BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082986.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 = 2,642,647 number of mapped reads = 2,277,956 (86.2%) number of supplementary alignments = 20,914 (0.79%) number of secondary alignments = 0 number of mapped bases = 156,555,777 bp number of sequenced bases = 156,496,788 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 433,909 duplication rate = 10.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1128 >>>>>>> ACTG content number of A's = 45,066,147 bp (28.8%) number of C's = 28,082,354 bp (17.94%) number of T's = 50,762,429 bp (32.44%) number of G's = 32,541,809 bp (20.79%) number of N's = 44,049 bp (0.03%) GC percentage = 38.74% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 1,481,654 number of insertions = 13,623 mapped reads with insertion percentage = 0.59% number of deletions = 36,501 mapped reads with deletion percentage = 1.58% homopolymer indels = 49.8% >>>>>>> Coverage mean coverageData = 0.0506X std coverageData = 0.5982X There is a 1.56% of reference with a coverageData >= 1X There is a 0.88% of reference with a coverageData >= 2X There is a 0.66% of reference with a coverageData >= 3X There is a 0.5% of reference with a coverageData >= 4X There is a 0.38% of reference with a coverageData >= 5X There is a 0.28% of reference with a coverageData >= 6X There is a 0.21% of reference with a coverageData >= 7X There is a 0.15% of reference with a coverageData >= 8X There is a 0.11% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 14021551 0.056254828749253145 0.6340715189514605 chr2 243199373 12875822 0.05294348353439217 0.5911807912573883 chr3 198022430 11267008 0.05689763528303334 0.6019116742018531 chr4 191154276 9245932 0.048368951997704725 0.5518565072228697 chr5 180915260 6994962 0.03866430062339683 0.48566380378661056 chr6 171115067 10729106 0.06270111795590741 0.6447137196405143 chr7 159138663 8237016 0.05175999247901184 0.6088394318754553 chr8 146364022 11925196 0.08147627973765302 0.9734385673415163 chr9 141213431 5365230 0.03799376562134518 0.4846802688339154 chr10 135534747 8116176 0.05988262183423709 0.6309671768448992 chr11 135006516 6821918 0.05053028699740685 0.5592683146684055 chr12 133851895 8333841 0.0622616586787957 0.6263785274586501 chr13 115169878 3371279 0.029272228629086506 0.41987753821239265 chr14 107349540 4697352 0.04375754195127431 0.5215776705506083 chr15 102531392 3682097 0.03591189906014346 0.4590274401111777 chr16 90354753 3769483 0.041718701837411915 0.4867397516771246 chr17 81195210 3182086 0.0391905630886354 0.47993961888807735 chr18 78077248 5457302 0.06989618793941098 0.7634428892047659 chr19 59128983 3083879 0.052155116552571185 0.5666002986955766 chr20 63025520 2581879 0.04096561202509714 0.4954548012061308 chr21 48129895 1228507 0.025524821942786286 0.3785392932603519 chr22 51304566 990573 0.019307696706760955 0.31039530835885276 chrMT 16571 615230 37.126908454528994 24.45760570408318 chrX 155270560 9700146 0.06247253825837944 0.6315301842038524 chrY 59373566 262206 0.00441620771102076 0.11948242354157684