BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038466.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 14,357,846 number of mapped reads = 13,702,088 (95.43%) number of supplementary alignments = 238,608 (1.66%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,926,263 number of mapped paired reads (second in pair) = 6,775,825 number of mapped paired reads (both in pair) = 13,530,202 number of mapped paired reads (singletons) = 171,886 number of mapped bases = 1,967,464,459 bp number of sequenced bases = 1,965,915,335 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,142,685 duplication rate = 9.5% >>>>>>> Insert size mean insert size = 86,053.6065 std insert size = 2,783,683.6172 median insert size = 255 >>>>>>> Mapping quality mean mapping quality = 53.7289 >>>>>>> ACTG content number of A's = 582,838,113 bp (29.65%) number of C's = 394,562,189 bp (20.07%) number of T's = 582,002,507 bp (29.6%) number of G's = 406,471,030 bp (20.68%) number of N's = 41,496 bp (0%) GC percentage = 40.75% >>>>>>> Mismatches and indels general error rate = 0.0153 number of mismatches = 28,969,100 number of insertions = 405,215 mapped reads with insertion percentage = 2.74% number of deletions = 769,385 mapped reads with deletion percentage = 5.36% homopolymer indels = 46.65% >>>>>>> Coverage mean coverageData = 0.6355X std coverageData = 9.397X There is a 24.19% of reference with a coverageData >= 1X There is a 13.66% of reference with a coverageData >= 2X There is a 7.6% of reference with a coverageData >= 3X There is a 4.69% of reference with a coverageData >= 4X There is a 2.88% of reference with a coverageData >= 5X There is a 1.85% of reference with a coverageData >= 6X There is a 1.2% of reference with a coverageData >= 7X There is a 0.8% of reference with a coverageData >= 8X There is a 0.55% of reference with a coverageData >= 9X There is a 0.38% of reference with a coverageData >= 10X There is a 0.27% of reference with a coverageData >= 11X There is a 0.2% of reference with a coverageData >= 12X There is a 0.15% of reference with a coverageData >= 13X There is a 0.11% of reference with a coverageData >= 14X There is a 0.09% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 127365671 0.5109943978835664 7.522384239897242 chr2 243199373 234030600 0.962299355928027 15.333189149826453 chr3 198022430 132958604 0.6714320392896905 1.6059603876126431 chr4 191154276 107188796 0.5607449555562126 8.557444438460537 chr5 180915260 72383349 0.40009532087011346 1.3975372787304743 chr6 171115067 110240053 0.6442451558050116 9.260668145318764 chr7 159138663 147661234 0.9278778093039527 9.49307696714248 chr8 146364022 90330738 0.6171649068238915 2.9455857174874716 chr9 141213431 84688422 0.5997193142343521 16.402865171999835 chr10 135534747 84385398 0.622610805478539 20.195000574660774 chr11 135006516 116249221 0.8610637800622898 6.846036193059238 chr12 133851895 63093888 0.4713708984097685 1.3637633152736222 chr13 115169878 119022511 1.0334517416090343 2.1316578872977683 chr14 107349540 37568849 0.34996748938095124 1.3655654453160921 chr15 102531392 34913996 0.3405200623824555 1.0507377239071165 chr16 90354753 79041220 0.8747876273869069 15.756472802628865 chr17 81195210 41873518 0.5157141412652299 5.855259744237896 chr18 78077248 33729259 0.4319985637813464 13.59531349001481 chr19 59128983 26018507 0.4400296720814562 4.631253286040441 chr20 63025520 60978693 0.9675238379627807 3.368702040152182 chr21 48129895 18769454 0.3899749625466667 4.307206777025309 chr22 51304566 11523295 0.22460564231261598 1.1690123686885787 chrMT 16571 1439828 86.88841952809125 53.98340770890867 chrX 155270560 102580632 0.6606573197134087 2.3259825887153167 chrY 59373566 29428723 0.49565362134388224 14.514067703176853