BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083677.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 = 1,738,850 number of mapped reads = 1,400,571 (80.55%) number of supplementary alignments = 9,372 (0.54%) number of secondary alignments = 0 number of mapped bases = 87,679,406 bp number of sequenced bases = 87,650,440 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 35,663 duplication rate = 2.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7778 >>>>>>> ACTG content number of A's = 25,986,975 bp (29.65%) number of C's = 16,143,776 bp (18.42%) number of T's = 26,062,646 bp (29.73%) number of G's = 19,445,957 bp (22.19%) number of N's = 11,086 bp (0.01%) GC percentage = 40.6% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 777,746 number of insertions = 6,122 mapped reads with insertion percentage = 0.43% number of deletions = 18,232 mapped reads with deletion percentage = 1.29% homopolymer indels = 46.27% >>>>>>> Coverage mean coverageData = 0.0283X std coverageData = 0.245X There is a 2.6% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0% 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 9591677 0.038482058586325446 0.49671253107218183 chr2 243199373 7770281 0.031950250957267064 0.2263745866952306 chr3 198022430 6789888 0.03428847934044643 0.19836661533174618 chr4 191154276 4483640 0.023455609227386574 0.16398983421785326 chr5 180915260 4186201 0.023139015470557873 0.1627889659562251 chr6 171115067 6091085 0.03559642705221277 0.2346052578652577 chr7 159138663 6343270 0.03986001817798356 0.3435076807453653 chr8 146364022 6261638 0.04278126492041876 0.2877225881343881 chr9 141213431 3296325 0.023342857521817455 0.18301410328840997 chr10 135534747 3633044 0.026805259023355833 0.21761697284316422 chr11 135006516 3185501 0.023595164843747244 0.1799489497511703 chr12 133851895 3188461 0.02382081329517225 0.16401916775389705 chr13 115169878 2876311 0.024974507657288654 0.16718494234082942 chr14 107349540 1878773 0.01750145366249357 0.14157963829210132 chr15 102531392 2158025 0.02104745637316618 0.15501512781979376 chr16 90354753 2261455 0.025028622456640438 0.17250844854460104 chr17 81195210 1662016 0.020469384831937745 0.15500892943902972 chr18 78077248 2317830 0.029686369068745867 0.2713598058454106 chr19 59128983 2189004 0.03702082953126388 0.3519615081545984 chr20 63025520 1563759 0.024811520793481753 0.16764708519893107 chr21 48129895 1095667 0.022764790989051608 0.16153639216818433 chr22 51304566 692219 0.013492346860511402 0.12202981692119326 chrMT 16571 2613 0.1576851125460141 0.4025272285813687 chrX 155270560 3989849 0.025696107491336412 0.17716338481326094 chrY 59373566 170874 0.0028779474017107207 0.06331963011729676