BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438273.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 = 1,399,701,716 number of mapped reads = 1,394,268,895 (99.61%) number of supplementary alignments = 16,862,238 (1.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 697,498,357 number of mapped paired reads (second in pair) = 696,770,538 number of mapped paired reads (both in pair) = 1,391,818,876 number of mapped paired reads (singletons) = 2,450,019 number of mapped bases = 153,484,110,332 bp number of sequenced bases = 153,448,802,838 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 680,672,207 duplication rate = 46.72% >>>>>>> Insert size mean insert size = 86,915.917 std insert size = 3,035,549.4532 median insert size = 124 >>>>>>> Mapping quality mean mapping quality = 53.1269 >>>>>>> ACTG content number of A's = 46,658,662,572 bp (30.41%) number of C's = 30,379,901,964 bp (19.8%) number of T's = 45,569,923,196 bp (29.7%) number of G's = 30,839,887,612 bp (20.1%) number of N's = 427,494 bp (0%) GC percentage = 39.9% >>>>>>> Mismatches and indels general error rate = 0.0034 number of mismatches = 496,816,277 number of insertions = 21,427,903 mapped reads with insertion percentage = 1.52% number of deletions = 15,255,746 mapped reads with deletion percentage = 1.08% homopolymer indels = 47.8% >>>>>>> Coverage mean coverageData = 49.5799X std coverageData = 573.7904X There is a 86.92% of reference with a coverageData >= 1X There is a 85.43% of reference with a coverageData >= 2X There is a 83.02% of reference with a coverageData >= 3X There is a 81.35% of reference with a coverageData >= 4X There is a 79.42% of reference with a coverageData >= 5X There is a 77.75% of reference with a coverageData >= 6X There is a 76.02% of reference with a coverageData >= 7X There is a 74.41% of reference with a coverageData >= 8X There is a 72.8% of reference with a coverageData >= 9X There is a 71.26% of reference with a coverageData >= 10X There is a 69.74% of reference with a coverageData >= 11X There is a 68.28% of reference with a coverageData >= 12X There is a 66.84% of reference with a coverageData >= 13X There is a 65.44% of reference with a coverageData >= 14X There is a 64.07% of reference with a coverageData >= 15X There is a 62.73% of reference with a coverageData >= 16X There is a 61.43% of reference with a coverageData >= 17X There is a 60.16% of reference with a coverageData >= 18X There is a 58.91% of reference with a coverageData >= 19X There is a 57.7% of reference with a coverageData >= 20X There is a 56.51% of reference with a coverageData >= 21X There is a 55.36% of reference with a coverageData >= 22X There is a 54.23% of reference with a coverageData >= 23X There is a 53.12% of reference with a coverageData >= 24X There is a 52.05% of reference with a coverageData >= 25X There is a 51% of reference with a coverageData >= 26X There is a 49.97% of reference with a coverageData >= 27X There is a 48.97% of reference with a coverageData >= 28X There is a 47.99% of reference with a coverageData >= 29X There is a 47.04% of reference with a coverageData >= 30X There is a 46.1% of reference with a coverageData >= 31X There is a 45.19% of reference with a coverageData >= 32X There is a 44.3% of reference with a coverageData >= 33X There is a 43.44% of reference with a coverageData >= 34X There is a 42.59% of reference with a coverageData >= 35X There is a 41.76% of reference with a coverageData >= 36X There is a 40.95% of reference with a coverageData >= 37X There is a 40.16% of reference with a coverageData >= 38X There is a 39.39% of reference with a coverageData >= 39X There is a 38.63% of reference with a coverageData >= 40X There is a 37.89% of reference with a coverageData >= 41X There is a 37.17% of reference with a coverageData >= 42X There is a 36.47% of reference with a coverageData >= 43X There is a 35.78% of reference with a coverageData >= 44X There is a 35.11% of reference with a coverageData >= 45X There is a 34.46% of reference with a coverageData >= 46X There is a 33.81% of reference with a coverageData >= 47X There is a 33.19% of reference with a coverageData >= 48X There is a 32.58% of reference with a coverageData >= 49X There is a 31.98% of reference with a coverageData >= 50X There is a 31.39% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 10937631722 43.88206407718439 67.84349387076075 chr2 243199373 13301160521 54.692412882988805 2032.3873464637622 chr3 198022430 12650647857 63.884923829083405 78.0770740642821 chr4 191154276 11065899225 57.88988588986626 70.51515979652962 chr5 180915260 8878856239 49.07743127362501 63.44123473027919 chr6 171115067 11157711192 65.20589558603861 82.50088323838011 chr7 159138663 8421096618 52.91672343634055 70.25663310303115 chr8 146364022 7849570058 53.63046157613788 69.30337016093958 chr9 141213431 6300412160 44.61623880521677 68.460332752481 chr10 135534747 6998624538 51.63712400628896 68.9198770987794 chr11 135006516 6954489822 51.512253097472716 71.78061793918984 chr12 133851895 7381947692 55.15011716494563 80.73427388049355 chr13 115169878 4644397442 40.32649441549291 58.235001378623416 chr14 107349540 5220410568 48.630022708993444 73.35897463467128 chr15 102531392 3965575531 38.67669650871413 65.05870585301702 chr16 90354753 3177330753 35.165064897028714 57.509087664533716 chr17 81195210 2266785594 27.91772561460214 49.597985083621296 chr18 78077248 4536313162 58.10032087708829 70.95378760380244 chr19 59128983 1011691946 17.10991623177419 33.22264316787662 chr20 63025520 2394603425 37.994187513248605 60.1864499513348 chr21 48129895 1688155734 35.07499307862608 58.14259524409314 chr22 51304566 782115542 15.244560143048476 37.14035019618735 chrMT 16571 315189 19.020517772011345 12.361235541530275 chrX 155270560 11791410461 75.94105708770549 103.80522521627789 chrY 59373566 106957341 1.801430303175659 10.861696984919995