BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038396.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 20,497,024 number of mapped reads = 18,730,269 (91.38%) number of supplementary alignments = 389,018 (1.9%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,489,672 number of mapped paired reads (second in pair) = 9,240,597 number of mapped paired reads (both in pair) = 18,408,346 number of mapped paired reads (singletons) = 321,923 number of mapped bases = 2,500,463,291 bp number of sequenced bases = 2,498,339,375 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,423,800 duplication rate = 15.79% >>>>>>> Insert size mean insert size = 92,712.4419 std insert size = 2,889,258.906 median insert size = 239 >>>>>>> Mapping quality mean mapping quality = 53.3357 >>>>>>> ACTG content number of A's = 712,661,079 bp (28.53%) number of C's = 499,216,227 bp (19.98%) number of T's = 727,410,852 bp (29.12%) number of G's = 558,855,512 bp (22.37%) number of N's = 195,705 bp (0.01%) GC percentage = 42.35% >>>>>>> Mismatches and indels general error rate = 0.0139 number of mismatches = 33,183,067 number of insertions = 534,943 mapped reads with insertion percentage = 2.66% number of deletions = 969,153 mapped reads with deletion percentage = 4.94% homopolymer indels = 45.76% >>>>>>> Coverage mean coverageData = 0.8077X std coverageData = 11.6981X There is a 28.28% of reference with a coverageData >= 1X There is a 17.13% of reference with a coverageData >= 2X There is a 10.07% of reference with a coverageData >= 3X There is a 6.47% of reference with a coverageData >= 4X There is a 4.1% of reference with a coverageData >= 5X There is a 2.7% of reference with a coverageData >= 6X There is a 1.79% of reference with a coverageData >= 7X There is a 1.22% of reference with a coverageData >= 8X There is a 0.84% of reference with a coverageData >= 9X There is a 0.58% of reference with a coverageData >= 10X There is a 0.41% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.22% of reference with a coverageData >= 13X There is a 0.17% of reference with a coverageData >= 14X There is a 0.13% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 195244517 0.7833261005195249 16.16329253586146 chr2 243199373 221071648 0.9090140540781739 12.93476052388246 chr3 198022430 161009894 0.81308917378703 1.9112494835667606 chr4 191154276 164531675 0.8607271489966565 14.03912176566162 chr5 180915260 148243809 0.8194101979014927 1.9148906040089553 chr6 171115067 141966131 0.8296530135478952 7.6314666408359795 chr7 159138663 129003331 0.8106347544216832 10.6014497394621 chr8 146364022 123927887 0.846710040531682 3.706074104681611 chr9 141213431 102994255 0.7293516931827823 16.651751086212506 chr10 135534747 136476477 1.0069482551216185 27.589189125899637 chr11 135006516 114687720 0.8494976642460724 6.762506626826072 chr12 133851895 104456886 0.7803915364814222 1.9133507281129147 chr13 115169878 74750584 0.6490463070560863 1.647272117551434 chr14 107349540 71751321 0.6683896456379785 1.926882953551643 chr15 102531392 66215008 0.6458022924335213 1.5951862158763037 chr16 90354753 91242443 1.009824497002388 18.028659208123496 chr17 81195210 63495303 0.7820079903728311 12.62005156544016 chr18 78077248 68246467 0.8740890431998832 13.692197289723095 chr19 59128983 38697237 0.6544546352167092 7.845636759622263 chr20 63025520 50446573 0.8004150223591967 4.386640407669945 chr21 48129895 32544049 0.6761712029498506 6.636345658929174 chr22 51304566 24669581 0.4808457204374363 1.737508029645166 chrMT 16571 14114624 851.7665801701768 425.18251365977244 chrX 155270560 147629959 0.9507916954765926 4.086986576766683 chrY 59373566 13045912 0.21972592988603717 17.04687888792179