BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080659.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 = 1,437,720 number of mapped reads = 1,278,660 (88.94%) number of supplementary alignments = 14,505 (1.01%) number of secondary alignments = 0 number of mapped bases = 84,142,916 bp number of sequenced bases = 84,111,697 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,716 duplication rate = 3.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1406 >>>>>>> ACTG content number of A's = 22,603,843 bp (26.87%) number of C's = 15,466,731 bp (18.39%) number of T's = 26,735,221 bp (31.79%) number of G's = 19,302,510 bp (22.95%) number of N's = 3,392 bp (0%) GC percentage = 41.34% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 589,665 number of insertions = 6,206 mapped reads with insertion percentage = 0.48% number of deletions = 19,312 mapped reads with deletion percentage = 1.5% homopolymer indels = 47.66% >>>>>>> Coverage mean coverageData = 0.0272X std coverageData = 0.2369X There is a 2.38% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.04% 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 10239356 0.04108056364682036 0.305368235106681 chr2 243199373 5639515 0.02318885501402999 0.34360557625887955 chr3 198022430 5333720 0.026934928533095974 0.1823042621391781 chr4 191154276 3596849 0.018816471570847832 0.15639285628304764 chr5 180915260 3912598 0.02162668864970263 0.16311868974869237 chr6 171115067 4983450 0.029123385142934256 0.2345224185122769 chr7 159138663 5390450 0.03387266110184676 0.4425983723410237 chr8 146364022 10132191 0.0692259672940663 0.3231436764130766 chr9 141213431 2595325 0.018378740475472194 0.17466837365178792 chr10 135534747 3967634 0.029273924862972592 0.1996110316455856 chr11 135006516 3503797 0.025952799196743957 0.18979750925994038 chr12 133851895 2756140 0.020590967352386007 0.1604359423990482 chr13 115169878 1739300 0.015102039093937392 0.1374269272074481 chr14 107349540 1642026 0.015296069270534368 0.13996622232199873 chr15 102531392 1596320 0.01556908541727396 0.14405355988074578 chr16 90354753 1967366 0.021773796448760145 0.16763505706507859 chr17 81195210 1377171 0.01696123453587964 0.14668447505585794 chr18 78077248 2608655 0.033411205784302234 0.2564563141254008 chr19 59128983 1332336 0.022532706168817414 0.2165457532544404 chr20 63025520 2064536 0.032757143455539914 0.20290032721137968 chr21 48129895 1291510 0.026833842043495003 0.18388652081595946 chr22 51304566 840217 0.016377041372886772 0.14045478569705414 chrMT 16571 33290 2.008931265463762 1.9601774068536424 chrX 155270560 5432411 0.03498674185241555 0.21508402740460872 chrY 59373566 166753 0.0028085394096086466 0.06105080719778421