BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1264621.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 = 1,422,593,592 number of mapped reads = 1,416,167,197 (99.55%) number of supplementary alignments = 9,434,789 (0.66%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 709,739,287 number of mapped paired reads (second in pair) = 706,427,910 number of mapped paired reads (both in pair) = 1,411,669,034 number of mapped paired reads (singletons) = 4,498,163 number of mapped bases = 142,174,613,612 bp number of sequenced bases = 142,142,164,276 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 498,381,561 duplication rate = 34.93% >>>>>>> Insert size mean insert size = 87,501.8737 std insert size = 2,847,108.9733 median insert size = 329 >>>>>>> Mapping quality mean mapping quality = 54.5628 >>>>>>> ACTG content number of A's = 43,916,409,149 bp (30.9%) number of C's = 27,124,747,741 bp (19.08%) number of T's = 43,632,300,185 bp (30.7%) number of G's = 27,425,420,733 bp (19.29%) number of N's = 43,286,468 bp (0.03%) GC percentage = 38.38% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 546,984,585 number of insertions = 15,543,085 mapped reads with insertion percentage = 1.08% number of deletions = 14,589,091 mapped reads with deletion percentage = 1.01% homopolymer indels = 48.63% >>>>>>> Coverage mean coverageData = 45.9266X std coverageData = 44.8483X There is a 90.83% of reference with a coverageData >= 1X There is a 89.62% of reference with a coverageData >= 2X There is a 88.42% of reference with a coverageData >= 3X There is a 87.21% of reference with a coverageData >= 4X There is a 85.99% of reference with a coverageData >= 5X There is a 84.76% of reference with a coverageData >= 6X There is a 83.52% of reference with a coverageData >= 7X There is a 82.29% of reference with a coverageData >= 8X There is a 81.04% of reference with a coverageData >= 9X There is a 79.8% of reference with a coverageData >= 10X There is a 78.56% of reference with a coverageData >= 11X There is a 77.31% of reference with a coverageData >= 12X There is a 76.07% of reference with a coverageData >= 13X There is a 74.84% of reference with a coverageData >= 14X There is a 73.6% of reference with a coverageData >= 15X There is a 72.38% of reference with a coverageData >= 16X There is a 71.16% of reference with a coverageData >= 17X There is a 69.95% of reference with a coverageData >= 18X There is a 68.74% of reference with a coverageData >= 19X There is a 67.54% of reference with a coverageData >= 20X There is a 66.35% of reference with a coverageData >= 21X There is a 65.16% of reference with a coverageData >= 22X There is a 63.98% of reference with a coverageData >= 23X There is a 62.81% of reference with a coverageData >= 24X There is a 61.65% of reference with a coverageData >= 25X There is a 60.5% of reference with a coverageData >= 26X There is a 59.36% of reference with a coverageData >= 27X There is a 58.23% of reference with a coverageData >= 28X There is a 57.11% of reference with a coverageData >= 29X There is a 56% of reference with a coverageData >= 30X There is a 54.9% of reference with a coverageData >= 31X There is a 53.82% of reference with a coverageData >= 32X There is a 52.74% of reference with a coverageData >= 33X There is a 51.68% of reference with a coverageData >= 34X There is a 50.63% of reference with a coverageData >= 35X There is a 49.59% of reference with a coverageData >= 36X There is a 48.57% of reference with a coverageData >= 37X There is a 47.56% of reference with a coverageData >= 38X There is a 46.56% of reference with a coverageData >= 39X There is a 45.57% of reference with a coverageData >= 40X There is a 44.6% of reference with a coverageData >= 41X There is a 43.65% of reference with a coverageData >= 42X There is a 42.7% of reference with a coverageData >= 43X There is a 41.77% of reference with a coverageData >= 44X There is a 40.86% of reference with a coverageData >= 45X There is a 39.96% of reference with a coverageData >= 46X There is a 39.07% of reference with a coverageData >= 47X There is a 38.2% of reference with a coverageData >= 48X There is a 37.35% of reference with a coverageData >= 49X There is a 36.51% of reference with a coverageData >= 50X There is a 35.68% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 11129573937 44.65214125584867 46.51520002137156 chr2 243199373 13190958127 54.23927687099753 46.16146327825347 chr3 198022430 11036622462 55.734203756614846 45.577462120596465 chr4 191154276 11561299340 60.48151044238215 47.12724738873739 chr5 180915260 10138536683 56.04025156860732 44.164966645043435 chr6 171115067 9770688980 57.100109016116036 46.979322039078376 chr7 159138663 7856401764 49.36827805320948 44.918513376707075 chr8 146364022 8132491545 55.563460431553324 45.63769751390638 chr9 141213431 6201664455 43.91695896830097 48.41264776354247 chr10 135534747 6276360270 46.308126948434854 41.81829048640002 chr11 135006516 6743613996 49.9502853328946 46.02539145081035 chr12 133851895 6653191885 49.705623405630526 46.66867600307044 chr13 115169878 5322495901 46.21430528041368 44.21167224673582 chr14 107349540 4534838704 42.24367150525284 44.33236764323599 chr15 102531392 3761760851 36.68886940499159 43.414003893698634 chr16 90354753 2582453240 28.581266112254216 34.21702408537011 chr17 81195210 2211310190 27.234490679930502 32.836661836435084 chr18 78077248 3854752974 49.37101489540205 41.00773039988681 chr19 59128983 1029155041 17.405255236674712 24.61110098143721 chr20 63025520 2139581049 33.94785237789391 40.76152846159795 chr21 48129895 1796408240 37.324167027582334 47.251672262815894 chr22 51304566 722374780 14.080126513495895 23.58980432172118 chrMT 16571 35560 2.1459175668336252 5.4536694031084565 chrX 155270560 4851283661 31.24406623509312 30.733917049660125 chrY 59373566 676759977 11.398338058387802 23.801791477851804