BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714114.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 638,140 number of mapped reads = 459,829 (72.06%) number of supplementary alignments = 15,163 (2.38%) number of secondary alignments = 0 number of mapped bases = 59,635,156 bp number of sequenced bases = 58,321,432 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 447,008 duplication rate = 35.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 26.7263 >>>>>>> ACTG content number of A's = 16,859,783 bp (28.91%) number of C's = 11,524,223 bp (19.76%) number of T's = 15,914,500 bp (27.29%) number of G's = 14,022,426 bp (24.04%) number of N's = 500 bp (0%) GC percentage = 43.8% >>>>>>> Mismatches and indels general error rate = 0.0422 number of mismatches = 2,365,844 number of insertions = 40,532 mapped reads with insertion percentage = 8.52% number of deletions = 206,139 mapped reads with deletion percentage = 43.41% homopolymer indels = 30.95% >>>>>>> Coverage mean coverageData = 0.0193X std coverageData = 13.0333X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% 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 1772691 0.007112082581330861 5.000567944159996 chr2 243199373 13754944 0.05655830370911359 29.534116017717924 chr3 198022430 7459884 0.0376719142371902 23.52542504862104 chr4 191154276 5487646 0.028707942688135316 15.016121535926432 chr5 180915260 1023394 0.005656758860474236 2.219736910995116 chr6 171115067 3832010 0.022394345905261515 11.607773038523648 chr7 159138663 559779 0.0035175550017031375 1.5485271429214968 chr8 146364022 1103412 0.007538819888401263 4.257837625474454 chr9 141213431 1147923 0.0081289930559084 5.805755970224766 chr10 135534747 820171 0.006051370723405711 3.8304089012782856 chr11 135006516 195883 0.0014509151543470687 0.452255980723663 chr12 133851895 5083219 0.037976444039137434 18.010427451967573 chr13 115169878 334728 0.0029063849490228687 1.2234444374040097 chr14 107349540 3483690 0.03245183910429425 9.681360713549543 chr15 102531392 2602400 0.025381494869395706 8.863259622164655 chr16 90354753 827554 0.009158942640239413 3.0176055804104585 chr17 81195210 2622953 0.03230428248168827 19.96264438318316 chr18 78077248 55764 7.14215746948458E-4 0.15121068662838474 chr19 59128983 644718 0.010903586824755637 3.4066031486887676 chr20 63025520 2145201 0.034037021828617994 15.62431348723571 chr21 48129895 216519 0.004498638528091532 2.2359784458482084 chr22 51304566 24810 4.835826893068348E-4 0.0991903142197711 chrMT 16571 820500 49.51421157443727 413.48994616431565 chrX 155270560 3595525 0.02315651466704313 6.692501724819535 chrY 59373566 19838 3.3412175377844076E-4 0.0558484989011746