BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080980.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 = 4,237,511 number of mapped reads = 3,550,445 (83.79%) number of supplementary alignments = 25,870 (0.61%) number of secondary alignments = 0 number of mapped bases = 239,670,479 bp number of sequenced bases = 239,584,341 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 243,654 duplication rate = 5.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.3248 >>>>>>> ACTG content number of A's = 67,562,336 bp (28.2%) number of C's = 42,233,714 bp (17.63%) number of T's = 78,203,513 bp (32.64%) number of G's = 51,106,936 bp (21.33%) number of N's = 477,842 bp (0.2%) GC percentage = 38.96% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 2,335,586 number of insertions = 18,107 mapped reads with insertion percentage = 0.51% number of deletions = 48,911 mapped reads with deletion percentage = 1.36% homopolymer indels = 49.52% >>>>>>> Coverage mean coverageData = 0.0774X std coverageData = 0.5871X There is a 5.58% of reference with a coverageData >= 1X There is a 1.44% of reference with a coverageData >= 2X There is a 0.41% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 19609650 0.07867442785629007 0.8950120862609432 chr2 243199373 16207364 0.0666422935226893 0.5133427880827635 chr3 198022430 21010796 0.1061031116525537 0.4280645912562163 chr4 191154276 15009997 0.07852294656489923 0.3880053511668661 chr5 180915260 13846092 0.07653357710123514 0.36337790544494264 chr6 171115067 20649341 0.12067517701407322 0.6979564126618735 chr7 159138663 11762389 0.07391283034720482 0.5942798034064325 chr8 146364022 18826191 0.1286258107883917 1.1279059376155478 chr9 141213431 12366131 0.08757050170390662 0.7086604007742292 chr10 135534747 10920376 0.08057251916366509 0.5080395970036414 chr11 135006516 10775384 0.0798138069128456 0.474287225548715 chr12 133851895 12112523 0.09049197996038831 0.4137370546440532 chr13 115169878 6602055 0.057324494170255175 0.31000449201575203 chr14 107349540 7020050 0.06539431841067973 0.4065813829282043 chr15 102531392 6069546 0.05919695306584739 0.31460115248280146 chr16 90354753 5371781 0.05945211316110841 0.38939647708300773 chr17 81195210 4835990 0.059560040549190035 0.3279661777128962 chr18 78077248 5896610 0.07552276945007078 1.1484434629381781 chr19 59128983 4232542 0.07158151189578214 0.6661450210177119 chr20 63025520 3671197 0.058249372635084964 0.3376420207517261 chr21 48129895 3302881 0.06862431343346999 0.43245791353688817 chr22 51304566 1957894 0.03816217839168545 0.24850369659006238 chrMT 16571 31082 1.875686440166556 1.5963120232445764 chrX 155270560 7074248 0.04556078112940405 0.3180972452155512 chrY 59373566 508369 0.008562211001441281 0.18563304184449148