BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053630.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 8,568,573 number of mapped reads = 6,615,809 (77.21%) number of supplementary alignments = 166 (0%) number of secondary alignments = 0 number of mapped bases = 311,572,209 bp number of sequenced bases = 311,509,735 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,528,007 duplication rate = 16.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9231 >>>>>>> ACTG content number of A's = 93,065,885 bp (29.88%) number of C's = 61,966,980 bp (19.89%) number of T's = 90,256,882 bp (28.97%) number of G's = 66,213,599 bp (21.26%) number of N's = 6,389 bp (0%) GC percentage = 41.15% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 2,056,504 number of insertions = 12,977 mapped reads with insertion percentage = 0.2% number of deletions = 42,018 mapped reads with deletion percentage = 0.63% homopolymer indels = 45.67% >>>>>>> Coverage mean coverageData = 0.1006X std coverageData = 0.837X There is a 4.26% of reference with a coverageData >= 1X There is a 1.76% of reference with a coverageData >= 2X There is a 1.04% of reference with a coverageData >= 3X There is a 0.68% of reference with a coverageData >= 4X There is a 0.48% of reference with a coverageData >= 5X There is a 0.35% of reference with a coverageData >= 6X There is a 0.26% of reference with a coverageData >= 7X There is a 0.2% of reference with a coverageData >= 8X There is a 0.16% of reference with a coverageData >= 9X There is a 0.13% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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 24823416 0.09959219319256982 0.8538739126745097 chr2 243199373 26138077 0.1074759226455736 0.9046671347627331 chr3 198022430 21476997 0.10845739545767619 0.8319595088398107 chr4 191154276 20337573 0.106393502806079 0.8607266402067485 chr5 180915260 19162003 0.1059170077748002 0.8191379643730464 chr6 171115067 18431921 0.10771652855093117 0.8806393874414101 chr7 159138663 16711976 0.10501518414792765 0.8704736592955082 chr8 146364022 15880144 0.10849759239330004 0.8720312143164028 chr9 141213431 12741624 0.090229547641258 0.765619718388365 chr10 135534747 14292924 0.10545579134773461 0.8619495393021522 chr11 135006516 14155852 0.1048531020532372 0.8742726218552371 chr12 133851895 14394523 0.10754067396655087 0.8501039565772337 chr13 115169878 10033167 0.0871162423216251 0.7463721187051746 chr14 107349540 9513169 0.08861862845429985 0.8182712911444469 chr15 102531392 9123327 0.08898081672391613 0.7574326036838228 chr16 90354753 8832231 0.09775059647387892 0.8272127839456827 chr17 81195210 8394532 0.10338703477705151 0.8141777640716645 chr18 78077248 8124641 0.10405900832980179 0.8700414072440932 chr19 59128983 5835586 0.09869248047104075 0.848671581250954 chr20 63025520 6365890 0.1010049579916199 0.8030294788930655 chr21 48129895 4011744 0.08335243615220851 0.8239987662967251 chr22 51304566 3494775 0.06811820608715412 0.6208938088336649 chrMT 16571 60356 3.6422666103433707 8.00209859600777 chrX 155270560 18454440 0.11885343879741272 0.9077870464065075 chrY 59373566 781321 0.013159408346805379 0.28589518761583793