BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438277.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP178894/SRP178894.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 = 724,014,094 number of mapped reads = 721,790,660 (99.69%) number of supplementary alignments = 11,464,179 (1.58%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 361,035,340 number of mapped paired reads (second in pair) = 360,755,320 number of mapped paired reads (both in pair) = 720,257,614 number of mapped paired reads (singletons) = 1,533,046 number of mapped bases = 103,568,927,587 bp number of sequenced bases = 103,541,230,182 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 327,454,892 duplication rate = 42.7% >>>>>>> Insert size mean insert size = 40,228.0259 std insert size = 1,962,749.2507 median insert size = 234 >>>>>>> Mapping quality mean mapping quality = 55.0253 >>>>>>> ACTG content number of A's = 31,373,184,179 bp (30.3%) number of C's = 20,638,421,159 bp (19.93%) number of T's = 29,980,773,753 bp (28.96%) number of G's = 21,548,210,362 bp (20.81%) number of N's = 640,729 bp (0%) GC percentage = 40.74% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 529,032,462 number of insertions = 12,791,017 mapped reads with insertion percentage = 1.74% number of deletions = 11,344,216 mapped reads with deletion percentage = 1.55% homopolymer indels = 48.29% >>>>>>> Coverage mean coverageData = 33.4558X std coverageData = 99.8735X There is a 91.56% of reference with a coverageData >= 1X There is a 90.95% of reference with a coverageData >= 2X There is a 90.25% of reference with a coverageData >= 3X There is a 89.49% of reference with a coverageData >= 4X There is a 88.62% of reference with a coverageData >= 5X There is a 87.66% of reference with a coverageData >= 6X There is a 86.6% of reference with a coverageData >= 7X There is a 85.45% of reference with a coverageData >= 8X There is a 84.2% of reference with a coverageData >= 9X There is a 82.87% of reference with a coverageData >= 10X There is a 81.45% of reference with a coverageData >= 11X There is a 79.95% of reference with a coverageData >= 12X There is a 78.38% of reference with a coverageData >= 13X There is a 76.75% of reference with a coverageData >= 14X There is a 75.06% of reference with a coverageData >= 15X There is a 73.32% of reference with a coverageData >= 16X There is a 71.54% of reference with a coverageData >= 17X There is a 69.73% of reference with a coverageData >= 18X There is a 67.89% of reference with a coverageData >= 19X There is a 66.04% of reference with a coverageData >= 20X There is a 64.17% of reference with a coverageData >= 21X There is a 62.3% of reference with a coverageData >= 22X There is a 60.44% of reference with a coverageData >= 23X There is a 58.57% of reference with a coverageData >= 24X There is a 56.73% of reference with a coverageData >= 25X There is a 54.89% of reference with a coverageData >= 26X There is a 53.08% of reference with a coverageData >= 27X There is a 51.3% of reference with a coverageData >= 28X There is a 49.54% of reference with a coverageData >= 29X There is a 47.81% of reference with a coverageData >= 30X There is a 46.12% of reference with a coverageData >= 31X There is a 44.46% of reference with a coverageData >= 32X There is a 42.84% of reference with a coverageData >= 33X There is a 41.26% of reference with a coverageData >= 34X There is a 39.71% of reference with a coverageData >= 35X There is a 38.21% of reference with a coverageData >= 36X There is a 36.75% of reference with a coverageData >= 37X There is a 35.34% of reference with a coverageData >= 38X There is a 33.96% of reference with a coverageData >= 39X There is a 32.63% of reference with a coverageData >= 40X There is a 31.34% of reference with a coverageData >= 41X There is a 30.09% of reference with a coverageData >= 42X There is a 28.88% of reference with a coverageData >= 43X There is a 27.72% of reference with a coverageData >= 44X There is a 26.59% of reference with a coverageData >= 45X There is a 25.5% of reference with a coverageData >= 46X There is a 24.46% of reference with a coverageData >= 47X There is a 23.45% of reference with a coverageData >= 48X There is a 22.48% of reference with a coverageData >= 49X There is a 21.54% of reference with a coverageData >= 50X There is a 20.64% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 8454121509 33.918156252056036 32.464008061323355 chr2 243199373 9169843150 37.705044371146464 130.55594502686185 chr3 198022430 7513065222 37.94047584407483 257.31595277103713 chr4 191154276 6981359301 36.52211944764448 35.16505981971029 chr5 180915260 6740440870 37.25744787918941 52.50298213412949 chr6 171115067 6219419161 36.3464145503914 29.435110814205423 chr7 159138663 5658444055 35.55668967132142 34.87141275603368 chr8 146364022 5433653167 37.124240593771056 29.572866790148712 chr9 141213431 4494389222 31.8269246074759 37.48528886744374 chr10 135534747 4988632785 36.807039489290524 43.44753896097208 chr11 135006516 4899817772 36.293194707728034 28.85611240841227 chr12 133851895 4850339075 36.23661118133591 28.584954184702468 chr13 115169878 3604441735 31.296740064272708 27.666669839287522 chr14 107349540 3311545611 30.84825152487845 32.82320450236235 chr15 102531392 3019063982 29.445264743894242 30.747598754807864 chr16 90354753 2805710441 31.05216214801672 53.112424541266364 chr17 81195210 2489525568 30.660990568285985 37.44286947545465 chr18 78077248 2908606508 37.25293324887681 28.828268677877485 chr19 59128983 1602743190 27.10588122241169 370.21111396567835 chr20 63025520 2266540970 35.962273218848495 32.692560989889564 chr21 48129895 1323374862 27.49590170516682 135.16579309755704 chr22 51304566 1115430734 21.741354054140132 28.364824572924302 chrMT 16571 134169340 8096.6350853901395 3083.0674159179475 chrX 155270560 3059184426 19.70228242881329 41.730540565327466 chrY 59373566 525064931 8.843412420267969 27.226941067791795