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Mutant Information

Mutant Name	FN1540-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1540-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000326 (Leaf Color) = Normal TO:0000346 (Tiller number) = Normal (Between 75% and 125%) TO:0000430 (Germination Rate) = Normal (Between 75% and 125%) For more information, please see this phenotype file
Mapping (Hover to Zoom-In)

Variant Information

Single base substitutions: 44

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	37110353	A-G	HET	INTERGENIC
SBS	Chr1	41132865	G-T	Homo	INTERGENIC
SBS	Chr1	8151655	T-G	HET	INTERGENIC
SBS	Chr11	12853748	T-A	HET	INTERGENIC
SBS	Chr11	14940458	G-A	Homo	NON_SYNONYMOUS_CODING	LOC_Os11g26110
SBS	Chr11	21050437	A-G	Homo	INTERGENIC
SBS	Chr11	21417941	T-C	HET	INTERGENIC
SBS	Chr11	26671416	G-A	HET	INTERGENIC
SBS	Chr11	27388322	G-T	HET	NON_SYNONYMOUS_CODING	LOC_Os11g45250
SBS	Chr11	9350055	G-T	HET	INTRON
SBS	Chr12	10743748	C-A	HET	INTERGENIC
SBS	Chr12	11108140	A-T	HET	STOP_GAINED	LOC_Os12g19130
SBS	Chr12	21851126	G-A	HET	INTERGENIC
SBS	Chr12	25454977	G-C	HET	INTERGENIC
SBS	Chr2	29084621	T-C	Homo	INTRON
SBS	Chr2	29486601	G-T	HET	INTERGENIC
SBS	Chr2	9346930	A-G	HET	NON_SYNONYMOUS_CODING	LOC_Os02g16400
SBS	Chr3	13559989	T-A	Homo	INTERGENIC
SBS	Chr3	24508700	C-A	HET	INTERGENIC
SBS	Chr4	1299323	A-G	HET	NON_SYNONYMOUS_CODING	LOC_Os04g03120
SBS	Chr4	268987	T-G	Homo	INTERGENIC
SBS	Chr4	27287594	T-A	HET	INTRON
SBS	Chr4	28299450	C-A	HET	INTRON
SBS	Chr5	12827777	A-T	Homo	INTRON
SBS	Chr5	1358777	T-C	HET	INTERGENIC
SBS	Chr5	15219045	C-T	HET	INTERGENIC
SBS	Chr5	24618489	G-A	HET	INTRON
SBS	Chr5	27002677	A-G	HET	INTERGENIC
SBS	Chr6	26052870	G-A	HET	NON_SYNONYMOUS_CODING	LOC_Os06g43340
SBS	Chr6	3785560	G-A	HET	INTRON
SBS	Chr6	3785561	C-A	HET	INTRON
SBS	Chr7	23876059	T-G	HET	INTERGENIC
SBS	Chr7	23952032	T-C	HET	INTERGENIC
SBS	Chr8	13091286	T-C	HET	INTERGENIC
SBS	Chr8	13108028	C-A	HET	INTERGENIC
SBS	Chr8	13108029	C-A	HET	INTERGENIC
SBS	Chr8	14495079	A-C	HET	INTERGENIC
SBS	Chr8	19553328	A-G	HET	INTERGENIC
SBS	Chr8	22561780	A-G	HET	INTERGENIC
SBS	Chr8	2961197	C-A	HET	INTERGENIC
SBS	Chr8	7424005	A-G	HET	INTRON
SBS	Chr9	22548434	G-C	Homo	NON_SYNONYMOUS_CODING	LOC_Os09g39250
SBS	Chr9	2990831	C-A	HET	INTERGENIC
SBS	Chr9	5294694	T-A	HET	INTRON

Deletions: 47

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Deletion	Chr11	1140651	1140652	1
Deletion	Chr2	3773884	3773899	15	LOC_Os02g07330
Deletion	Chr9	4014674	4014679	5
Deletion	Chr12	4764436	4764443	7
Deletion	Chr4	5038570	5038571	1
Deletion	Chr1	5357247	5357251	4
Deletion	Chr8	5807996	5807997	1
Deletion	Chr8	6711427	6711453	26
Deletion	Chr2	8876043	8876049	6	LOC_Os02g15750
Deletion	Chr2	9004995	9005008	13
Deletion	Chr2	9223591	9223602	11	LOC_Os02g16230
Deletion	Chr12	9992697	9992709	12	LOC_Os12g17424
Deletion	Chr4	10158058	10158064	6
Deletion	Chr11	10934850	10934866	16
Deletion	Chr1	11777722	11777736	14
Deletion	Chr3	12094166	12094167	1
Deletion	Chr11	12766849	12766852	3
Deletion	Chr11	12835720	12835725	5
Deletion	Chr3	13348416	13348417	1
Deletion	Chr2	14305804	14305806	2	LOC_Os02g24660
Deletion	Chr8	14544001	14580000	36000	9
Deletion	Chr2	14551685	14551687	2
Deletion	Chr4	14633790	14633791	1
Deletion	Chr8	14811001	14875000	64000	7
Deletion	Chr7	16124930	16124931	1
Deletion	Chr3	16355128	16355148	20
Deletion	Chr2	16589453	16589454	1
Deletion	Chr2	16761704	16761720	16
Deletion	Chr11	18637846	18637847	1
Deletion	Chr6	21091100	21091101	1	LOC_Os06g36070
Deletion	Chr8	22143805	22143818	13
Deletion	Chr8	22606823	22606859	36
Deletion	Chr8	22985603	22985613	10
Deletion	Chr4	23550883	23550884	1
Deletion	Chr7	23785377	23785400	23	LOC_Os07g39690
Deletion	Chr6	23952746	23952753	7
Deletion	Chr12	24513920	24513921	1
Deletion	Chr8	24547563	24547571	8
Deletion	Chr6	25488349	25488350	1
Deletion	Chr3	25492868	25492886	18
Deletion	Chr2	25544977	25544978	1
Deletion	Chr5	26272127	26272128	1
Deletion	Chr12	26607112	26607113	1
Deletion	Chr3	27485722	27485724	2
Deletion	Chr1	30816716	30817736	1020
Deletion	Chr1	31626963	31626964	1
Deletion	Chr3	32216685	32216686	1

Insertions: 15

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Insertion	Chr1	12362031	12362034	4
Insertion	Chr1	2377850	2377855	6	LOC_Os01g05064
Insertion	Chr10	7138490	7138490	1
Insertion	Chr12	24258197	24258197	1
Insertion	Chr12	5315490	5315490	1
Insertion	Chr12	6046886	6046886	1
Insertion	Chr2	25564944	25564965	22
Insertion	Chr2	28165371	28165384	14
Insertion	Chr2	28613584	28613635	52
Insertion	Chr3	7404429	7404448	20
Insertion	Chr4	12363255	12363258	4
Insertion	Chr4	2242568	2242568	1
Insertion	Chr5	11182632	11182633	2
Insertion	Chr6	22075505	22075507	3
Insertion	Chr8	20085411	20085412	2

Inversions: 6

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr3	2982898	3181507
Inversion	Chr3	3181515	3280355
Inversion	Chr8	12353779	12999858	LOC_Os08g20570
Inversion	Chr8	12355081	12999888	LOC_Os08g20570
Inversion	Chr5	22515160	27300379
Inversion	Chr5	22515186	27300419

Translocations: 5

Variant Type	Chromosome	Position 1	Chromosome	Position 2	Number of Genes
Translocation	Chr3	2982902	Chr2	26193205	LOC_Os02g43400
Translocation	Chr3	3280348	Chr2	26193894	LOC_Os02g43400
Translocation	Chr11	14321747	Chr8	12353778	LOC_Os08g20570
Translocation	Chr11	14321786	Chr8	12355101	LOC_Os08g20570
Translocation	Chr12	17386184	Chr8	17758594

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