BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354870.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP408873/SRP408873.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 = 25,767,118 number of mapped reads = 25,511,874 (99.01%) number of supplementary alignments = 1,186,085 (4.6%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 12,767,278 number of mapped paired reads (second in pair) = 12,744,596 number of mapped paired reads (both in pair) = 25,470,008 number of mapped paired reads (singletons) = 41,866 number of mapped bases = 3,194,552,251 bp number of sequenced bases = 3,193,008,614 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,426,992 duplication rate = 64.51% >>>>>>> Insert size mean insert size = 440,047.5372 std insert size = 7,677,871.4801 median insert size = 160 >>>>>>> Mapping quality mean mapping quality = 53.6286 >>>>>>> ACTG content number of A's = 890,000,093 bp (27.87%) number of C's = 674,212,133 bp (21.12%) number of T's = 900,877,179 bp (28.21%) number of G's = 727,889,977 bp (22.8%) number of N's = 29,232 bp (0%) GC percentage = 43.91% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 17,395,986 number of insertions = 531,941 mapped reads with insertion percentage = 1.95% number of deletions = 550,564 mapped reads with deletion percentage = 2.06% homopolymer indels = 44.2% >>>>>>> Coverage mean coverageData = 1.0319X std coverageData = 62.0755X There is a 26.19% of reference with a coverageData >= 1X There is a 21.69% of reference with a coverageData >= 2X There is a 13.46% of reference with a coverageData >= 3X There is a 11.12% of reference with a coverageData >= 4X There is a 6.68% of reference with a coverageData >= 5X There is a 5.54% of reference with a coverageData >= 6X There is a 3.29% of reference with a coverageData >= 7X There is a 2.73% of reference with a coverageData >= 8X There is a 1.62% of reference with a coverageData >= 9X There is a 1.34% of reference with a coverageData >= 10X There is a 0.8% of reference with a coverageData >= 11X There is a 0.66% of reference with a coverageData >= 12X There is a 0.4% of reference with a coverageData >= 13X There is a 0.33% of reference with a coverageData >= 14X There is a 0.21% of reference with a coverageData >= 15X There is a 0.17% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.04% 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 0.03% 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 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 261256621 1.0481683855062491 30.5408506481905 chr2 243199373 307931666 1.2661696541462713 215.81465762991513 chr3 198022430 210010173 1.0605372987292399 2.8477489287540276 chr4 191154276 216788977 1.1341047740935704 13.048557082669321 chr5 180915260 189232165 1.045971274064996 2.3746442768518894 chr6 171115067 180494323 1.0548125665637615 5.225045023402191 chr7 159138663 170443126 1.0710353020874632 17.940256947842222 chr8 146364022 156940605 1.0722621779278516 5.832886189790755 chr9 141213431 136525409 0.9668018688675584 15.57837894125971 chr10 135534747 174154262 1.2849418016768792 35.01586511229442 chr11 135006516 146358577 1.084085282224452 5.7805314528538885 chr12 133851895 137268955 1.0255286636024092 2.3099333435028226 chr13 115169878 99156495 0.8609585832851191 2.071473891692726 chr14 107349540 96329406 0.8973434446016256 7.533883653532461 chr15 102531392 88606406 0.864188072273514 2.081926622129972 chr16 90354753 101316046 1.1213139612035683 6.194578031117163 chr17 81195210 90120791 1.1099274329113749 6.882424924767495 chr18 78077248 86983155 1.1140653292493097 13.712035025903784 chr19 59128983 67032534 1.133666276654885 15.357859348816833 chr20 63025520 67080939 1.064345665057583 4.839809508092893 chr21 48129895 44529584 0.9251959514975048 7.344917551520163 chr22 51304566 40369146 0.7868528894679666 3.233794804813722 chrMT 16571 3854690 232.6166193953292 49.01936795111111 chrX 155270560 84369192 0.5433688910505636 2.5102453053805003 chrY 59373566 37399008 0.6298932423900562 17.32193316190534