BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514721.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 143,514,543 number of mapped reads = 115,699,644 (80.62%) number of supplementary alignments = 8,860,873 (6.17%) number of secondary alignments = 0 number of mapped bases = 10,170,941,339 bp number of sequenced bases = 10,152,093,040 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 110,205,093 duplication rate = 43.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5501 >>>>>>> ACTG content number of A's = 2,674,748,169 bp (26.35%) number of C's = 2,319,606,731 bp (22.85%) number of T's = 2,663,496,683 bp (26.24%) number of G's = 2,304,818,690 bp (22.7%) number of N's = 189,422,767 bp (1.87%) GC percentage = 45.55% >>>>>>> Mismatches and indels general error rate = 0.0128 number of mismatches = 114,483,055 number of insertions = 7,413,942 mapped reads with insertion percentage = 5.96% number of deletions = 5,943,861 mapped reads with deletion percentage = 4.7% homopolymer indels = 27.66% >>>>>>> Coverage mean coverageData = 3.2855X std coverageData = 712.3088X There is a 7.95% of reference with a coverageData >= 1X There is a 4.35% of reference with a coverageData >= 2X There is a 2.85% of reference with a coverageData >= 3X There is a 2.17% of reference with a coverageData >= 4X There is a 1.76% of reference with a coverageData >= 5X There is a 1.5% of reference with a coverageData >= 6X There is a 1.31% of reference with a coverageData >= 7X There is a 1.18% of reference with a coverageData >= 8X There is a 1.08% of reference with a coverageData >= 9X There is a 1% of reference with a coverageData >= 10X There is a 0.93% of reference with a coverageData >= 11X There is a 0.88% of reference with a coverageData >= 12X There is a 0.83% of reference with a coverageData >= 13X There is a 0.79% of reference with a coverageData >= 14X There is a 0.76% of reference with a coverageData >= 15X There is a 0.73% of reference with a coverageData >= 16X There is a 0.7% of reference with a coverageData >= 17X There is a 0.68% of reference with a coverageData >= 18X There is a 0.66% of reference with a coverageData >= 19X There is a 0.64% of reference with a coverageData >= 20X There is a 0.62% of reference with a coverageData >= 21X There is a 0.6% of reference with a coverageData >= 22X There is a 0.59% of reference with a coverageData >= 23X There is a 0.57% of reference with a coverageData >= 24X There is a 0.56% of reference with a coverageData >= 25X There is a 0.55% of reference with a coverageData >= 26X There is a 0.54% of reference with a coverageData >= 27X There is a 0.53% of reference with a coverageData >= 28X There is a 0.52% of reference with a coverageData >= 29X There is a 0.51% of reference with a coverageData >= 30X There is a 0.5% of reference with a coverageData >= 31X There is a 0.49% of reference with a coverageData >= 32X There is a 0.48% of reference with a coverageData >= 33X There is a 0.47% of reference with a coverageData >= 34X There is a 0.47% of reference with a coverageData >= 35X There is a 0.46% of reference with a coverageData >= 36X There is a 0.45% of reference with a coverageData >= 37X There is a 0.45% of reference with a coverageData >= 38X There is a 0.44% of reference with a coverageData >= 39X There is a 0.43% of reference with a coverageData >= 40X There is a 0.43% of reference with a coverageData >= 41X There is a 0.42% of reference with a coverageData >= 42X There is a 0.42% of reference with a coverageData >= 43X There is a 0.41% of reference with a coverageData >= 44X There is a 0.41% of reference with a coverageData >= 45X There is a 0.4% of reference with a coverageData >= 46X There is a 0.4% of reference with a coverageData >= 47X There is a 0.39% of reference with a coverageData >= 48X There is a 0.39% of reference with a coverageData >= 49X There is a 0.39% of reference with a coverageData >= 50X There is a 0.38% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 441681471 1.7720375950437453 147.5667998530723 chr2 243199373 1292227997 5.313451186405814 614.1592278562814 chr3 198022430 510196644 2.5764588587262565 89.4843880407953 chr4 191154276 520013992 2.7203890118576264 176.8379840441648 chr5 180915260 427557462 2.3633023659806254 92.35634492357637 chr6 171115067 552570808 3.2292352607383195 184.0743582281244 chr7 159138663 287737702 1.808094252997463 105.001392508196 chr8 146364022 381059196 2.603503175117721 115.70202334586082 chr9 141213431 396933412 2.8108757728576115 341.6392191691446 chr10 135534747 405912232 2.9948942318090577 140.48399805927278 chr11 135006516 620860133 4.598741982201807 300.9519672903867 chr12 133851895 430751302 3.2181188170701653 133.63616211317816 chr13 115169878 124378145 1.0799537792338376 48.932874478705976 chr14 107349540 262036909 2.4409690903193435 86.09048017490632 chr15 102531392 264421307 2.5789302363124067 82.03988749520572 chr16 90354753 233274773 2.5817653776332055 102.37094335241666 chr17 81195210 264192222 3.253790734699744 310.0081432187177 chr18 78077248 184088071 2.3577684372277057 74.36302783605854 chr19 59128983 230838889 3.9039888272727437 215.5038847870506 chr20 63025520 106224407 1.6854189699664517 88.89514899936492 chr21 48129895 160036659 3.3250988600743883 159.0884722981839 chr22 51304566 1732460941 33.768162876575154 5224.7800543529975 chrMT 16571 3339942 201.5534367268119 341.4375477348875 chrX 155270560 245170177 1.5789868794187385 156.09689931012565 chrY 59373566 92976546 1.56595859510948 152.4204178295175