BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818936.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,754,767 number of mapped reads = 1,699,272 (96.84%) number of supplementary alignments = 21,988 (1.25%) number of secondary alignments = 0 number of mapped bases = 157,562,575 bp number of sequenced bases = 157,478,096 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 643,424 duplication rate = 32.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2435 >>>>>>> ACTG content number of A's = 44,153,755 bp (28.04%) number of C's = 33,853,271 bp (21.5%) number of T's = 46,249,863 bp (29.37%) number of G's = 33,214,232 bp (21.09%) number of N's = 6,975 bp (0%) GC percentage = 42.59% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 1,022,784 number of insertions = 21,736 mapped reads with insertion percentage = 1.25% number of deletions = 46,770 mapped reads with deletion percentage = 2.7% homopolymer indels = 42.33% >>>>>>> Coverage mean coverageData = 0.0509X std coverageData = 0.5802X There is a 2.74% of reference with a coverageData >= 1X There is a 1.14% of reference with a coverageData >= 2X There is a 0.54% of reference with a coverageData >= 3X There is a 0.26% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 17810659 0.0714568289882014 1.0572488725679883 chr2 243199373 14027541 0.05767918242124744 0.7871653271942315 chr3 198022430 10646117 0.05376217734526336 0.3812400651609035 chr4 191154276 10800920 0.05650367978166494 0.43471151221753596 chr5 180915260 8284614 0.045792787186664075 0.3588290344158447 chr6 171115067 8489761 0.04961433933810165 0.3996802026768656 chr7 159138663 7711861 0.048460008740930545 0.4599187278645383 chr8 146364022 10666898 0.07287923530825083 0.5142642379284851 chr9 141213431 5780538 0.04093476066026609 0.6158964707914307 chr10 135534747 7690992 0.05674553699502608 0.6899149897214335 chr11 135006516 6261833 0.04638170945763832 0.4421059468624479 chr12 133851895 6797265 0.05078198556695817 0.38208487855552414 chr13 115169878 2664821 0.023138176806959888 0.24773357367101342 chr14 107349540 3249437 0.030269687229214023 0.31626951690105987 chr15 102531392 4637337 0.04522846037240965 0.350335067232293 chr16 90354753 4923683 0.054492794640255394 0.6139545015053357 chr17 81195210 3374531 0.04156071521953081 0.3819730601926136 chr18 78077248 3965322 0.05078716401479724 0.8154139084124726 chr19 59128983 2577908 0.04359804395756308 1.0084534373733187 chr20 63025520 3326440 0.05277925513347609 0.39929452399957616 chr21 48129895 2087312 0.043368305706879266 0.38222775252055424 chr22 51304566 1938696 0.037787981677888084 0.34617717928204794 chrMT 16571 181485 10.951964274938145 7.732619782988042 chrX 155270560 9193625 0.05921035513750965 0.4775601779878709 chrY 59373566 472979 0.007966154500472482 0.41772240831929025