BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084344.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 = 2,910,641 number of mapped reads = 2,631,222 (90.4%) number of supplementary alignments = 17,210 (0.59%) number of secondary alignments = 0 number of mapped bases = 175,735,214 bp number of sequenced bases = 175,671,983 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 99,390 duplication rate = 3.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.144 >>>>>>> ACTG content number of A's = 49,373,374 bp (28.11%) number of C's = 33,919,648 bp (19.31%) number of T's = 53,862,170 bp (30.66%) number of G's = 38,287,575 bp (21.79%) number of N's = 229,216 bp (0.13%) GC percentage = 41.1% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 1,774,797 number of insertions = 11,911 mapped reads with insertion percentage = 0.45% number of deletions = 36,176 mapped reads with deletion percentage = 1.36% homopolymer indels = 47.35% >>>>>>> Coverage mean coverageData = 0.0568X std coverageData = 0.3503X There is a 4.66% of reference with a coverageData >= 1X There is a 0.75% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% 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 17426337 0.06991491908860681 0.5258647970543257 chr2 243199373 17234005 0.07086369009676682 0.40258049547062646 chr3 198022430 12007545 0.060637297502106204 0.29110021086064386 chr4 191154276 8371407 0.04379398240612729 0.253156464120666 chr5 180915260 9071014 0.0501395736324288 0.26134173865335253 chr6 171115067 8443005 0.04934109630451186 0.28862178805622735 chr7 159138663 9935182 0.062430975683137414 0.48873694995701716 chr8 146364022 8729937 0.059645375145539525 0.36212432991947596 chr9 141213431 6485135 0.04592434978794616 0.30356665218907863 chr10 135534747 12555427 0.09263622265071259 0.4491386723352941 chr11 135006516 10271537 0.07608178704500455 0.38115835508131346 chr12 133851895 6526723 0.04876078145923896 0.25892575373186194 chr13 115169878 4352239 0.0377897335273725 0.2264293707105365 chr14 107349540 4768691 0.044422090676867365 0.2559155595433844 chr15 102531392 3886489 0.03790535682964297 0.2330334141759859 chr16 90354753 3802879 0.04208831161322526 0.2591200579791733 chr17 81195210 4974888 0.061270707964176704 0.31359158591373615 chr18 78077248 4790948 0.0613616402053515 0.48506410249117055 chr19 59128983 3913264 0.06618182490979085 0.40410381214848906 chr20 63025520 3605370 0.057204922704326755 0.2835006700747555 chr21 48129895 1846653 0.0383681078049308 0.24024916965909765 chr22 51304566 1423567 0.027747374375996087 0.19388495497621838 chrMT 16571 33061 1.9951119425502384 1.875790976566632 chrX 155270560 10918457 0.07031891299934771 0.3381042884882379 chrY 59373566 361454 0.0060877933456110755 0.11914619785616659