BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818768.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 = 304,161 number of mapped reads = 288,440 (94.83%) number of supplementary alignments = 2,370 (0.78%) number of secondary alignments = 0 number of mapped bases = 19,575,864 bp number of sequenced bases = 19,567,788 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 55,661 duplication rate = 17.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.9856 >>>>>>> ACTG content number of A's = 5,634,886 bp (28.8%) number of C's = 4,434,664 bp (22.66%) number of T's = 5,507,507 bp (28.15%) number of G's = 3,989,435 bp (20.39%) number of N's = 1,296 bp (0.01%) GC percentage = 43.05% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 98,838 number of insertions = 2,440 mapped reads with insertion percentage = 0.84% number of deletions = 5,048 mapped reads with deletion percentage = 1.73% homopolymer indels = 40.06% >>>>>>> Coverage mean coverageData = 0.0063X std coverageData = 0.1158X There is a 0.48% of reference with a coverageData >= 1X There is a 0.11% 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 1715067 0.006880893588626204 0.14610437880307597 chr2 243199373 1704885 0.007010236000896269 0.16648485524128578 chr3 198022430 1318307 0.006657361996820259 0.10341967459448194 chr4 191154276 1176893 0.0061567704611535864 0.10222971453295712 chr5 180915260 1222641 0.0067580866312769855 0.10394903377785863 chr6 171115067 1183278 0.006915101169904576 0.1092255325562547 chr7 159138663 1005770 0.0063200857732479505 0.10645145936533257 chr8 146364022 994102 0.006791983346836424 0.10793318882590304 chr9 141213431 830599 0.005881869692692333 0.1016066933504739 chr10 135534747 932350 0.00687904777658234 0.11985761075278549 chr11 135006516 942588 0.0069817963452964 0.10908990971076596 chr12 133851895 907574 0.00678043444958325 0.10646529075083241 chr13 115169878 586535 0.005092781291302575 0.09010314844050611 chr14 107349540 616818 0.00574588396000579 0.10010149015164632 chr15 102531392 576422 0.005621907483709965 0.09500775383968604 chr16 90354753 644916 0.007137599059121993 0.13522581738663295 chr17 81195210 588636 0.007249639479964397 0.1096732842722201 chr18 78077248 502693 0.006438405718398272 0.11681003319113534 chr19 59128983 422958 0.0071531418018808135 0.13075954458959807 chr20 63025520 436903 0.006932160178924346 0.10822228779945003 chr21 48129895 263859 0.005482226794801859 0.09636044798103377 chr22 51304566 251544 0.0049029554211607596 0.0938736595072378 chrMT 16571 15851 0.9565506004465633 1.488073298282482 chrX 155270560 561723 0.0036177044766245448 0.07803995946375927 chrY 59373566 172952 0.0029129461417223956 0.13255083921473848