BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094020.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 577,080 number of mapped reads = 438,157 (75.93%) number of supplementary alignments = 12,456 (2.16%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 219,536 number of mapped paired reads (second in pair) = 218,621 number of mapped paired reads (both in pair) = 434,014 number of mapped paired reads (singletons) = 4,143 number of mapped bases = 59,310,683 bp number of sequenced bases = 58,657,422 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 437,604 duplication rate = 39.8% >>>>>>> Insert size mean insert size = 170,443.6868 std insert size = 3,854,176.0371 median insert size = 191 >>>>>>> Mapping quality mean mapping quality = 23.3224 >>>>>>> ACTG content number of A's = 17,387,024 bp (29.64%) number of C's = 12,174,097 bp (20.75%) number of T's = 16,663,567 bp (28.41%) number of G's = 12,431,968 bp (21.19%) number of N's = 766 bp (0%) GC percentage = 41.95% >>>>>>> Mismatches and indels general error rate = 0.0272 number of mismatches = 1,557,698 number of insertions = 20,278 mapped reads with insertion percentage = 4.52% number of deletions = 120,207 mapped reads with deletion percentage = 26.48% homopolymer indels = 22.9% >>>>>>> Coverage mean coverageData = 0.0192X std coverageData = 19.4648X There is a 0.01% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 307668 0.0012343720499697372 0.6637973910463224 chr2 243199373 678492 0.002789859166289874 1.7102121104498442 chr3 198022430 614717 0.0031042796515526046 1.8646769614482357 chr4 191154276 671486 0.003512796124947788 2.7799314734375526 chr5 180915260 2298392 0.012704246175806287 12.009704474925677 chr6 171115067 2079793 0.012154353421139706 11.244718007050539 chr7 159138663 173461 0.001089999103486247 0.5750913057476764 chr8 146364022 474769 0.0032437548074485136 1.6331085453774838 chr9 141213431 147947 0.001047683630036579 0.5257027638879126 chr10 135534747 137122 0.0010117110411546346 0.3310125787713353 chr11 135006516 781724 0.005790268671180286 3.3786372882817997 chr12 133851895 276304 0.002064251686537572 1.026492260629248 chr13 115169878 4822698 0.04187464711910175 27.313296888965006 chr14 107349540 114702 0.0010684908384330292 1.0264348634265745 chr15 102531392 247243 0.0024113883092506927 1.3110446155905628 chr16 90354753 764721 0.008463539267270202 6.612322509379941 chr17 81195210 299705 0.0036911660182909803 2.3788687525800074 chr18 78077248 648619 0.008307400896097158 4.83944154657334 chr19 59128983 81970 0.0013862913894527832 0.4868016427541135 chr20 63025520 127757 0.002027067765565441 1.509508970239269 chr21 48129895 4989 1.0365698907092982E-4 0.01765231761213691 chr22 51304566 3504 6.82980146445445E-5 0.013066766138469924 chrMT 16571 24118767 1455.480477943395 7120.325250144976 chrX 155270560 19422357 0.12508718330120017 31.30807980200105 chrY 59373566 11776 1.9833742174084676E-4 0.08750384230380022