. 2021 Jan 14;1:617338. doi: 10.3389/ffunb.2020.617338

Table 1.

Characterization of SNPs associated with ITCZ sensitivity.

Chr.	Pos.	Ref	Alt.	Tassel p-value	RoadTrips p-value	Gene ID	Predicted effect
2	476106	G	T	0.00826	0.0043564^*	Afu2g01910	Missense variant
2	478090	C	T	0.00826	0.0043564^*	Afu2g01910	Synonymous variant
2	482083	T	C	0.00415	0.0016581^*	Afu2g01930	Missense variant
2	483220	T	A	0.0028	0.00221361^*	Afu2g01930	Missense variant
2	506066	C	G	0.00474	0.0043564^*	Afu2g02040	Intron variant
2	534384	C	T	0.00173	0.00221361^*	Afu2g02140	Synonymous variant
2	535564	G	C	0.00082113^*	0.00231196^*	Afu2g02140	Missense variant
2	536173	T	C	0.00109	0.00231196^*	Afu2g02140	Missense variant
2	541570	T	C	0.00109	0.00231196^*	Afu2g02170	5 prime UTR variant
2	543033	T	C	0.00109	0.00231196^*	Afu2g02170	Synonymous variant
2	543252	G	A	0.00109	0.00231196^*	Afu2g02170	Synonymous variant
2	549368	T	C	0.00109	0.00231196^*	Afu2g02180	Upstream gene variant
2	550095	A	T	0.00109	0.00231196^*	Afu2g02190	3 prime UTR variant
2	550165	T	G	0.00109	0.00231196^*	Afu2g02190	3 prime UTR variant
2	561450	T	C	0.00081303^*	0.000825977^*	Afu2g02220	Synonymous variant
2	579284	C	T	0.00173	0.00221361^*	Afu2g02290	Synonymous variant
2	3496859	C	A	0.00104^*	0.00851735	Afu2g13480	3 prime UTR variant
3	953774	C	A	0.00028012^*	0.108915	Afu3g03560	3 prime UTR variant
3	953900	T	C	0.00028012^*	0.108915	Afu3g03560	3 prime UTR variant
3	953968	C	G	0.00084242^*	0.108915	Afu3g03560	3 prime UTR variant
3	953975	G	C	0.00084242^*	0.108915	Afu3g03560	3 prime UTR variant
3	954072	A	C	0.00084242^*	0.108915	Afu3g03560	3 prime UTR variant
3	954106	T	C	0.00084242^*	0.108915	Afu3g03560	3 prime UTR variant
3	3551729	A	T	0.00084242^*	0.347887	Afu3g13420	5 prime UTR variant
3	3551730	A	T	0.00084242^*	0.347887	Afu3g13420	5 prime UTR variant
4	95177	G	C	0.00061923^*	0.354433	Afu4g00350	Missense variant
5	1649986	A	G	0.00067773^*	0.221647	Afu5g06720	Intron variant
6	2995822	G	A	0.00097218^*	0.221647	Afu6g11980	Missense variant
2	3271604	A	G	0.00053335^*	0.153849	Afu2g12760-Afu2g12770	Intergenic region
2	3894996	G	C	0.00109^*	0.120241	Afu2g14770-Afu2g14780	Intergenic region
2	3908952	A	C	0.0008576^*	0.250408	Afu2g14800-Afu2g14810	Intergenic region
4	93588	G	C	0.00056303^*	0.884311	Afu4g00340-Afu4g00350	Intergenic region
5	399165	A	T	0.000099305^*	0.118454	Afu5g01540-Afu5g01550	Intergenic region
8	627169	G	C	0.00023513^*	0.135283	Afu8g02340-Afu8g02350	Intergenic region
2	413387	G	A	0.00173	0.00221361^*	Afu2g01680-Afu2g01690	Intergenic region
2	505989	C	T	0.00474	0.0043564^*	Afu2g02030-Afu2g02040	Intergenic region
2	514248	T	C	0.00474	0.0043564^*	Afu2g02070-Afu2g02080	Intergenic region
8	590672	C	T	0.02195	0.00238334^*	Afu8g02250-Afu8g02255	Intergenic region

p-value is significant in the corresponding method.

Chr., chromosome; Pos., position; Ref., reference allele; Alt., Alternate allele.