BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013306.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 = 2,366,524 number of mapped reads = 2,126,523 (89.86%) number of supplementary alignments = 12,063 (0.51%) number of secondary alignments = 0 number of mapped bases = 139,619,264 bp number of sequenced bases = 139,560,443 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,372 duplication rate = 3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4191 >>>>>>> ACTG content number of A's = 37,873,801 bp (27.14%) number of C's = 26,735,529 bp (19.16%) number of T's = 42,942,704 bp (30.77%) number of G's = 31,976,178 bp (22.91%) number of N's = 32,231 bp (0.02%) GC percentage = 42.07% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,099,581 number of insertions = 9,290 mapped reads with insertion percentage = 0.43% number of deletions = 33,809 mapped reads with deletion percentage = 1.57% homopolymer indels = 45.27% >>>>>>> Coverage mean coverageData = 0.0451X std coverageData = 0.3522X There is a 3.78% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% 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 10382618 0.041655334531744255 0.5022592521379217 chr2 243199373 14161129 0.05822847660055439 0.46078439395016674 chr3 198022430 8720847 0.04403969287721598 0.24101685017634905 chr4 191154276 8641134 0.04520502591320531 0.25126177020435714 chr5 180915260 7516110 0.041544919980768896 0.23503245597445432 chr6 171115067 7402989 0.04326322123346391 0.2865719870902679 chr7 159138663 8714629 0.05476123046226673 0.6175066826417814 chr8 146364022 7649603 0.05226423061809548 0.3458540866641171 chr9 141213431 5019536 0.035545740688079454 0.29815284324863256 chr10 135534747 6619489 0.048839793090107 0.37461912214546 chr11 135006516 5853746 0.04335898868762749 0.28192284860876865 chr12 133851895 6887728 0.05145782956602893 0.26644371438522424 chr13 115169878 3509067 0.030468617844676367 0.2058412318441087 chr14 107349540 4634090 0.04316823341767464 0.25476663400840516 chr15 102531392 3970699 0.03872666626821959 0.22939841820012197 chr16 90354753 4731454 0.05236530279707588 0.2850271848088464 chr17 81195210 3843114 0.047331782256613414 0.2747064979788442 chr18 78077248 3374282 0.04321722507432639 0.5021577549617842 chr19 59128983 2921645 0.04941138595263849 0.4446792523199119 chr20 63025520 3179088 0.05044128156340479 0.26446033457771423 chr21 48129895 2373327 0.04931087009435612 0.2678770971391821 chr22 51304566 1484735 0.02893962693301021 0.1941396191312436 chrMT 16571 288848 17.430933558626517 12.232505136000002 chrX 155270560 7436001 0.04789060463232695 0.27163655860658764 chrY 59373566 303356 0.00510927708131932 0.11333479904188748