BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173879.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 = 1,815,154 number of mapped reads = 1,768,740 (97.44%) number of supplementary alignments = 171,538 (9.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 885,651 number of mapped paired reads (second in pair) = 883,089 number of mapped paired reads (both in pair) = 1,739,388 number of mapped paired reads (singletons) = 29,352 number of mapped bases = 208,980,557 bp number of sequenced bases = 208,862,784 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,328,402 duplication rate = 62.83% >>>>>>> Insert size mean insert size = 1,064,995.5015 std insert size = 9,732,605.6182 median insert size = 197 >>>>>>> Mapping quality mean mapping quality = 53.0753 >>>>>>> ACTG content number of A's = 63,370,975 bp (30.34%) number of C's = 40,419,123 bp (19.35%) number of T's = 63,217,507 bp (30.27%) number of G's = 41,853,199 bp (20.04%) number of N's = 1,980 bp (0%) GC percentage = 39.39% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 2,153,738 number of insertions = 22,936 mapped reads with insertion percentage = 1.25% number of deletions = 48,336 mapped reads with deletion percentage = 2.66% homopolymer indels = 43.31% >>>>>>> Coverage mean coverageData = 0.0675X std coverageData = 1.1486X There is a 1.56% of reference with a coverageData >= 1X There is a 1.18% of reference with a coverageData >= 2X There is a 0.88% of reference with a coverageData >= 3X There is a 0.7% of reference with a coverageData >= 4X There is a 0.52% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.3% of reference with a coverageData >= 7X There is a 0.24% of reference with a coverageData >= 8X There is a 0.17% of reference with a coverageData >= 9X There is a 0.15% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% 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 0.01% 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 16956323 0.0680292106473829 0.903726406783118 chr2 243199373 18750962 0.07710119384230485 3.0033206775071095 chr3 198022430 14349388 0.07246344770135384 0.758409869672392 chr4 191154276 14489544 0.07580026093687803 0.8727609983824288 chr5 180915260 13016719 0.07194925955942025 0.7514643789185912 chr6 171115067 12390251 0.07240888378344848 0.802048401965105 chr7 159138663 11663407 0.07329084447567591 0.8581615087292567 chr8 146364022 11074915 0.07566692175212293 1.0220158551606051 chr9 141213431 8786540 0.062221701843644034 0.8226871482429036 chr10 135534747 10150513 0.07489233000892384 1.0674783893568351 chr11 135006516 9659111 0.07154551710674469 0.7520809108682655 chr12 133851895 9726688 0.0726675404931697 0.7588016304857496 chr13 115169878 6904764 0.05995286371667425 0.6855138962884512 chr14 107349540 6175379 0.05752590090278915 0.6667855186779946 chr15 102531392 6064577 0.05914848985957393 0.6749946072996592 chr16 90354753 6146983 0.06803165075333668 0.7856472190930617 chr17 81195210 5637907 0.06943644828309453 0.7803104138364189 chr18 78077248 5953317 0.07624906297926894 1.0645418554402921 chr19 59128983 3554049 0.060106716193647367 0.7476013212415787 chr20 63025520 4515587 0.0716469614213417 0.7488167089405627 chr21 48129895 3133814 0.06511159020812325 0.8792380875247595 chr22 51304566 2344376 0.04569527008570738 0.6142534946624203 chrMT 16571 326041 19.675396777502865 17.22094764018235 chrX 155270560 5546329 0.035720416027352514 0.5358413186953529 chrY 59373566 1663073 0.028010327019940152 0.5556837064867322