BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237304.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,970,419 number of mapped reads = 2,712,310 (91.31%) number of supplementary alignments = 30,054 (1.01%) number of secondary alignments = 0 number of mapped bases = 169,841,704 bp number of sequenced bases = 169,766,767 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 741,513 duplication rate = 19.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7308 >>>>>>> ACTG content number of A's = 43,238,586 bp (25.47%) number of C's = 29,776,765 bp (17.54%) number of T's = 56,167,668 bp (33.09%) number of G's = 40,565,956 bp (23.9%) number of N's = 17,792 bp (0.01%) GC percentage = 41.43% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 1,016,850 number of insertions = 13,507 mapped reads with insertion percentage = 0.49% number of deletions = 42,692 mapped reads with deletion percentage = 1.56% homopolymer indels = 42.78% >>>>>>> Coverage mean coverageData = 0.0549X std coverageData = 0.768X There is a 2.6% of reference with a coverageData >= 1X There is a 1.27% of reference with a coverageData >= 2X There is a 0.68% of reference with a coverageData >= 3X There is a 0.36% of reference with a coverageData >= 4X There is a 0.2% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 14568533 0.05844933481630122 0.9958036174344744 chr2 243199373 13160391 0.054113589347123854 1.4082192152085862 chr3 198022430 12813303 0.06470632140005554 0.4609360776563033 chr4 191154276 10220307 0.05346627453941967 0.6143686865332694 chr5 180915260 9813432 0.05424325178539389 0.4180977513900435 chr6 171115067 14544420 0.08499789209094019 0.8236060298637448 chr7 159138663 10453617 0.0656887320964862 0.8992912289345572 chr8 146364022 14351858 0.09805591431478974 1.411057634569247 chr9 141213431 6103107 0.04321902638283748 0.46991452299979697 chr10 135534747 5333478 0.03935137016930426 0.7184508870189762 chr11 135006516 8532469 0.06320042360029497 0.5296957642195339 chr12 133851895 3383968 0.025281435126488123 0.29109122994276637 chr13 115169878 3850975 0.03343734548368628 0.3784318188911979 chr14 107349540 7362084 0.06858048949254929 0.47601909349142174 chr15 102531392 2675423 0.026093696260360923 0.3117095645444775 chr16 90354753 2837134 0.03139994195988782 0.3594307711928529 chr17 81195210 4136021 0.05093922412418171 0.4472241766641985 chr18 78077248 6005780 0.0769210000844292 1.035891049468678 chr19 59128983 2500550 0.04228975154198069 0.6380769603193273 chr20 63025520 3751058 0.05951649427089217 0.4685626535455072 chr21 48129895 2616239 0.054357878819390734 0.5046738574246296 chr22 51304566 1782944 0.03475215052009211 0.332564338985166 chrMT 16571 20017 1.2079536539738096 2.0186039272765472 chrX 155270560 8355675 0.05381364632162079 0.45365057712285695 chrY 59373566 668921 0.011266309993912106 0.4630914273074903