BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084832.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 = 1,093,963 number of mapped reads = 990,217 (90.52%) number of supplementary alignments = 11,355 (1.04%) number of secondary alignments = 0 number of mapped bases = 66,464,349 bp number of sequenced bases = 66,440,464 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 36,099 duplication rate = 2.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1737 >>>>>>> ACTG content number of A's = 18,462,372 bp (27.79%) number of C's = 12,565,141 bp (18.91%) number of T's = 20,073,889 bp (30.21%) number of G's = 15,329,784 bp (23.07%) number of N's = 9,278 bp (0.01%) GC percentage = 41.98% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 566,792 number of insertions = 6,180 mapped reads with insertion percentage = 0.62% number of deletions = 13,975 mapped reads with deletion percentage = 1.39% homopolymer indels = 44.22% >>>>>>> Coverage mean coverageData = 0.0215X std coverageData = 0.3125X There is a 1.97% of reference with a coverageData >= 1X There is a 0.1% 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 5544096 0.022243057922010152 0.5932726471010272 chr2 243199373 5768219 0.023718066904720187 0.429062672583013 chr3 198022430 4973257 0.025114614541393115 0.16653691717240515 chr4 191154276 3578092 0.01871834664059516 0.1463192625929095 chr5 180915260 3476753 0.01921757733427241 0.1553116604571609 chr6 171115067 3630966 0.021219440600166437 0.1682004296779643 chr7 159138663 3837529 0.02411437250795553 0.37164624432983256 chr8 146364022 3698428 0.02526869615539808 0.3219506938270272 chr9 141213431 4485712 0.031765477038795266 0.37313955049480246 chr10 135534747 2279292 0.0168170306910301 0.20088030050783634 chr11 135006516 2864823 0.021219886897903505 0.32345624511523063 chr12 133851895 2783535 0.020795633860842985 0.16192983804858846 chr13 115169878 1709841 0.014846251725646527 0.12658101814715064 chr14 107349540 1371054 0.012771866558533925 0.15134595444688959 chr15 102531392 1645878 0.01605243006941718 0.13855078141258753 chr16 90354753 1405503 0.015555385337614724 0.1722936146653304 chr17 81195210 2011044 0.02476801279287288 0.19096461244001497 chr18 78077248 2593799 0.03322093268451265 0.7092559965154138 chr19 59128983 1657835 0.02803760382619806 0.3715380507432555 chr20 63025520 1383630 0.021953488047381443 0.17083954064105705 chr21 48129895 612139 0.012718477777688898 0.14331671621727066 chr22 51304566 683741 0.013327098410695064 0.1193942452488445 chrMT 16571 25836 1.5591092873091545 1.5383812294098154 chrX 155270560 4260822 0.02744127412176526 0.21610126305252778 chrY 59373566 182525 0.0030741795094470156 0.10807300069164362