BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082741.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,978,347 number of mapped reads = 2,622,676 (88.06%) number of supplementary alignments = 11,470 (0.39%) number of secondary alignments = 0 number of mapped bases = 174,392,848 bp number of sequenced bases = 174,326,228 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 100,454 duplication rate = 2.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8868 >>>>>>> ACTG content number of A's = 48,114,641 bp (27.6%) number of C's = 30,312,746 bp (17.39%) number of T's = 57,602,972 bp (33.04%) number of G's = 38,249,111 bp (21.94%) number of N's = 46,758 bp (0.03%) GC percentage = 39.33% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 1,652,420 number of insertions = 15,970 mapped reads with insertion percentage = 0.6% number of deletions = 40,832 mapped reads with deletion percentage = 1.54% homopolymer indels = 49.18% >>>>>>> Coverage mean coverageData = 0.0563X std coverageData = 0.4371X There is a 4.75% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% 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 13494500 0.0541402863746526 0.7435685195511871 chr2 243199373 15136630 0.06223959302724025 0.5258230313846264 chr3 198022430 12072783 0.06096674502984334 0.28232880685489165 chr4 191154276 12020732 0.06288497569366432 0.3096836362699321 chr5 180915260 10885165 0.06016720203701999 0.28183910387701877 chr6 171115067 10381290 0.060668474039168044 0.36340357036394205 chr7 159138663 9758121 0.061318354798544465 0.5942787445520044 chr8 146364022 8947673 0.06113300849302979 0.4544196165947688 chr9 141213431 7408679 0.05246440758174058 0.490949613562359 chr10 135534747 8049456 0.059390349546304906 0.37797264729106295 chr11 135006516 7854276 0.058177014211669605 0.3691349891940016 chr12 133851895 7874518 0.05883008230850972 0.2845040973345821 chr13 115169878 5983370 0.05195256002615545 0.2604953529579091 chr14 107349540 5163345 0.048098436192646934 0.2807538106855828 chr15 102531392 4815638 0.04696744973480902 0.2470766084270875 chr16 90354753 4568761 0.05056470023220583 0.3043434918631535 chr17 81195210 4233363 0.05213808794878417 0.3143641885458412 chr18 78077248 4886338 0.0625833789633569 0.8821504631580229 chr19 59128983 2902279 0.04908386467597456 0.5235946383609672 chr20 63025520 3309670 0.05251317244189338 0.27837695387237826 chr21 48129895 2412379 0.05012225769451606 0.2869517144631099 chr22 51304566 1727077 0.0336632220999589 0.20757809696702828 chrMT 16571 2987 0.18025466175849375 0.45109244116966907 chrX 155270560 10071722 0.06486562552489022 0.3325640762944556 chrY 59373566 432096 0.007277582080887646 0.18152973806270167