Project: ex Cluster: 1.0k Pairs: 846 Seqs: 707 Hits: 2.2k PCC Stats KaKs Multi
Created: 13-Jul-22 v4.0.3
DATASETS: 3
Type #Seq #annotated #annoDB Created Remark
bar NT 250 250 3 06-Jul-22 exBar
fly NT 207 207 3 06-Jul-22 exFly
foo NT 250 250 3 06-Jul-22 exFoo
CLUSTER SETS: 5
Statistics
Prefix Method conLen sdLen Score1 SD Score2 SD
CL Closure 579.80 58.52 3.72 1.06 0.78 0.15
OM orthoMCL.OM-4 606.33 85.28 3.30 1.40 0.75 0.16
B12 BBH bar,fly 540.34 62.71 3.58 1.10 0.72 0.18
B13 BBH bar,foo 558.76 34.07 4.09 0.83 0.79 0.15
B23 BBH fly,foo 559.57 70.82 3.98 1.28 0.80 0.21
Sizes
Prefix =2 =3 4-5 6-10 11-15 16-20 21-25 >25 Total #Seqs
CL 93 150 1 1 0 0 0 0 245 91.5%
OM 50 186 3 3 0 0 0 0 242 98.0%
B12 157 0 0 0 0 0 0 0 157 44.4%
B13 239 0 0 0 0 0 0 0 239 67.6%
B23 166 0 0 0 0 0 0 0 166 47.0%
PAIRS: 846
Hits
AA Diff 753 Same 60 Similarity 76.4% Coverage 84.7%
NT Diff 663 Same 4 Similarity 86.4% Coverage 59.4%
Aligned: 700 CDS: 1.0Mb 5UTR: 61.5kb 3UTR: 96.5kb
Codons 311.0k Amino Acids Nucleotides
Exact 57.8% Exact 86.3% CDS Diff 24.9%
Synonymous 28.5% Substitution >0 5.9% Gaps 7.6%
Fourfold 14.8% Substitution<=0 7.8% SNPs 17.3%
Twofold 11.1% 5UTR Diff 35.4%
Nonsynonymous 13.7% 3UTR Diff 37.0%
Pos1 Pos2 Pos3 Total GC CpG-Nt CpG-Cd
Transition 9.3% 5.1% 35.0% 49.4% Both 38.0% 3.9% 2.2%
Transversion 12.1% 8.3% 30.3% 50.6% Either 54.6% 11.4% 5.8%
ts/tv 0.77 0.62 1.16 0.98 Jaccard 0.70 0.35 0.37
KaKs method: YN Pairs: 700
Ka/Ks Quartiles Average P-value
NA 16 Q1(Lower) 0.019 Ka 0.102 NA 48
KaKs<1 675 Q2(Median) 0.044 Ks 2.793 <1E-100 419
KaKs~1 0 Q3(Upper) 0.113 P-value 0.036 <1E-10 85
KaKs>1 9 <1.0 148
SEQUENCES: 707
Average Lengths %GC CpG O/E
5UTR CDS 3UTR 5UTR CDS 3UTR 5UTR CDS 3UTR
bar 170.8 1612.4 229.6 39.1% 51.0% 38.4% 0.754 0.695 0.730
fly 135.2 1520.2 314.4 36.8% 46.6% 35.5% 0.751 0.693 0.663
foo 193.2 1539.8 336.8 40.5% 47.0% 36.7% 0.779 0.702 0.742
Counts
Cx Cy Cz
bar 812,745 665,939 853,758
fly 736,627 605,318 772,927
foo 1,009,851 706,578 537,403
Differential Expression (p-value < 0.001)
CxCy CxCz CyCz
bar 0 17 17
fly 0 16 14
foo 6 16 18
----------------------------------------------------
PROCESSING:
AA: diamond --masking 0 --query-cover 25 --subject-cover 25
NT: blastn -evalue 1e-05 -max_hsps 1 -max_target_seqs 25
MSA: Score1=Sum-of-Pairs Score2=Wentropy
Cluster Sets
Prefix Method Parameters
CL Closure Sim 60; Cov 40(Both); AA
OM User Defined orthoMCL.OM-4
B12 BBH Sim 60; Cov 40(Both); AA; bar,fly
B13 BBH Sim 60; Cov 40(Both); AA; bar,foo
B23 BBH Sim 60; Cov 40(Both); AA; fly,foo
|