BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10251061.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP224945/SRP224945.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 = 1,635,576 number of mapped reads = 1,552,591 (94.93%) number of supplementary alignments = 42,516 (2.6%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 778,312 number of mapped paired reads (second in pair) = 774,279 number of mapped paired reads (both in pair) = 1,545,042 number of mapped paired reads (singletons) = 7,549 number of mapped bases = 191,192,200 bp number of sequenced bases = 191,028,690 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 261,079 duplication rate = 15.24% >>>>>>> Insert size mean insert size = 87,236.7344 std insert size = 2,787,250.3078 median insert size = 192 >>>>>>> Mapping quality mean mapping quality = 53.2304 >>>>>>> ACTG content number of A's = 56,029,281 bp (29.33%) number of C's = 38,848,670 bp (20.34%) number of T's = 56,131,733 bp (29.38%) number of G's = 40,013,279 bp (20.95%) number of N's = 5,727 bp (0%) GC percentage = 41.28% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 1,334,964 number of insertions = 32,128 mapped reads with insertion percentage = 1.94% number of deletions = 76,800 mapped reads with deletion percentage = 4.75% homopolymer indels = 44.16% >>>>>>> Coverage mean coverageData = 0.0618X std coverageData = 0.6849X There is a 3.77% of reference with a coverageData >= 1X There is a 1.52% of reference with a coverageData >= 2X There is a 0.37% of reference with a coverageData >= 3X There is a 0.23% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% 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 17370128 0.06968940711285128 1.3256103668788475 chr2 243199373 16581446 0.0681804636067051 1.0560173042071357 chr3 198022430 12628855 0.06377487136179472 0.37004092458232846 chr4 191154276 11628478 0.060832947310056514 0.44199395361892996 chr5 180915260 11116154 0.061443982116268135 0.37546015455392073 chr6 171115067 9986078 0.05835884691556706 0.38739918619406355 chr7 159138663 10984886 0.06902713515948038 0.9840831246984673 chr8 146364022 8566860 0.05853118739795221 0.41745544465280715 chr9 141213431 8919141 0.063160713091094 0.8518540138760707 chr10 135534747 11062968 0.08162458885912112 0.767416996524636 chr11 135006516 8702690 0.06446125904026737 0.45601551331288803 chr12 133851895 8645741 0.06459184608480889 0.3825342119353061 chr13 115169878 5684913 0.04936110985547801 0.3241786331858957 chr14 107349540 5928883 0.05522970103085677 0.3581384993987503 chr15 102531392 5907641 0.05761787570386248 0.3537433049510955 chr16 90354753 5482578 0.06067835745176571 0.6756222314257684 chr17 81195210 5935048 0.073096036083902 0.48060092616276373 chr18 78077248 4368295 0.05594837307790357 0.6498923224639095 chr19 59128983 3847531 0.06507013658597849 0.6659041183900394 chr20 63025520 3927958 0.06232329380225661 0.37943387334545636 chr21 48129895 2176308 0.04521738516155084 0.33420163599620983 chr22 51304566 2262461 0.04409862857040833 0.3183095915003963 chrMT 16571 90921 5.486753967775028 4.231098270673164 chrX 155270560 8956431 0.05768273779652756 0.3653612173711584 chrY 59373566 429807 0.007239029570836287 0.5534488289545401