BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080652.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 = 1,454,243 number of mapped reads = 1,333,729 (91.71%) number of supplementary alignments = 11,439 (0.79%) number of secondary alignments = 0 number of mapped bases = 89,384,691 bp number of sequenced bases = 89,351,307 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 48,197 duplication rate = 3.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9974 >>>>>>> ACTG content number of A's = 24,665,263 bp (27.6%) number of C's = 16,475,271 bp (18.44%) number of T's = 28,334,604 bp (31.71%) number of G's = 19,872,276 bp (22.24%) number of N's = 3,893 bp (0%) GC percentage = 40.68% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 598,487 number of insertions = 6,907 mapped reads with insertion percentage = 0.51% number of deletions = 20,768 mapped reads with deletion percentage = 1.54% homopolymer indels = 49.02% >>>>>>> Coverage mean coverageData = 0.0289X std coverageData = 0.2252X There is a 2.48% of reference with a coverageData >= 1X There is a 0.32% of reference with a coverageData >= 2X There is a 0.05% 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 10730844 0.04305242633678333 0.25713540407135477 chr2 243199373 5809916 0.023889518827007832 0.3142291468353519 chr3 198022430 5606758 0.028313752134038552 0.18977991217741255 chr4 191154276 3740713 0.019569078329171145 0.15960624420527955 chr5 180915260 4095447 0.02263737730028965 0.16960782739397287 chr6 171115067 5318907 0.031083802807382238 0.22651991220330397 chr7 159138663 5438710 0.034175918645238335 0.35462532673537905 chr8 146364022 12169720 0.08314693620540163 0.36321114099152785 chr9 141213431 2730143 0.019333451362710675 0.1709931538833402 chr10 135534747 4180369 0.030843522362571717 0.20577289485261305 chr11 135006516 3695908 0.027375774958891614 0.1959963891081685 chr12 133851895 2838399 0.021205519727606398 0.1647200355170164 chr13 115169878 1748551 0.015182363916370564 0.13989591550434058 chr14 107349540 1626361 0.015150144099359905 0.14136568712753847 chr15 102531392 1590398 0.015511327496655854 0.14544473104139824 chr16 90354753 2225155 0.024626872700321586 0.180077342769041 chr17 81195210 1433025 0.017649132257925068 0.15183019792305144 chr18 78077248 2703828 0.034630165243529076 0.24800872090472062 chr19 59128983 1325981 0.022425229265316468 0.17910388095828852 chr20 63025520 2243783 0.035601181870455016 0.21459372678778219 chr21 48129895 1297170 0.026951440471665273 0.18822511785698 chr22 51304566 820972 0.016001928561290235 0.14213640787121987 chrMT 16571 5244 0.31645646008086414 0.6496868114330862 chrX 155270560 5835720 0.037584201409462295 0.22471413468686033 chrY 59373566 172669 0.0029081797108160895 0.061767737117264195