BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708511.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,241,806 number of mapped reads = 2,157,656 (66.56%) number of supplementary alignments = 651 (0.02%) number of secondary alignments = 0 number of mapped bases = 102,252,911 bp number of sequenced bases = 102,228,797 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 96,076 duplication rate = 3.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.5613 >>>>>>> ACTG content number of A's = 29,157,846 bp (28.52%) number of C's = 18,779,214 bp (18.37%) number of T's = 32,838,365 bp (32.12%) number of G's = 21,451,998 bp (20.98%) number of N's = 1,374 bp (0%) GC percentage = 39.35% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 544,102 number of insertions = 5,683 mapped reads with insertion percentage = 0.26% number of deletions = 16,021 mapped reads with deletion percentage = 0.74% homopolymer indels = 47.72% >>>>>>> Coverage mean coverageData = 0.033X std coverageData = 0.3586X There is a 2.89% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 8142734 0.03266886143485275 0.6078888955583945 chr2 243199373 8883121 0.03652608512276057 0.5089574986648077 chr3 198022430 7274235 0.03673439922942063 0.22628739974295833 chr4 191154276 7186618 0.0375959049956068 0.2320515969442006 chr5 180915260 6534345 0.036118263323945146 0.21918840369245807 chr6 171115067 6246744 0.03650610147614879 0.3032839907670293 chr7 159138663 5842191 0.03671132388488145 0.42711930096147577 chr8 146364022 5423215 0.03705292411273038 0.6602920880301847 chr9 141213431 4355425 0.030842852334633807 0.2687275583547499 chr10 135534747 4759702 0.03511794654399584 0.2782674712714761 chr11 135006516 4759559 0.035254290985481024 0.31447753931772876 chr12 133851895 4701776 0.03512670478068316 0.22088325515205917 chr13 115169878 3496407 0.0303586932687382 0.23542239317892155 chr14 107349540 3148697 0.029331257497703298 0.20716460168859477 chr15 102531392 2804389 0.027351515914267505 0.19782958328345746 chr16 90354753 2660620 0.029446375665483807 0.20765428701265998 chr17 81195210 2507754 0.030885491890469893 0.2608472192712192 chr18 78077248 2792244 0.035762582205766266 0.42585560146058216 chr19 59128983 1837685 0.031079259387904574 0.42662913813382336 chr20 63025520 1952178 0.030974405288524395 0.20343965997007554 chr21 48129895 1379196 0.02865570348740632 0.2176407030663419 chr22 51304566 997330 0.019439400383973623 0.17340137293375568 chrMT 16571 61689 3.7227083459054975 2.8137571657240437 chrX 155270560 3672423 0.023651766310368173 0.21109925646282587 chrY 59373566 832634 0.014023648166930044 0.15860782701416742