BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438256.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 = 753,173,218 number of mapped reads = 749,242,464 (99.48%) number of supplementary alignments = 20,412,598 (2.71%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 374,808,414 number of mapped paired reads (second in pair) = 374,434,050 number of mapped paired reads (both in pair) = 746,789,744 number of mapped paired reads (singletons) = 2,452,720 number of mapped bases = 106,254,315,680 bp number of sequenced bases = 106,219,821,954 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 300,311,948 duplication rate = 35.16% >>>>>>> Insert size mean insert size = 111,115.5898 std insert size = 3,249,529.7857 median insert size = 445 >>>>>>> Mapping quality mean mapping quality = 54.3315 >>>>>>> ACTG content number of A's = 32,443,015,145 bp (30.54%) number of C's = 20,317,460,943 bp (19.13%) number of T's = 30,551,972,573 bp (28.76%) number of G's = 22,907,176,415 bp (21.57%) number of N's = 196,878 bp (0%) GC percentage = 40.69% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 570,461,494 number of insertions = 14,309,116 mapped reads with insertion percentage = 1.86% number of deletions = 12,658,212 mapped reads with deletion percentage = 1.64% homopolymer indels = 48.36% >>>>>>> Coverage mean coverageData = 34.3233X std coverageData = 85.0499X There is a 91.02% of reference with a coverageData >= 1X There is a 90.34% of reference with a coverageData >= 2X There is a 89.61% of reference with a coverageData >= 3X There is a 88.79% of reference with a coverageData >= 4X There is a 87.86% of reference with a coverageData >= 5X There is a 86.83% of reference with a coverageData >= 6X There is a 85.69% of reference with a coverageData >= 7X There is a 84.43% of reference with a coverageData >= 8X There is a 83.08% of reference with a coverageData >= 9X There is a 81.62% of reference with a coverageData >= 10X There is a 80.08% of reference with a coverageData >= 11X There is a 78.47% of reference with a coverageData >= 12X There is a 76.78% of reference with a coverageData >= 13X There is a 75.04% of reference with a coverageData >= 14X There is a 73.26% of reference with a coverageData >= 15X There is a 71.43% of reference with a coverageData >= 16X There is a 69.59% of reference with a coverageData >= 17X There is a 67.72% of reference with a coverageData >= 18X There is a 65.86% of reference with a coverageData >= 19X There is a 63.99% of reference with a coverageData >= 20X There is a 62.12% of reference with a coverageData >= 21X There is a 60.27% of reference with a coverageData >= 22X There is a 58.44% of reference with a coverageData >= 23X There is a 56.62% of reference with a coverageData >= 24X There is a 54.84% of reference with a coverageData >= 25X There is a 53.08% of reference with a coverageData >= 26X There is a 51.36% of reference with a coverageData >= 27X There is a 49.67% of reference with a coverageData >= 28X There is a 48.02% of reference with a coverageData >= 29X There is a 46.4% of reference with a coverageData >= 30X There is a 44.83% of reference with a coverageData >= 31X There is a 43.3% of reference with a coverageData >= 32X There is a 41.81% of reference with a coverageData >= 33X There is a 40.35% of reference with a coverageData >= 34X There is a 38.94% of reference with a coverageData >= 35X There is a 37.58% of reference with a coverageData >= 36X There is a 36.25% of reference with a coverageData >= 37X There is a 34.96% of reference with a coverageData >= 38X There is a 33.72% of reference with a coverageData >= 39X There is a 32.51% of reference with a coverageData >= 40X There is a 31.35% of reference with a coverageData >= 41X There is a 30.22% of reference with a coverageData >= 42X There is a 29.13% of reference with a coverageData >= 43X There is a 28.07% of reference with a coverageData >= 44X There is a 27.06% of reference with a coverageData >= 45X There is a 26.08% of reference with a coverageData >= 46X There is a 25.13% of reference with a coverageData >= 47X There is a 24.21% of reference with a coverageData >= 48X There is a 23.33% of reference with a coverageData >= 49X There is a 22.48% of reference with a coverageData >= 50X There is a 21.66% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 8816588872 35.3723847773282 40.16652307449128 chr2 243199373 9328573641 38.3577207701107 158.55807122751608 chr3 198022430 7679879953 38.78287905567061 30.00124821632038 chr4 191154276 6612652813 34.593276966506366 33.07114459248663 chr5 180915260 6778671958 37.468768295167585 30.243201545233703 chr6 171115067 6533425355 38.181473259745154 33.36901703334683 chr7 159138663 5499239447 34.55627528427834 29.807273723715138 chr8 146364022 5363158835 36.64260356961221 31.554581265688295 chr9 141213431 4411564659 31.240404172319842 44.45300091996229 chr10 135534747 4871263755 35.94106945136364 65.91908737398661 chr11 135006516 4899956781 36.29422435432672 33.031857974594665 chr12 133851895 5074115089 37.908429230680674 32.25124351840202 chr13 115169878 3456571206 30.012806004708974 29.536329585940695 chr14 107349540 3374594513 31.435574973120517 31.78906344907626 chr15 102531392 3211632022 31.32340212449276 31.737424674216303 chr16 90354753 2907570184 32.17949346837349 73.38962059372763 chr17 81195210 2807486437 34.57699582278314 46.37098299108888 chr18 78077248 2769838265 35.475613395082775 53.164365510603716 chr19 59128983 1601013617 27.076630372621157 31.784104579111652 chr20 63025520 2145311317 34.03877218307758 32.11766247641533 chr21 48129895 1268030273 26.346001232705785 38.45765361855146 chr22 51304566 1176447293 22.930654807605233 30.488283727726195 chrMT 16571 417950155 25221.782330577516 9443.673857136437 chrX 155270560 5130215947 33.04049361965333 26.655939559898062 chrY 59373566 118563293 1.9969036894297372 31.30725307321008