BamQC report ----------------------------------- >>>>>>> Input bam file = SRR21671999.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP398595/SRP398595.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 = 335,285,616 number of mapped reads = 333,045,864 (99.33%) number of supplementary alignments = 1,121,121 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 166,594,419 number of mapped paired reads (second in pair) = 166,451,445 number of mapped paired reads (both in pair) = 332,478,200 number of mapped paired reads (singletons) = 567,664 number of mapped bases = 49,451,281,173 bp number of sequenced bases = 49,432,565,925 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 100,783,646 duplication rate = 27.24% >>>>>>> Insert size mean insert size = 16,575.8039 std insert size = 1,162,202.5454 median insert size = 338 >>>>>>> Mapping quality mean mapping quality = 54.5948 >>>>>>> ACTG content number of A's = 15,240,894,778 bp (30.83%) number of C's = 9,514,409,417 bp (19.25%) number of T's = 15,126,539,503 bp (30.6%) number of G's = 9,550,464,534 bp (19.32%) number of N's = 257,693 bp (0%) GC percentage = 38.57% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 304,333,222 number of insertions = 5,895,705 mapped reads with insertion percentage = 1.69% number of deletions = 7,049,199 mapped reads with deletion percentage = 2.01% homopolymer indels = 44.28% >>>>>>> Coverage mean coverageData = 15.9742X std coverageData = 220.7576X There is a 91.48% of reference with a coverageData >= 1X There is a 91% of reference with a coverageData >= 2X There is a 90.18% of reference with a coverageData >= 3X There is a 88.95% of reference with a coverageData >= 4X There is a 87.27% of reference with a coverageData >= 5X There is a 85.14% of reference with a coverageData >= 6X There is a 82.57% of reference with a coverageData >= 7X There is a 79.58% of reference with a coverageData >= 8X There is a 76.21% of reference with a coverageData >= 9X There is a 72.5% of reference with a coverageData >= 10X There is a 68.51% of reference with a coverageData >= 11X There is a 64.29% of reference with a coverageData >= 12X There is a 59.91% of reference with a coverageData >= 13X There is a 55.44% of reference with a coverageData >= 14X There is a 50.94% of reference with a coverageData >= 15X There is a 46.47% of reference with a coverageData >= 16X There is a 42.1% of reference with a coverageData >= 17X There is a 37.87% of reference with a coverageData >= 18X There is a 33.84% of reference with a coverageData >= 19X There is a 30.03% of reference with a coverageData >= 20X There is a 26.47% of reference with a coverageData >= 21X There is a 23.19% of reference with a coverageData >= 22X There is a 20.18% of reference with a coverageData >= 23X There is a 17.46% of reference with a coverageData >= 24X There is a 15.02% of reference with a coverageData >= 25X There is a 12.84% of reference with a coverageData >= 26X There is a 10.93% of reference with a coverageData >= 27X There is a 9.25% of reference with a coverageData >= 28X There is a 7.79% of reference with a coverageData >= 29X There is a 6.54% of reference with a coverageData >= 30X There is a 5.46% of reference with a coverageData >= 31X There is a 4.55% of reference with a coverageData >= 32X There is a 3.78% of reference with a coverageData >= 33X There is a 3.13% of reference with a coverageData >= 34X There is a 2.59% of reference with a coverageData >= 35X There is a 2.15% of reference with a coverageData >= 36X There is a 1.78% of reference with a coverageData >= 37X There is a 1.47% of reference with a coverageData >= 38X There is a 1.23% of reference with a coverageData >= 39X There is a 1.02% of reference with a coverageData >= 40X There is a 0.86% of reference with a coverageData >= 41X There is a 0.73% of reference with a coverageData >= 42X There is a 0.62% of reference with a coverageData >= 43X There is a 0.53% of reference with a coverageData >= 44X There is a 0.46% of reference with a coverageData >= 45X There is a 0.41% of reference with a coverageData >= 46X There is a 0.36% of reference with a coverageData >= 47X There is a 0.32% of reference with a coverageData >= 48X There is a 0.29% of reference with a coverageData >= 49X There is a 0.27% of reference with a coverageData >= 50X There is a 0.25% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3717137114 14.913251164979043 367.2861214394436 chr2 243199373 4507968080 18.53610074891106 96.27285093357992 chr3 198022430 3651217386 18.438403094033337 10.034774205193036 chr4 191154276 3876965818 20.281868128338388 60.972284076584806 chr5 180915260 3334099906 18.42906953233243 13.08409622235293 chr6 171115067 3199777581 18.69956653787828 45.762956069602865 chr7 159138663 2765496698 17.377905820410216 128.8044468780583 chr8 146364022 2749704020 18.786748153176607 649.0466777423892 chr9 141213431 1980993286 14.028363109455219 264.4947926566336 chr10 135534747 2418705933 17.845652030471566 343.419445406424 chr11 135006516 2129995287 15.776981364366147 83.84712992476373 chr12 133851895 2228175560 16.64657463385184 13.698959177651247 chr13 115169878 1854656255 16.103657372980805 10.631396792064537 chr14 107349540 1459793865 13.598510668979113 11.789005099559342 chr15 102531392 1162035652 11.333462165421494 9.332682641843055 chr16 90354753 1043392412 11.547731329640179 63.74592228305722 chr17 81195210 924571218 11.38701677106322 60.21081331989741 chr18 78077248 1380628111 17.682848030196965 190.9664902177991 chr19 59128983 577828146 9.77233357793419 168.48521073897763 chr20 63025520 755317234 11.984307848630205 24.649262463951185 chr21 48129895 629683928 13.083010631957539 29.747666216447783 chr22 51304566 309366965 6.0300084206930045 16.0494867887521 chrMT 16571 527410749 31827.333836219903 3538.5755889309694 chrX 155270560 2183215448 14.060717292447455 29.63046340756447 chrY 59373566 83144521 1.4003625957046273 66.67331830619814