BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971284.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 12,730,370 number of mapped reads = 10,732,059 (84.3%) number of secondary alignments = 0 number of mapped bases = 422,494,855 bp number of sequenced bases = 422,451,201 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 943,120 duplication rate = 6.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 37.2106 >>>>>>> ACTG content number of A's = 121,567,841 bp (28.78%) number of C's = 86,418,118 bp (20.46%) number of T's = 125,546,148 bp (29.72%) number of G's = 88,915,928 bp (21.05%) number of N's = 3,166 bp (0%) GC percentage = 41.5% >>>>>>> Mismatches and indels general error rate = 0.0033 number of mismatches = 1,379,811 number of insertions = 15,879 mapped reads with insertion percentage = 0.15% number of deletions = 35,011 mapped reads with deletion percentage = 0.33% homopolymer indels = 38.73% >>>>>>> Coverage mean coverageData = 0.1365X std coverageData = 1.4769X There is a 10.27% of reference with a coverageData >= 1X There is a 2.26% of reference with a coverageData >= 2X There is a 0.54% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 0.01% 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 33358198 0.13383396144076207 2.8709805901755336 chr2 243199373 35764392 0.14705791202841628 1.0743252977122444 chr3 198022430 29001784 0.14645706549505527 0.4941546834789914 chr4 191154276 29287771 0.1532153588863479 0.5388449419126876 chr5 180915260 27680561 0.15300290865458227 0.5458043626691041 chr6 171115067 25107709 0.1467299720602628 0.5758042262306611 chr7 159138663 24264483 0.1524738397481698 1.9601659686438608 chr8 146364022 21976697 0.15015095034762027 3.592215492435006 chr9 141213431 17454768 0.1236055796987186 1.0741791340853348 chr10 135534747 19973891 0.14737099852335284 1.0581599102019306 chr11 135006516 19241708 0.1425242911979152 0.8986088218232836 chr12 133851895 19597699 0.1464133100244864 0.5702386278442098 chr13 115169878 10049181 0.08725528909564356 0.3606624152294088 chr14 107349540 13076656 0.12181380562972137 0.7487323360840207 chr15 102531392 11686950 0.11398411522590077 0.42320877077074626 chr16 90354753 10750926 0.11898572729206619 0.5778684361287796 chr17 81195210 10318222 0.12707919592793712 0.5670487129033006 chr18 78077248 11331272 0.14512898815286113 2.4846277812417528 chr19 59128983 8094183 0.1368902793406746 2.765993488116517 chr20 63025520 7874191 0.1249365495120072 0.5355143927034826 chr21 48129895 5173897 0.10749861390721921 0.5692576256846025 chr22 51304566 4211320 0.08208470177878514 0.3614499323439638 chrMT 16571 26341 1.589584213384829 1.8824632501066676 chrX 155270560 25532232 0.16443704460137196 0.8140494838932919 chrY 59373566 1659823 0.0279555888558218 0.3317872292699974