 23,578 mapped reads with deletion percentage = 1.12% homopolymer indels = 45.36% >>>>>>> Coverage mean coverageData = 0.0397X std coverageData = 0.3292X There is a 3.4% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 14205496 0.05699282089251043 0.6656643300843339 chr2 243199373 9565902 0.039333580025307055 0.2911016026516347 chr3 198022430 8634002 0.04360113144758399 0.23628226318787768 chr4 191154276 5902279 0.030877044047918654 0.204088953526585 chr5 180915260 7211458 0.039860971374111834 0.2264119916318327 chr6 171115067 5878757 0.034355577817118815 0.24446662298836588 chr7 159138663 7974788 0.05011219680788697 0.4021893246965006 chr8 146364022 10071210 0.06880932801914941 0.47270368563109094 chr9 141213431 5890739 0.04171514676957321 0.29442041131850577 chr10 135534747 4836035 0.03568114529331729 0.2992116722813617 chr11 135006516 5139469 0.03806830331063428 0.24588250118087526 chr12 133851895 4268204 0.031887512687063566 0.2046271165980841 chr13 115169878 4350662 0.03777604071092269 0.21985071200114512 chr14 107349540 2203125 0.02052291048475848 0.172063780727477 chr15 102531392 2976719 0.029032269453632308 0.1940720374464459 chr16 90354753 3097482 0.03428133990914678 0.22822870025387076 chr17 81195210 2240367 0.02759235427804177 0.1958999277944776 chr18 78077248 2608358 0.03340740185924586 0.5014953889456872 chr19 59128983 2703867 0.04572828523027362 0.4078852814130622 chr20 63025520 1964826 0.031175085901710926 0.20662333977824246 chr21 48129895 1229432 0.02554404076717807 0.18827388503611403 chr22 51304566 1090528 0.021255963845401207 0.1630604148657476 chrMT 16571 49396 2.9808701949188343 2.302598579967076 chrX 155270560 8376214 0.05394592510003184 0.28024680050115425 chrY 59373566 333481 0.005616657756416382 0.11497384061337804