BamQC report ----------------------------------- >>>>>>> Input bam file = SRR21671988.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 = 300,462,430 number of mapped reads = 187,840,387 (62.52%) number of supplementary alignments = 1,301,180 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 93,921,205 number of mapped paired reads (second in pair) = 93,919,182 number of mapped paired reads (both in pair) = 186,151,848 number of mapped paired reads (singletons) = 1,688,539 number of mapped bases = 27,802,998,792 bp number of sequenced bases = 27,791,033,435 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 43,978,133 duplication rate = 19.97% >>>>>>> Insert size mean insert size = 110,361.4992 std insert size = 3,212,764.6351 median insert size = 363 >>>>>>> Mapping quality mean mapping quality = 54.4725 >>>>>>> ACTG content number of A's = 8,165,943,898 bp (29.38%) number of C's = 5,755,153,068 bp (20.71%) number of T's = 8,104,673,101 bp (29.16%) number of G's = 5,765,024,816 bp (20.74%) number of N's = 238,552 bp (0%) GC percentage = 41.45% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 163,198,655 number of insertions = 4,017,787 mapped reads with insertion percentage = 2.02% number of deletions = 4,330,498 mapped reads with deletion percentage = 2.21% homopolymer indels = 45.78% >>>>>>> Coverage mean coverageData = 8.9812X std coverageData = 87.4992X There is a 92.04% of reference with a coverageData >= 1X There is a 91.18% of reference with a coverageData >= 2X There is a 89.41% of reference with a coverageData >= 3X There is a 86.35% of reference with a coverageData >= 4X There is a 81.73% of reference with a coverageData >= 5X There is a 75.45% of reference with a coverageData >= 6X There is a 67.7% of reference with a coverageData >= 7X There is a 58.91% of reference with a coverageData >= 8X There is a 49.66% of reference with a coverageData >= 9X There is a 40.53% of reference with a coverageData >= 10X There is a 32.07% of reference with a coverageData >= 11X There is a 24.63% of reference with a coverageData >= 12X There is a 18.4% of reference with a coverageData >= 13X There is a 13.41% of reference with a coverageData >= 14X There is a 9.56% of reference with a coverageData >= 15X There is a 6.69% of reference with a coverageData >= 16X There is a 4.63% of reference with a coverageData >= 17X There is a 3.18% of reference with a coverageData >= 18X There is a 2.18% of reference with a coverageData >= 19X There is a 1.52% of reference with a coverageData >= 20X There is a 1.08% of reference with a coverageData >= 21X There is a 0.79% of reference with a coverageData >= 22X There is a 0.6% of reference with a coverageData >= 23X There is a 0.48% of reference with a coverageData >= 24X There is a 0.4% of reference with a coverageData >= 25X There is a 0.35% of reference with a coverageData >= 26X There is a 0.31% of reference with a coverageData >= 27X There is a 0.28% of reference with a coverageData >= 28X There is a 0.26% of reference with a coverageData >= 29X There is a 0.24% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.14% of reference with a coverageData >= 42X There is a 0.14% of reference with a coverageData >= 43X There is a 0.13% of reference with a coverageData >= 44X There is a 0.13% of reference with a coverageData >= 45X There is a 0.12% of reference with a coverageData >= 46X There is a 0.12% of reference with a coverageData >= 47X There is a 0.12% of reference with a coverageData >= 48X There is a 0.11% of reference with a coverageData >= 49X There is a 0.11% of reference with a coverageData >= 50X There is a 0.11% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2306983198 9.255676831392929 190.2337154230014 chr2 243199373 2427784114 9.982690679058617 64.03978588421901 chr3 198022430 1838000918 9.28178145273745 7.028336109768067 chr4 191154276 1821950127 9.531307199217453 57.104422597134025 chr5 180915260 1682786895 9.301519921536746 8.860704297692834 chr6 171115067 1610237151 9.410259302297442 45.08373743605749 chr7 159138663 1514211436 9.515044348462322 52.98540311032971 chr8 146364022 1394533626 9.52784439061124 60.334124330777435 chr9 141213431 1240920709 8.787554414707197 180.57998354972744 chr10 135534747 1434889314 10.586874183636466 162.11905547036108 chr11 135006516 1295198255 9.593598097146659 47.07613337978905 chr12 133851895 1239461249 9.259945471821673 9.61599584978638 chr13 115169878 886516179 7.697465642882769 6.654718389391039 chr14 107349540 841533081 7.839186651382018 7.973984875232788 chr15 102531392 787370968 7.679316086920969 5.858033293385718 chr16 90354753 894416025 9.898937192601258 56.55445572619416 chr17 81195210 810949902 9.987656931979116 50.54350873787259 chr18 78077248 798757789 10.23035275269948 149.83364741064634 chr19 59128983 590155721 9.980819744523595 84.16957943214797 chr20 63025520 601384567 9.541921542257803 24.751129419196523 chr21 48129895 400017889 8.311214661906078 36.47406375171076 chr22 51304566 365844155 7.130830324146977 25.899619475973697 chrMT 16571 8627263 520.6241626938628 78.31567422154224 chrX 155270560 739449238 4.762327372297749 16.127333652721774 chrY 59373566 271019023 4.56464115697548 77.7408937027601