BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083771.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 = 1,958,803 number of mapped reads = 1,516,269 (77.41%) number of supplementary alignments = 10,717 (0.55%) number of secondary alignments = 0 number of mapped bases = 97,515,951 bp number of sequenced bases = 97,482,749 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 48,505 duplication rate = 2.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3008 >>>>>>> ACTG content number of A's = 27,840,505 bp (28.56%) number of C's = 17,814,261 bp (18.27%) number of T's = 30,259,997 bp (31.04%) number of G's = 21,566,888 bp (22.12%) number of N's = 1,098 bp (0%) GC percentage = 40.4% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 805,530 number of insertions = 7,052 mapped reads with insertion percentage = 0.46% number of deletions = 20,856 mapped reads with deletion percentage = 1.36% homopolymer indels = 46.94% >>>>>>> Coverage mean coverageData = 0.0315X std coverageData = 0.2485X There is a 2.84% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 7615073 0.03055187172432361 0.34219993904870194 chr2 243199373 7911824 0.03253225492485131 0.292720379678286 chr3 198022430 7125947 0.0359855547677099 0.24631929641408992 chr4 191154276 6305133 0.03298452502312844 0.2009950919158424 chr5 180915260 6599653 0.036479250009092655 0.2068226099941682 chr6 171115067 5652110 0.03303104804908851 0.22249916505641548 chr7 159138663 5512485 0.0346395080622237 0.2908609143853441 chr8 146364022 5010131 0.034230618505413854 0.2793343354652673 chr9 141213431 4101637 0.029045657845392907 0.226071341858112 chr10 135534747 4588838 0.033857280893437605 0.24960909923208827 chr11 135006516 4438239 0.03287425771360547 0.2227518522621053 chr12 133851895 4585399 0.034257258741088426 0.20330969465703239 chr13 115169878 3331181 0.028924064676008426 0.18441274889449485 chr14 107349540 2951568 0.02749492918181112 0.1883276999156872 chr15 102531392 2868777 0.027979499195719494 0.18654264489810027 chr16 90354753 2452805 0.027146385979274382 0.19022824889099618 chr17 81195210 2337983 0.028794592685947855 0.20113610224269582 chr18 78077248 2666449 0.03415142142305016 0.4158187019227245 chr19 59128983 1615705 0.027325093685443568 0.26111844175121257 chr20 63025520 1841196 0.02921349954748489 0.19053924286988858 chr21 48129895 1299425 0.026998292848966324 0.1830721233340013 chr22 51304566 955293 0.01862003861410698 0.3165971873599953 chrMT 16571 5947 0.35887997103373365 0.6411897552445348 chrX 155270560 5525938 0.03558909042383823 0.22009188072102065 chrY 59373566 217215 0.003658446251990322 0.07803241077142273