BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080765.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 = 7,391,624 number of mapped reads = 3,491,994 (47.24%) number of supplementary alignments = 26,791 (0.36%) number of secondary alignments = 0 number of mapped bases = 219,027,781 bp number of sequenced bases = 218,951,646 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 556,611 duplication rate = 12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6117 >>>>>>> ACTG content number of A's = 67,235,462 bp (30.71%) number of C's = 44,508,817 bp (20.33%) number of T's = 56,519,710 bp (25.81%) number of G's = 50,616,880 bp (23.12%) number of N's = 70,777 bp (0.03%) GC percentage = 43.45% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 2,057,032 number of insertions = 16,860 mapped reads with insertion percentage = 0.48% number of deletions = 40,677 mapped reads with deletion percentage = 1.15% homopolymer indels = 41.96% >>>>>>> Coverage mean coverageData = 0.0708X std coverageData = 0.659X There is a 4.43% of reference with a coverageData >= 1X There is a 1.36% of reference with a coverageData >= 2X There is a 0.56% of reference with a coverageData >= 3X There is a 0.27% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% 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 0.01% 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 26757349 0.10735118288832668 0.670835649452173 chr2 243199373 16520807 0.06793112497045788 1.367676969363037 chr3 198022430 13291081 0.06711906827928533 0.40195767110482167 chr4 191154276 12038985 0.06298046401012761 0.4422430995920389 chr5 180915260 16072991 0.08884264931548616 0.4689927633898206 chr6 171115067 13336239 0.07793725727261644 1.1057743893177556 chr7 159138663 14593137 0.09170076413171827 0.652029990706338 chr8 146364022 9956678 0.06802681331071922 0.5943940974064676 chr9 141213431 7753454 0.05490592463545482 0.3950924010907311 chr10 135534747 8986175 0.06630163259905594 0.53196228143388 chr11 135006516 8990562 0.06659354130729513 0.4755767319610167 chr12 133851895 7717215 0.057654880418390786 0.4263354742369087 chr13 115169878 8036225 0.06977714259626115 0.4150742201644662 chr14 107349540 6600144 0.06148274133265964 0.556297153410859 chr15 102531392 6002307 0.058541163666245746 0.39137511431094896 chr16 90354753 7114189 0.07873619000430447 0.48505953416067543 chr17 81195210 5671189 0.06984634931050736 0.4354493628972315 chr18 78077248 2944147 0.03770812977424614 0.49155773062862224 chr19 59128983 4543360 0.07683812183950467 0.7657361514818762 chr20 63025520 4679440 0.07424674957065011 0.4557109242154516 chr21 48129895 3704643 0.0769717656770288 0.5007959465322535 chr22 51304566 1791761 0.034924006568927995 0.30562731388173714 chrMT 16571 45878 2.768571600989681 3.7274546950910237 chrX 155270560 11243861 0.0724146354595488 0.43109781009220566 chrY 59373566 635964 0.01071123132472791 0.30095749403949923