evg12aedes aaeval_genesets_summary.txt
see tables in aaeval/ for per-gene matches.

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Aedes_aegypti x REFERENCE Highly conserved BUSCO/drosmel1g_busco (n=3055)
       Evigene  PubTrinVb3 Vecbase3  
found  99.5%     98.6%      98.3%   
align  91.3%     86.5%      85.1%   
best   42.3%      5.2%       3.0%     equal 52% 
                  
Aedes_aegypti x REFERENCE Drosophila mel. model/drosmel1g (n=11146)
       Evigene  PubTrinVb3 Vecbase3  
found  99.0%     97.5%      97.1%   
align  86.4%     82.4%      81.1%   
best   44.0%      9.2%       6.1%    equal 47%                 

Aedes_aegypti x REFERENCE  Anopheles gambia/AGAP (n=14014)
       Evigene  PubTrinVb3 Vecbase3  
found  99.1%     97.3%      96.6%   
align  94.3%     89.7%      87.2%   
best   44.3%     10.4%       8.5%     equal 45%                 
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Evigene gene set has >= 90% best genes versus <= 55% best for others

Aedes PubTrinVb3 ref = RNA-seq data source for EVm gene construction
  doi:10.1186/s12864-015-2239-0; Matthews et al. BMC Genomics (2016) 17:32, The neurotranscriptome of Aedes_aegypti 
Aedes_aegypti RNA-seq SRA accessions used for Evigene: 
 evg1aedes = SRP037535 (male+fem, 10 of 68 SRX read sets) from PubTrinVb3
 evg2aedes = SRP047470 (male+fem, 4 of 6 SRX) and SRP046160 (embryo) from
 doi:10.1126/science.aaa2850, Hall A.B. et al. 2015. A male-determining factor in the mosquito Aedes aegypti. 
evg2aedes gene set is less complete than evg1, using less effort/data,
but contains ~3000 better gene loci (some replace evg1, some are unfound in evg1)
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REFERENCE AGAP
==> trasm16aedes_evg12aedesmerge-AGAP.hodiff.txt <==
#stat a,b=trasm16aedes EVm, nr=14010, aved(a-b)=-29, refalign%(a,b)=89.7 94.3, sumd=-407851
#best (equal,abest,bbest,amiss,bmiss)=6337,45.2% 1464,10.4% 6209,44.3% 384,2.7% 137,0.9%

==> vbase3aedes_evg12aedesmerge-AGAP.hodiff.txt <==
#stat a,b=EVm AAEL, nr=14013, aved(a-b)=44, refalign%(a,b)=94.3 87.8, sumd=629401
#best (equal,abest,bbest,amiss,bmiss)=5654,40.3% 7124,50.8% 1235,8.8% 140,0.9% 473,3.3%

REFERENCE drosmel1g
==> trasm16aedes_evg12aedesmerge-drosmel1g.hodiff.txt <==
#stat a,b=trasm16aedes EVm, nr=11141, aved(a-b)=-29, refalign%(a,b)=82.4 86.4, sumd=-325275
#best (equal,abest,bbest,amiss,bmiss)=5206,46.7% 1028,9.2% 4907,44% 277,2.4% 117,1%

==> vbase3aedes_evg12aedesmerge-drosmel1g.hodiff.txt <==
#stat a,b=EVm AAEL, nr=11139, aved(a-b)=42, refalign%(a,b)=86.4 81, sumd=468512
#best (equal,abest,bbest,amiss,bmiss)=4746,42.6% 5563,49.9% 830,7.4% 115,1% 320,2.8%

REFERENCE drosmel conserved BUSCO
==> trasm16aedes_evg12aedesmerge-drosmel1g_busco.hodiff.txt <==
#stat a,b=trasm16aedes EVm, nr=3047, aved(a-b)=-32, refalign%(a,b)=86.5 91.3, sumd=-98272
#best (equal,abest,bbest,amiss,bmiss)=1598,52.4% 159,5.2% 1290,42.3% 34,1.1% 6,0.1%

==> vbase3aedes_evg12aedesmerge-drosmel1g_busco.hodiff.txt <==
#stat a,b=EVm AAEL, nr=3047, aved(a-b)=45, refalign%(a,b)=91.3 85.1, sumd=137635
#best (equal,abest,bbest,amiss,bmiss)=1470,48.2% 1474,48.3% 103,3.3% 6,0.1% 42,1.3%
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