BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173866.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 1,549,252 number of mapped reads = 1,509,291 (97.42%) number of supplementary alignments = 145,022 (9.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 755,497 number of mapped paired reads (second in pair) = 753,794 number of mapped paired reads (both in pair) = 1,484,254 number of mapped paired reads (singletons) = 25,037 number of mapped bases = 178,340,736 bp number of sequenced bases = 178,244,997 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,134,135 duplication rate = 62.96% >>>>>>> Insert size mean insert size = 1,070,245.6205 std insert size = 9,316,084.2322 median insert size = 202 >>>>>>> Mapping quality mean mapping quality = 52.92 >>>>>>> ACTG content number of A's = 53,895,109 bp (30.24%) number of C's = 34,735,100 bp (19.49%) number of T's = 53,644,289 bp (30.1%) number of G's = 35,968,026 bp (20.18%) number of N's = 2,473 bp (0%) GC percentage = 39.67% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 1,864,741 number of insertions = 21,047 mapped reads with insertion percentage = 1.35% number of deletions = 39,149 mapped reads with deletion percentage = 2.53% homopolymer indels = 43.08% >>>>>>> Coverage mean coverageData = 0.0576X std coverageData = 1.0053X There is a 1.32% of reference with a coverageData >= 1X There is a 1.01% of reference with a coverageData >= 2X There is a 0.75% of reference with a coverageData >= 3X There is a 0.61% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.36% of reference with a coverageData >= 6X There is a 0.26% of reference with a coverageData >= 7X There is a 0.21% of reference with a coverageData >= 8X There is a 0.15% of reference with a coverageData >= 9X There is a 0.12% of reference with a coverageData >= 10X There is a 0.09% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 14322697 0.05746303436491739 0.7811117793039852 chr2 243199373 15404604 0.06334146264431365 2.540054224421972 chr3 198022430 12080563 0.061006033508426295 0.68419025599446 chr4 191154276 12563898 0.06572648157763418 0.8276196475569922 chr5 180915260 11582324 0.06402071334391582 0.708740219827038 chr6 171115067 10964354 0.06407591214629861 0.7506362741899817 chr7 159138663 9635359 0.06054693949514958 0.7486002968492724 chr8 146364022 9133014 0.06239931012554438 0.8205160086778625 chr9 141213431 7688019 0.05444254803213442 0.8359906254181778 chr10 135534747 9125155 0.06732705230194586 0.9351212351709715 chr11 135006516 8124440 0.060178132439177974 0.6868499173650141 chr12 133851895 8486020 0.06339857945231182 0.7067104159238167 chr13 115169878 5827511 0.05059926346366365 0.6266917146857961 chr14 107349540 5399991 0.050302879732880085 0.6239453887408993 chr15 102531392 5249463 0.05119859291484114 0.623275744798752 chr16 90354753 5415388 0.05993473304055184 0.7462073222927174 chr17 81195210 4665873 0.05746488000954736 0.6895117809263576 chr18 78077248 5141908 0.06585667568611024 1.055761965802279 chr19 59128983 3112265 0.052635185692268716 0.6889929495725436 chr20 63025520 3682449 0.05842790349052257 0.6926433810008911 chr21 48129895 2536162 0.05269411038607086 0.7314017839896141 chr22 51304566 2027385 0.0395166582249229 0.543070812730472 chrMT 16571 243676 14.704966507754511 14.235875309622536 chrX 155270560 4462368 0.02873930512004336 0.46774494350110046 chrY 59373566 1465850 0.02468859626858188 0.5485408622803319