BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083632.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 = 2,414,425 number of mapped reads = 2,021,267 (83.72%) number of supplementary alignments = 12,896 (0.53%) number of secondary alignments = 0 number of mapped bases = 122,139,946 bp number of sequenced bases = 122,098,659 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,751 duplication rate = 1.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8044 >>>>>>> ACTG content number of A's = 36,693,899 bp (30.05%) number of C's = 24,011,217 bp (19.67%) number of T's = 35,573,880 bp (29.14%) number of G's = 25,802,962 bp (21.13%) number of N's = 16,701 bp (0.01%) GC percentage = 40.8% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,018,224 number of insertions = 8,749 mapped reads with insertion percentage = 0.43% number of deletions = 25,966 mapped reads with deletion percentage = 1.27% homopolymer indels = 45.77% >>>>>>> Coverage mean coverageData = 0.0395X std coverageData = 0.2949X There is a 3.54% of reference with a coverageData >= 1X There is a 0.31% 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% 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 7836260 0.0314392797440613 0.49168423259470717 chr2 243199373 11615203 0.04776000388783897 0.31899165507926774 chr3 198022430 9369279 0.04731423101918303 0.23485824666294317 chr4 191154276 8839858 0.046244625989951695 0.24148089996623462 chr5 180915260 6639482 0.03669940280327928 0.2076701555230333 chr6 171115067 7043079 0.04115989972992851 0.23330563632217827 chr7 159138663 6723919 0.04225195105478547 0.31176699851570583 chr8 146364022 5861324 0.04004620753042711 0.45098516422820745 chr9 141213431 5204836 0.0368579388174486 0.263883038502346 chr10 135534747 5987852 0.04417946048919839 0.29453759186657624 chr11 135006516 5321859 0.039419275140764314 0.24906845385991655 chr12 133851895 5349904 0.039968832716189784 0.21857795457376572 chr13 115169878 4546411 0.03947569519870465 0.21391930907587892 chr14 107349540 3766333 0.03508476142515375 0.2101426633273735 chr15 102531392 2630805 0.025658531974285494 0.17327231829880402 chr16 90354753 3369808 0.037295304210504567 0.2299965256056447 chr17 81195210 3197121 0.039375734110423506 0.24462862377138267 chr18 78077248 3508171 0.04493205242070007 0.44064275822059107 chr19 59128983 2202565 0.03725017560339233 0.36100062469014776 chr20 63025520 2606211 0.04135167786001607 0.22514314955390677 chr21 48129895 1527817 0.03174361797381856 0.20336232970118204 chr22 51304566 1286313 0.025072095922222596 0.16973540078439434 chrMT 16571 26083 1.5740148452115141 1.4878719739230406 chrX 155270560 7359227 0.0473961515949965 0.251869638202416 chrY 59373566 320226 0.005393410259373675 0.1330818777552305