BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1264618.sorted.bam outfile = /home/yangyx/scDNA/SRP041470/SRP041470.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 = 1,085,673,012 number of mapped reads = 1,080,944,839 (99.56%) number of supplementary alignments = 11,641,336 (1.07%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 541,656,825 number of mapped paired reads (second in pair) = 539,288,014 number of mapped paired reads (both in pair) = 1,077,555,784 number of mapped paired reads (singletons) = 3,389,055 number of mapped bases = 107,310,984,399 bp number of sequenced bases = 107,285,948,424 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 357,137,562 duplication rate = 32.62% >>>>>>> Insert size mean insert size = 139,569.4356 std insert size = 3,592,175.2864 median insert size = 304 >>>>>>> Mapping quality mean mapping quality = 54.3725 >>>>>>> ACTG content number of A's = 33,060,718,185 bp (30.82%) number of C's = 20,454,395,582 bp (19.07%) number of T's = 32,968,906,749 bp (30.73%) number of G's = 20,747,898,711 bp (19.34%) number of N's = 54,029,197 bp (0.05%) GC percentage = 38.4% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 398,933,554 number of insertions = 11,508,666 mapped reads with insertion percentage = 1.05% number of deletions = 11,159,772 mapped reads with deletion percentage = 1.01% homopolymer indels = 47.26% >>>>>>> Coverage mean coverageData = 34.6646X std coverageData = 34.4324X There is a 89.96% of reference with a coverageData >= 1X There is a 88.21% of reference with a coverageData >= 2X There is a 86.49% of reference with a coverageData >= 3X There is a 84.8% of reference with a coverageData >= 4X There is a 83.12% of reference with a coverageData >= 5X There is a 81.45% of reference with a coverageData >= 6X There is a 79.79% of reference with a coverageData >= 7X There is a 78.15% of reference with a coverageData >= 8X There is a 76.51% of reference with a coverageData >= 9X There is a 74.88% of reference with a coverageData >= 10X There is a 73.26% of reference with a coverageData >= 11X There is a 71.66% of reference with a coverageData >= 12X There is a 70.07% of reference with a coverageData >= 13X There is a 68.48% of reference with a coverageData >= 14X There is a 66.92% of reference with a coverageData >= 15X There is a 65.36% of reference with a coverageData >= 16X There is a 63.82% of reference with a coverageData >= 17X There is a 62.3% of reference with a coverageData >= 18X There is a 60.8% of reference with a coverageData >= 19X There is a 59.31% of reference with a coverageData >= 20X There is a 57.84% of reference with a coverageData >= 21X There is a 56.38% of reference with a coverageData >= 22X There is a 54.95% of reference with a coverageData >= 23X There is a 53.54% of reference with a coverageData >= 24X There is a 52.14% of reference with a coverageData >= 25X There is a 50.77% of reference with a coverageData >= 26X There is a 49.43% of reference with a coverageData >= 27X There is a 48.1% of reference with a coverageData >= 28X There is a 46.8% of reference with a coverageData >= 29X There is a 45.52% of reference with a coverageData >= 30X There is a 44.26% of reference with a coverageData >= 31X There is a 43.03% of reference with a coverageData >= 32X There is a 41.83% of reference with a coverageData >= 33X There is a 40.65% of reference with a coverageData >= 34X There is a 39.49% of reference with a coverageData >= 35X There is a 38.36% of reference with a coverageData >= 36X There is a 37.25% of reference with a coverageData >= 37X There is a 36.17% of reference with a coverageData >= 38X There is a 35.12% of reference with a coverageData >= 39X There is a 34.08% of reference with a coverageData >= 40X There is a 33.08% of reference with a coverageData >= 41X There is a 32.1% of reference with a coverageData >= 42X There is a 31.14% of reference with a coverageData >= 43X There is a 30.21% of reference with a coverageData >= 44X There is a 29.3% of reference with a coverageData >= 45X There is a 28.41% of reference with a coverageData >= 46X There is a 27.55% of reference with a coverageData >= 47X There is a 26.71% of reference with a coverageData >= 48X There is a 25.89% of reference with a coverageData >= 49X There is a 25.1% of reference with a coverageData >= 50X There is a 24.33% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 8499634578 34.100755873342436 36.29220807526319 chr2 243199373 9777467590 40.20350656907327 34.408476056481454 chr3 198022430 8564495294 43.250127240636324 35.188792940051144 chr4 191154276 9007957147 47.124015928369815 35.93521090919046 chr5 180915260 7254473540 40.09873760787232 34.543847837351585 chr6 171115067 7616606465 44.51160612875779 36.15770406393564 chr7 159138663 5914680133 37.166833134698386 34.34237502886453 chr8 146364022 6038459599 41.25644756468909 34.87979630489355 chr9 141213431 4602610501 32.59329136334065 36.86284117321747 chr10 135534747 4591079847 33.87382164811213 31.351302931191494 chr11 135006516 5146185293 38.118051227986655 35.59045179231489 chr12 133851895 5019198594 37.498151176716625 34.502762336949 chr13 115169878 4265627912 37.03770452895678 34.94810064376961 chr14 107349540 3550111995 33.07058414036986 35.112262923450764 chr15 102531392 2835950679 27.65934045838371 32.00482535341047 chr16 90354753 1984450699 21.962881122590197 27.11223523955568 chr17 81195210 1648961143 20.308601246305045 24.411240542263748 chr18 78077248 3159211159 40.46263463333134 34.14632660182959 chr19 59128983 801756135 13.559444020878898 19.20188397735415 chr20 63025520 1685660702 26.745684954285185 33.28809445635145 chr21 48129895 1296273473 26.932813233853928 33.86110190852479 chr22 51304566 541669411 10.557918197768206 17.70253132126075 chrMT 16571 353603 21.338663930963733 8.015882085538555 chrX 155270560 2992108510 19.270288649696376 21.347273718771135 chrY 59373566 516000397 8.690742897268457 18.124864745732655