BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6432718.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP127755/SRP127755.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 = 363,228,698 number of mapped reads = 363,041,066 (99.95%) number of supplementary alignments = 2,622,520 (0.72%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 181,523,864 number of mapped paired reads (second in pair) = 181,517,202 number of mapped paired reads (both in pair) = 362,978,192 number of mapped paired reads (singletons) = 62,874 number of mapped bases = 51,204,562,963 bp number of sequenced bases = 51,150,890,696 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 184,617,699 duplication rate = 34.97% >>>>>>> Insert size mean insert size = 37,992.3092 std insert size = 1,925,548.4897 median insert size = 322 >>>>>>> Mapping quality mean mapping quality = 57.1012 >>>>>>> ACTG content number of A's = 14,300,940,525 bp (27.96%) number of C's = 10,873,542,186 bp (21.26%) number of T's = 14,139,948,111 bp (27.64%) number of G's = 11,829,069,335 bp (23.13%) number of N's = 7,390,539 bp (0.01%) GC percentage = 44.38% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 378,299,249 number of insertions = 11,434,333 mapped reads with insertion percentage = 3.08% number of deletions = 37,763,494 mapped reads with deletion percentage = 9.88% homopolymer indels = 53.71% >>>>>>> Coverage mean coverageData = 16.5406X std coverageData = 55.36X There is a 37.38% of reference with a coverageData >= 1X There is a 33.81% of reference with a coverageData >= 2X There is a 31.47% of reference with a coverageData >= 3X There is a 29.64% of reference with a coverageData >= 4X There is a 28.1% of reference with a coverageData >= 5X There is a 26.75% of reference with a coverageData >= 6X There is a 25.55% of reference with a coverageData >= 7X There is a 24.46% of reference with a coverageData >= 8X There is a 23.48% of reference with a coverageData >= 9X There is a 22.59% of reference with a coverageData >= 10X There is a 21.76% of reference with a coverageData >= 11X There is a 21% of reference with a coverageData >= 12X There is a 20.3% of reference with a coverageData >= 13X There is a 19.65% of reference with a coverageData >= 14X There is a 19.04% of reference with a coverageData >= 15X There is a 18.47% of reference with a coverageData >= 16X There is a 17.94% of reference with a coverageData >= 17X There is a 17.44% of reference with a coverageData >= 18X There is a 16.96% of reference with a coverageData >= 19X There is a 16.51% of reference with a coverageData >= 20X There is a 16.09% of reference with a coverageData >= 21X There is a 15.68% of reference with a coverageData >= 22X There is a 15.29% of reference with a coverageData >= 23X There is a 14.92% of reference with a coverageData >= 24X There is a 14.57% of reference with a coverageData >= 25X There is a 14.23% of reference with a coverageData >= 26X There is a 13.91% of reference with a coverageData >= 27X There is a 13.6% of reference with a coverageData >= 28X There is a 13.3% of reference with a coverageData >= 29X There is a 13.01% of reference with a coverageData >= 30X There is a 12.74% of reference with a coverageData >= 31X There is a 12.47% of reference with a coverageData >= 32X There is a 12.22% of reference with a coverageData >= 33X There is a 11.97% of reference with a coverageData >= 34X There is a 11.73% of reference with a coverageData >= 35X There is a 11.5% of reference with a coverageData >= 36X There is a 11.28% of reference with a coverageData >= 37X There is a 11.06% of reference with a coverageData >= 38X There is a 10.85% of reference with a coverageData >= 39X There is a 10.65% of reference with a coverageData >= 40X There is a 10.46% of reference with a coverageData >= 41X There is a 10.27% of reference with a coverageData >= 42X There is a 10.08% of reference with a coverageData >= 43X There is a 9.9% of reference with a coverageData >= 44X There is a 9.73% of reference with a coverageData >= 45X There is a 9.56% of reference with a coverageData >= 46X There is a 9.4% of reference with a coverageData >= 47X There is a 9.24% of reference with a coverageData >= 48X There is a 9.08% of reference with a coverageData >= 49X There is a 8.93% of reference with a coverageData >= 50X There is a 8.79% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4431442825 17.779064329793584 55.763698190754255 chr2 243199373 3393190019 13.952297562050047 50.41653625541391 chr3 198022430 4745319833 23.96354712443434 66.16606976741107 chr4 191154276 1545222750 8.083642083946895 34.115868919312256 chr5 180915260 1514107956 8.369155570403514 32.688287006207005 chr6 171115067 2145848317 12.540382063491814 41.59844087041244 chr7 159138663 1365605530 8.581230382713471 32.177649970003905 chr8 146364022 3363978794 22.983645489053313 64.71144670053211 chr9 141213431 2373441405 16.807476372413895 54.85694418116687 chr10 135534747 3277946739 24.185286884403155 66.30039351803842 chr11 135006516 3354660843 24.848140240875484 70.82134430376357 chr12 133851895 2083529042 15.565928610872486 49.73406299751515 chr13 115169878 2267956873 19.692274684878974 61.327139834444786 chr14 107349540 2643520784 24.62535735132167 71.23241102216133 chr15 102531392 2681345311 26.15145721419641 75.64786275707802 chr16 90354753 961153395 10.637552127445913 48.897089069693195 chr17 81195210 1684820973 20.75025082144624 60.44348190475179 chr18 78077248 1627811887 20.848735434425148 61.66205354057895 chr19 59128983 1385263935 23.42783292924216 67.73645422908945 chr20 63025520 2018079862 32.02004302384177 81.32143911751244 chr21 48129895 890228562 18.496374488246857 60.07437847115882 chr22 51304566 1171586101 22.83590316308299 70.60413022214541 chrMT 16571 394850 23.827771407881237 39.809892183973254 chrX 155270560 125814187 0.8102900317999755 9.56458685483667 chrY 59373566 152292190 2.564983043127307 24.079106220793815