# Lack of enrichment for conservation in RNA modification sites
#
# Notes:
# - SNV conservation means lack of SNVs in SARS-CoV-2
# - SNV-A, etc, refer to counts in sites with base A, etc.
# - For SNV(weighted) lines, ConservedInGenome is the fraction of sites with each base in 
#    the whole genome that are conserved (i.e., no SNV) weighted by the fraction of each 
#    base in the RNA modification sites in the study, times the size of the genome. In 
#    other words, the number of conserved sites that would be expected if the whole genome
#    had the same base composition as the RNA modification sites in the study.
# - The Taiaroa study looked only for 5-methylcytosine modifications, but one of the
#    reported sites is an adenine in the reference genome, suggesting the isolate used in
#    the study had a SNV at that site, though it was not included among the SNVs we
#    studied.
Study	ConservationType	GenomeSubset	ConservedInStudy	NumInStudy	FractionConservedInStudy	ConservedInGenome	NumInGenome	FracConservedInGenome	NominalPvalue
Kim	ConservedNucleotide	WholeGenome	21	41	0.512195121951	15989	29903	0.5346955155	0.672770851724
Kim	ConservedAminoAcid	WholeGenome	24	40	0.6	19438	29230	0.665001710571	0.850317086752
Kim	SynonymouslyConstrained	WholeGenome	5	40	0.125	4181	29230	0.143037974684	0.695445929207
Kim	InSCE	WholeGenome	7	40	0.175	3656	29230	0.12507697571	0.227973894644
Kim	SNV-A	WholeGenome	23	23	1.0	8662	8954	0.96738887648	0.466471435722
Kim	SNV-C	WholeGenome	6	6	1.0	4725	5492	0.860342316096	0.405534405566
Kim	SNV-G	WholeGenome	6	6	1.0	5392	5863	0.919665700154	0.605034216572
Kim	SNV-T	WholeGenome	6	6	1.0	9291	9594	0.968417761101	0.824852843128
Kim	SNV(weighted)	WholeGenome	41	41	1.0	28255.0521051	29903	0.944890215198	0.0978668069162
Taiaroa	ConservedNucleotide	WholeGenome	25	42	0.595238095238	15989	29903	0.5346955155	0.264689676358
Taiaroa	ConservedAminoAcid	WholeGenome	27	37	0.72972972973	19438	29230	0.665001710571	0.258483112427
Taiaroa	SynonymouslyConstrained	WholeGenome	4	37	0.108108108108	4181	29230	0.143037974684	0.795353348831
Taiaroa	InSCE	WholeGenome	7	37	0.189189189189	3656	29230	0.12507697571	0.172905070032
Taiaroa	SNV-A	WholeGenome	1	1	1.0	8662	8954	0.96738887648	0.96738887648
Taiaroa	SNV-C	WholeGenome	35	41	0.853658536585	4725	5492	0.860342316096	0.653958326691
Taiaroa	SNV-G	WholeGenome	0	0	0.0	5392	5863	0.919665700154	1.0
Taiaroa	SNV-T	WholeGenome	0	0	0.0	9291	9594	0.968417761101	1.0
Taiaroa	SNV(weighted)	WholeGenome	36	42	0.857142857143	25803.0308805	29903	0.862891043724	0.648272766855
Both	ConservedNucleotide	WholeGenome	46	83	0.55421686747	15989	29903	0.5346955155	0.40366064796
Both	ConservedAminoAcid	WholeGenome	51	77	0.662337662338	19438	29230	0.665001710571	0.572610001633
Both	SynonymouslyConstrained	WholeGenome	9	77	0.116883116883	4181	29230	0.143037974684	0.789740958383
Both	InSCE	WholeGenome	14	77	0.181818181818	3656	29230	0.12507697571	0.0955139898013
Both	SNV-A	WholeGenome	24	24	1.0	8662	8954	0.96738887648	0.451259278113
Both	SNV-C	WholeGenome	41	47	0.872340425532	4725	5492	0.860342316096	0.509872284331
Both	SNV-G	WholeGenome	6	6	1.0	5392	5863	0.919665700154	0.605034216572
Both	SNV-T	WholeGenome	6	6	1.0	9291	9594	0.968417761101	0.824852843128
Both	SNV(weighted)	WholeGenome	77	83	0.927710843373	27014.2702806	29903	0.903396658549	0.298658688443
Kim	ConservedNucleotide	AfterS	17	35	0.485714285714	2380	4519	0.526665191414	0.743864356424
Kim	ConservedAminoAcid	AfterS	21	34	0.617647058824	2384	4124	0.578079534433	0.388036713428
Kim	SynonymouslyConstrained	AfterS	2	34	0.0588235294118	480	4124	0.11639185257	0.918435835787
Kim	InSCE	AfterS	4	34	0.117647058824	561	4124	0.136032977692	0.697602070102
Kim	SNV-A	AfterS	20	20	1.0	1286	1333	0.964741185296	0.4877714575
Kim	SNV-C	AfterS	5	5	1.0	791	960	0.823958333333	0.379774894961
Kim	SNV-G	AfterS	6	6	1.0	723	874	0.827231121281	0.320450672962
Kim	SNV-T	AfterS	4	4	1.0	1286	1352	0.951183431953	0.81857241995
Kim	SNV(weighted)	AfterS	35	35	1.0	4155.25094878	4519	0.919506737946	0.0530178436479
Taiaroa	ConservedNucleotide	AfterS	24	41	0.585365853659	2380	4519	0.526665191414	0.276336062435
Taiaroa	ConservedAminoAcid	AfterS	27	37	0.72972972973	2384	4124	0.578079534433	0.042102523716
Taiaroa	SynonymouslyConstrained	AfterS	4	37	0.108108108108	480	4124	0.11639185257	0.638584818204
Taiaroa	InSCE	AfterS	7	37	0.189189189189	561	4124	0.136032977692	0.231634452656
Taiaroa	SNV-A	AfterS	1	1	1.0	1286	1333	0.964741185296	0.964741185296
Taiaroa	SNV-C	AfterS	34	40	0.85	791	960	0.823958333333	0.428387835011
Taiaroa	SNV-G	AfterS	0	0	0.0	723	874	0.827231121281	1.0
Taiaroa	SNV-T	AfterS	0	0	0.0	1286	1352	0.951183431953	1.0
Taiaroa	SNV(weighted)	AfterS	35	41	0.853658536585	3738.9847256	4519	0.82739206143	0.423082998112
Both	ConservedNucleotide	AfterS	41	76	0.539473684211	2380	4519	0.526665191414	0.457545194044
Both	ConservedAminoAcid	AfterS	48	71	0.676056338028	2384	4124	0.578079534433	0.0589856746626
Both	SynonymouslyConstrained	AfterS	6	71	0.0845070422535	480	4124	0.11639185257	0.848167807208
Both	InSCE	AfterS	11	71	0.154929577465	561	4124	0.136032977692	0.370846959391
Both	SNV-A	AfterS	21	21	1.0	1286	1333	0.964741185296	0.470573214062
Both	SNV-C	AfterS	39	45	0.866666666667	791	960	0.823958333333	0.299640358188
Both	SNV-G	AfterS	6	6	1.0	723	874	0.827231121281	0.320450672962
Both	SNV-T	AfterS	4	4	1.0	1286	1352	0.951183431953	0.81857241995
Both	SNV(weighted)	AfterS	70	76	0.921052631579	3930.68627575	4519	0.869813294036	0.119598117173