BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3212675.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 = 2,167,871 number of mapped reads = 1,984,407 (91.54%) number of supplementary alignments = 12,438 (0.57%) number of secondary alignments = 0 number of mapped bases = 134,299,492 bp number of sequenced bases = 134,249,713 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 83,983 duplication rate = 3.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.057 >>>>>>> ACTG content number of A's = 36,847,941 bp (27.45%) number of C's = 25,934,866 bp (19.32%) number of T's = 41,232,787 bp (30.71%) number of G's = 30,232,629 bp (22.52%) number of N's = 1,490 bp (0%) GC percentage = 41.84% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,111,805 number of insertions = 9,847 mapped reads with insertion percentage = 0.49% number of deletions = 27,793 mapped reads with deletion percentage = 1.39% homopolymer indels = 47.7% >>>>>>> Coverage mean coverageData = 0.0434X std coverageData = 0.3352X There is a 3.61% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.1% 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% 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 10499598 0.042124661346380356 0.4862684939596623 chr2 243199373 9133553 0.03755582461966298 0.3550077003300498 chr3 198022430 9847037 0.049726876899753227 0.2585550700394324 chr4 191154276 8659062 0.045298814032284584 0.26235355358093365 chr5 180915260 9298060 0.0513945589775014 0.26386625775592104 chr6 171115067 8316759 0.048603312062519895 0.3219398342638229 chr7 159138663 7401434 0.04650933883992729 0.4899784371651159 chr8 146364022 6083144 0.04156174390998903 0.3348991878692042 chr9 141213431 5072369 0.03591987648823574 0.3152810797044375 chr10 135534747 6549137 0.048320723245973224 0.3265849228860739 chr11 135006516 6030632 0.04466919211514206 0.3365153408101462 chr12 133851895 5780274 0.043184102847404586 0.2449878929167716 chr13 115169878 4367373 0.03792113941459589 0.22612175403957857 chr14 107349540 4181343 0.038950730482869324 0.24431332960146898 chr15 102531392 4811397 0.04692608679300872 0.25529272236944367 chr16 90354753 3645203 0.04034323462762385 0.25750100665828846 chr17 81195210 3221334 0.03967394135688546 0.2592197847149813 chr18 78077248 3008364 0.03853061009527385 0.6116025648115376 chr19 59128983 3311970 0.056012632586628454 0.41905847276223246 chr20 63025520 3399956 0.05394570326432848 0.27984894898773943 chr21 48129895 2035605 0.04229398381193227 0.2588381973125192 chr22 51304566 1723650 0.03359642492638959 0.21396790181952066 chrMT 16571 25133 1.516685776356285 1.7302596896934355 chrX 155270560 7558061 0.04867671630732832 0.2902462484327177 chrY 59373566 339044 0.00571035265087497 0.14023129361552017