BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695974.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 400,168,992 number of mapped reads = 392,184,680 (98%) number of supplementary alignments = 1,181,070 (0.3%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 197,766,943 number of mapped paired reads (second in pair) = 194,417,737 number of mapped paired reads (both in pair) = 387,385,938 number of mapped paired reads (singletons) = 4,798,742 number of mapped bases = 38,640,899,304 bp number of sequenced bases = 38,629,610,789 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 60,367,009 duplication rate = 10.03% >>>>>>> Insert size mean insert size = 47,073.0844 std insert size = 2,050,415.7192 median insert size = 308 >>>>>>> Mapping quality mean mapping quality = 53.7074 >>>>>>> ACTG content number of A's = 11,296,833,002 bp (29.24%) number of C's = 7,998,459,664 bp (20.71%) number of T's = 11,287,538,629 bp (29.22%) number of G's = 8,038,055,715 bp (20.81%) number of N's = 8,723,779 bp (0.02%) GC percentage = 41.51% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 265,119,419 number of insertions = 3,938,749 mapped reads with insertion percentage = 0.97% number of deletions = 4,633,860 mapped reads with deletion percentage = 1.15% homopolymer indels = 41.84% >>>>>>> Coverage mean coverageData = 12.4821X std coverageData = 137.4573X There is a 92.01% of reference with a coverageData >= 1X There is a 91.71% of reference with a coverageData >= 2X There is a 91.16% of reference with a coverageData >= 3X There is a 90.22% of reference with a coverageData >= 4X There is a 88.71% of reference with a coverageData >= 5X There is a 86.52% of reference with a coverageData >= 6X There is a 83.48% of reference with a coverageData >= 7X There is a 79.5% of reference with a coverageData >= 8X There is a 74.48% of reference with a coverageData >= 9X There is a 68.45% of reference with a coverageData >= 10X There is a 61.55% of reference with a coverageData >= 11X There is a 54.02% of reference with a coverageData >= 12X There is a 46.22% of reference with a coverageData >= 13X There is a 38.52% of reference with a coverageData >= 14X There is a 31.25% of reference with a coverageData >= 15X There is a 24.7% of reference with a coverageData >= 16X There is a 19.03% of reference with a coverageData >= 17X There is a 14.32% of reference with a coverageData >= 18X There is a 10.54% of reference with a coverageData >= 19X There is a 7.61% of reference with a coverageData >= 20X There is a 5.41% of reference with a coverageData >= 21X There is a 3.81% of reference with a coverageData >= 22X There is a 2.68% of reference with a coverageData >= 23X There is a 1.9% of reference with a coverageData >= 24X There is a 1.36% of reference with a coverageData >= 25X There is a 1.01% of reference with a coverageData >= 26X There is a 0.78% of reference with a coverageData >= 27X There is a 0.62% of reference with a coverageData >= 28X There is a 0.52% of reference with a coverageData >= 29X There is a 0.45% of reference with a coverageData >= 30X There is a 0.4% of reference with a coverageData >= 31X There is a 0.37% of reference with a coverageData >= 32X There is a 0.34% of reference with a coverageData >= 33X There is a 0.32% of reference with a coverageData >= 34X There is a 0.3% of reference with a coverageData >= 35X There is a 0.29% of reference with a coverageData >= 36X There is a 0.27% of reference with a coverageData >= 37X There is a 0.26% of reference with a coverageData >= 38X There is a 0.25% of reference with a coverageData >= 39X There is a 0.24% of reference with a coverageData >= 40X There is a 0.23% of reference with a coverageData >= 41X There is a 0.22% of reference with a coverageData >= 42X There is a 0.21% of reference with a coverageData >= 43X There is a 0.2% of reference with a coverageData >= 44X There is a 0.2% of reference with a coverageData >= 45X There is a 0.19% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3217283285 12.907824550615663 313.6673798360428 chr2 243199373 3366806761 13.84381349124613 87.15708858798196 chr3 198022430 2532703100 12.789980912768316 13.888024428766782 chr4 191154276 2509492494 13.12810022622774 94.33136180132382 chr5 180915260 2302010306 12.724246180228246 11.970310740962402 chr6 171115067 2209432872 12.911971521479169 52.718891335792414 chr7 159138663 2087849734 13.119688796178965 114.06420092662027 chr8 146364022 1921234656 13.126413375002771 78.74619159265278 chr9 141213431 1632528236 11.560715042749722 116.47904682968868 chr10 135534747 2137801834 15.773090527110366 358.9788515172499 chr11 135006516 1784953087 13.221236573499905 61.547755167093875 chr12 133851895 1722312159 12.867297538073705 11.581343607438347 chr13 115169878 1189879829 10.33151940127956 8.850720728307238 chr14 107349540 1175259345 10.947968151516998 11.095336297025616 chr15 102531392 1116754945 10.891834424719407 9.803348614715707 chr16 90354753 1259575036 13.940329580669653 98.51426236819611 chr17 81195210 1130268689 13.920386301113084 58.07660999269725 chr18 78077248 1050853879 13.459156232043425 150.12140335907858 chr19 59128983 819366204 13.857268676513513 167.64255372612263 chr20 63025520 834745724 13.244567026182409 45.08118648886761 chr21 48129895 535426308 11.124609933181862 55.89591119039705 chr22 51304566 512924535 9.997639099022882 52.98810473493767 chrMT 16571 109688953 6619.332146521031 1033.0893649329553 chrX 155270560 1006917553 6.484922531354302 23.94732356689559 chrY 59373566 474829780 7.997326284899243 137.5544749315163