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Mutant Information

Mutant Name	FN1273-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1273-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000430 (Germination Rate) = Very Low (Below 24%) For more information, please see this phenotype file
Mapping (Hover to Zoom-In)

Variant Information

Single base substitutions: 32

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	15972390	T-C	HOMO	NON_SYNONYMOUS_CODING	LOC_Os01g28530
SBS	Chr1	16838106	C-T	HET	INTRON
SBS	Chr1	34655731	C-T	HOMO	INTERGENIC
SBS	Chr1	4976696	G-A	HET	INTERGENIC
SBS	Chr10	12575307	A-C	HET	INTERGENIC
SBS	Chr11	13792222	C-T	HET	INTERGENIC
SBS	Chr11	14111218	T-A	HET	INTRON
SBS	Chr11	23879726	G-A	HET	NON_SYNONYMOUS_CODING	LOC_Os11g40050
SBS	Chr11	8239495	C-T	HET	INTERGENIC
SBS	Chr12	20211648	T-C	HOMO	NON_SYNONYMOUS_CODING	LOC_Os12g33450
SBS	Chr12	20351894	A-G	HOMO	INTERGENIC
SBS	Chr12	2874431	G-T	HET	INTERGENIC
SBS	Chr12	2874432	A-T	HET	INTERGENIC
SBS	Chr12	320291	G-C	HET	UTR_3_PRIME
SBS	Chr2	1548800	T-A	HET	INTERGENIC
SBS	Chr2	2754197	C-T	HET	INTERGENIC
SBS	Chr2	31095157	T-A	HOMO	INTERGENIC
SBS	Chr2	4371180	A-T	HET	INTERGENIC
SBS	Chr3	13778519	C-A	HET	SPLICE_SITE_REGION
SBS	Chr3	15588400	C-A	HET	INTERGENIC
SBS	Chr3	28257341	G-C	HET	STOP_GAINED	LOC_Os03g49620
SBS	Chr3	32509034	A-C	HET	INTERGENIC
SBS	Chr5	21876949	C-T	HOMO	INTRON
SBS	Chr5	21876963	A-T	HOMO	INTRON
SBS	Chr5	3024378	C-T	HOMO	INTERGENIC
SBS	Chr5	9847410	C-T	HOMO	INTERGENIC
SBS	Chr6	27291380	A-T	HET	INTRON
SBS	Chr6	30937224	T-C	HET	INTERGENIC
SBS	Chr7	27055014	A-G	HOMO	INTERGENIC
SBS	Chr8	1160456	A-T	HET	INTERGENIC
SBS	Chr8	4468494	C-T	HOMO	SYNONYMOUS_CODING
SBS	Chr9	13496969	C-T	HOMO	NON_SYNONYMOUS_CODING	LOC_Os09g22340

Deletions: 23

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Deletion	Chr12	2019113	2019191	78	LOC_Os12g04750
Deletion	Chr10	2702948	2702952	4
Deletion	Chr8	7771235	7771242	7	LOC_Os08g13080
Deletion	Chr9	8343355	8343359	4
Deletion	Chr8	8425383	8425384	1
Deletion	Chr9	10048873	10048877	4
Deletion	Chr5	10648001	10670000	22000	2
Deletion	Chr6	11400836	11400843	7
Deletion	Chr7	11716591	11716594	3
Deletion	Chr12	16901001	17398000	497000	70
Deletion	Chr2	17802752	17802753	1
Deletion	Chr11	18038516	18038519	3
Deletion	Chr4	18437001	18451000	14000	2
Deletion	Chr8	19080532	19080533	1
Deletion	Chr12	19391966	19391967	1	LOC_Os12g32150
Deletion	Chr11	20616772	20616773	1
Deletion	Chr5	21877555	21877591	36
Deletion	Chr6	23827034	23827042	8	LOC_Os06g40050
Deletion	Chr6	24414618	24414620	2
Deletion	Chr6	27500344	27500345	1
Deletion	Chr11	28237508	28237509	1	LOC_Os11g46980
Deletion	Chr6	29823289	29823325	36
Deletion	Chr2	32491185	32491200	15	LOC_Os02g53100

Insertions: 6

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Insertion	Chr1	2329880	2329881	2
Insertion	Chr1	31468985	31468985	1	LOC_Os01g54690
Insertion	Chr12	5714279	5714282	4
Insertion	Chr2	5710753	5710753	1
Insertion	Chr3	14444878	14444878	1
Insertion	Chr8	27389256	27389256	1

Inversions: 2

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr2	4388655	4449927	LOC_Os02g08364
Inversion	Chr2	4394509	4449938	LOC_Os02g08364

Translocations: 3

Variant Type	Chromosome	Position 1	Chromosome	Position 2	Number of Genes
Translocation	Chr6	14638022	Chr2	4388664
Translocation	Chr6	14638054	Chr2	4394511
Translocation	Chr12	17220099	Chr8	4874715	2

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