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Mutant Information

Mutant Name	FN1421-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN1421-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	TO:0000326 (Leaf Color) = Normal TO:0000137 (Days to heading) = Normal (Between 75% and 125%) TO:0000346 (Tiller number) = Normal (Between 75% and 125%) TO:0000430 (Germination Rate) = Very Low (Below 24%) For more information, please see this phenotype file

Variant Information

Single base substitutions: 36

Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

SBS Chr1 1931432 C-T Hetero INTERGENIC
SBS Chr1 20518154 C-T Homo INTERGENIC
SBS Chr1 28959554 T-C Hetero INTERGENIC
SBS Chr1 32003774 C-T Hetero INTERGENIC
SBS Chr1 35782458 A-T Homo INTRON
SBS Chr2 2221153 A-T Hetero INTERGENIC
SBS Chr2 19292604 A-G Hetero INTERGENIC
SBS Chr3 11686929 C-A Hetero UTR_5_PRIME
SBS Chr4 1455266 T-A Hetero INTERGENIC
SBS Chr4 16494332 C-A Hetero INTRON
SBS Chr5 5843708 G-T Hetero INTERGENIC
SBS Chr5 16531046 C-A Homo NON_SYNONYMOUS_CODING OsKitaake05g126400
SBS Chr5 21317067 G-A Hetero INTERGENIC
SBS Chr7 5736072 C-T Hetero INTERGENIC
SBS Chr7 9975232 A-G Hetero INTERGENIC
SBS Chr7 12902247 C-T Hetero INTERGENIC
SBS Chr7 15024253 C-T Hetero INTERGENIC
SBS Chr7 28733423 C-T Hetero INTERGENIC
SBS Chr8 9331923 C-T Hetero INTERGENIC
SBS Chr8 13101510 C-A Hetero INTERGENIC
SBS Chr8 13247444 G-C Hetero INTERGENIC
SBS Chr8 13268419 C-A Hetero INTRON
SBS Chr8 17639987 G-T Hetero INTERGENIC
SBS Chr8 18810422 A-T Hetero INTERGENIC
SBS Chr8 27509278 T-C Homo INTERGENIC
SBS Chr8 27761250 A-G Homo INTRON
SBS Chr9 15606879 C-T Hetero INTERGENIC
SBS Chr9 15670153 C-G Hetero INTERGENIC
SBS Chr10 759033 T-A Hetero INTERGENIC
SBS Chr11 17329228 C-T Homo INTERGENIC
SBS Chr11 23303435 T-C Hetero NON_SYNONYMOUS_CODING OsKitaake11g185600
SBS Chr11 29419607 G-A Hetero INTERGENIC
SBS Chr12 1845881 C-A Hetero INTERGENIC
SBS Chr12 9008677 A-T Homo INTERGENIC
SBS Chr12 12881336 C-T Hetero INTERGENIC
SBS Chr12 19090294 T-C Hetero INTERGENIC

Deletions: 126

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Deletion Chr6 85068 85076 8
Deletion Chr5 164001 190000 25999 7
Deletion Chr10 345001 355000 9999 2
Deletion Chr2 591001 612000 20999 2
Deletion Chr5 1121001 1138000 16999 3
Deletion Chr10 1377344 1377345 1
Deletion Chr2 1708001 1741000 32999 4
Deletion Chr3 1844001 1860000 15999 2
Deletion Chr2 2304015 2304024 9
Deletion Chr4 3356001 3373000 16999 OsKitaake04g017201
Deletion Chr9 3712001 3728000 15999
Deletion Chr10 4043001 4053000 9999 OsKitaake10g030600
Deletion Chr10 4143001 4173000 29999 2
Deletion Chr7 4459001 4476000 16999 2
Deletion Chr8 5296001 5309000 12999 3
Deletion Chr2 5458001 5467000 8999 2
Deletion Chr7 5988001 6002000 13999 OsKitaake07g072200
Deletion Chr5 6194001 6212000 17999 OsKitaake05g064100
Deletion Chr7 6224001 6232000 7999 OsKitaake07g073800
Deletion Chr8 6264001 6279000 14999 OsKitaake08g067400
Deletion Chr2 7436001 7453000 16999
Deletion Chr6 7610001 7624000 13999
Deletion Chr9 7829001 7854000 24999 4
Deletion Chr2 8387001 8399000 11999 OsKitaake02g106600
Deletion Chr9 8750001 8777000 26999 OsKitaake09g051400
Deletion Chr4 8930001 8950000 19999 OsKitaake04g046100
Deletion Chr7 9015001 9026000 10999 2
Deletion Chr2 9029001 9049000 19999 OsKitaake02g113050
Deletion Chr11 9276001 9286000 9999 3
Deletion Chr2 9327001 9343000 15999 OsKitaake02g116000
Deletion Chr1 9650001 9660000 9999 OsKitaake01g123400
Deletion Chr6 9765001 9777000 11999 OsKitaake06g114000
Deletion Chr6 9915001 9933000 17999 OsKitaake06g115100
Deletion Chr10 10114848 10114850 2
Deletion Chr4 10192001 10218000 25999
Deletion Chr10 10309001 10329000 19999 3
Deletion Chr2 10502001 10532000 29999 3
Deletion Chr2 10580001 10591000 10999 2
Deletion Chr7 10728001 10746000 17999 3
Deletion Chr6 10916001 10927000 10999 OsKitaake06g121600
Deletion Chr11 10993001 11007000 13999
Deletion Chr7 11244001 11259000 14999 OsKitaake07g105700
Deletion Chr12 11444001 11460000 15999
Deletion Chr12 11648001 11656000 7999
Deletion Chr11 11665001 11855000 189999 13
Deletion Chr4 12019001 12033000 13999
Deletion Chr11 12132001 12141000 8999 OsKitaake11g112400
Deletion Chr2 12495001 12510000 14999 3
Deletion Chr9 12606001 12621000 14999
Deletion Chr5 13039001 13053000 13999 OsKitaake05g101400
Deletion Chr5 13070001 13080000 9999 OsKitaake05g101700
Deletion Chr3 13106001 13124000 17999 2
Deletion Chr10 13295285 13295287 2
Deletion Chr5 13807633 13807635 2
Deletion Chr4 13953001 13969000 15999 OsKitaake04g067000
Deletion Chr1 13996001 14010000 13999 2
Deletion Chr3 14101001 14112000 10999 OsKitaake03g184300
Deletion Chr3 14506001 14517000 10999 OsKitaake03g189000
Deletion Chr10 14598001 14612000 13999 OsKitaake10g091900
Deletion Chr10 14623001 14637000 13999 2
Deletion Chr9 14860235 14860237 2
Deletion Chr9 14992001 15005000 12999
Deletion Chr11 15024001 15037000 12999 OsKitaake11g123300
Deletion Chr6 15222001 15233000 10999
Deletion Chr8 15244001 15259000 14999 OsKitaake08g119000
Deletion Chr2 15368001 15378000 9999
Deletion Chr11 15545001 15589000 43999
Deletion Chr3 15546001 15584000 37999
Deletion Chr2 16304001 16321000 16999 OsKitaake02g167700
Deletion Chr7 16382001 16409000 26999
Deletion Chr8 16565001 16581000 15999 OsKitaake08g127300
Deletion Chr5 16860001 16881000 20999 2
Deletion Chr12 17377001 17401000 23999 3
Deletion Chr1 17464001 17491000 26999 OsKitaake01g179300
Deletion Chr6 17733001 17758000 24999 OsKitaake06g163600
Deletion Chr8 18074001 18111000 36999 2
Deletion Chr7 18216001 18228000 11999 2
Deletion Chr1 18816001 18826000 9999 3
Deletion Chr10 19010001 19019000 8999 OsKitaake10g136000
Deletion Chr5 19092001 19113000 20999 2
Deletion Chr8 19690001 19706000 15999 OsKitaake08g144800
Deletion Chr3 20273001 20289000 15999
Deletion Chr4 20584001 20603000 18999 OsKitaake04g110900
Deletion Chr1 20688001 20703000 14999 OsKitaake01g202700
Deletion Chr8 20942001 20954000 11999 3
Deletion Chr1 21044001 21053000 8999 2
Deletion Chr1 21242001 21253000 10999
Deletion Chr9 21306001 21332000 25999 3
Deletion Chr1 21547001 21575000 27999
Deletion Chr2 22553001 22570000 16999 3
Deletion Chr4 22742001 22752000 9999 3
Deletion Chr1 23752001 23776000 23999 OsKitaake01g228000
Deletion Chr12 23796001 23821000 24999 3
Deletion Chr12 23830001 23864000 33999 5
Deletion Chr10 24020001 24035000 14999 4
Deletion Chr6 24031001 24047000 15999
Deletion Chr12 24381001 24405000 23999 4
Deletion Chr1 24582001 24602000 19999 2
Deletion Chr8 24966001 24992000 25999 OsKitaake08g194166
Deletion Chr12 25021001 25035000 13999 OsKitaake12g202800
Deletion Chr11 25110001 25125000 14999 2
Deletion Chr12 25395001 25415000 19999 7
Deletion Chr8 25757001 25770000 12999
Deletion Chr3 25804001 25813000 8999 OsKitaake03g272200
Deletion Chr1 26055001 26067000 11999
Deletion Chr3 26450649 26450654 5
Deletion Chr7 26841001 26861000 19999 2
Deletion Chr8 27058001 27071000 12999 2
Deletion Chr3 27428001 27443000 14999 3
Deletion Chr8 27761150 27761176 26
Deletion Chr8 27889001 27905000 15999 2
Deletion Chr5 28109001 28124000 14999 2
Deletion Chr1 28149001 28159000 9999 3
Deletion Chr3 28181001 28203000 21999 OsKitaake03g291400
Deletion Chr5 28978830 28978831 1
Deletion Chr4 29083001 29098000 14999 OsKitaake04g219900
Deletion Chr6 29196001 29206000 9999 2
Deletion Chr2 29996068 29996081 13 OsKitaake02g304500
Deletion Chr6 30573001 30601000 27999 4
Deletion Chr6 30826001 30833000 6999 OsKitaake06g291700
Deletion Chr3 31016001 31031000 14999 OsKitaake03g325700
Deletion Chr3 37293024 37293026 2
Deletion Chr3 37706001 37720000 13999 OsKitaake03g423700
Deletion Chr1 41444001 41451000 6999 2
Deletion Chr1 41460001 41481000 20999
Deletion Chr1 44224001 44238000 13999 2

Insertions: 6

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Insertion Chr8 11619652 11619657 4
Insertion Chr8 21322688 21322692 3
Insertion Chr10 2987395 2987398 2
Insertion Chr10 21959930 21959933 2
Insertion Chr12 1136387 1136390 2
Insertion Chr12 12111760 12111765 4

Inversions: 5

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Inversion Chr9 947745 971123 2
Inversion Chr9 947791 971122 OsKitaake09g006112
Inversion Chr12 7672644 7673831
Inversion Chr1 42622212 42772206
Inversion Chr1 42772209 43171184

Translocations: 4

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes

Translocation Chr11 22216184 Chr7 28523374 2
Translocation Chr11 22216186 Chr7 28523744 2
Translocation Chr12 25279429 Chr7 28523374 OsKitaake07g271700
Translocation Chr12 25279432 Chr7 28523742 OsKitaake07g271800

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr1	1931432	C-T	Hetero	INTERGENIC
SBS	Chr1	20518154	C-T	Homo	INTERGENIC
SBS	Chr1	28959554	T-C	Hetero	INTERGENIC
SBS	Chr1	32003774	C-T	Hetero	INTERGENIC
SBS	Chr1	35782458	A-T	Homo	INTRON
SBS	Chr2	2221153	A-T	Hetero	INTERGENIC
SBS	Chr2	19292604	A-G	Hetero	INTERGENIC
SBS	Chr3	11686929	C-A	Hetero	UTR_5_PRIME
SBS	Chr4	1455266	T-A	Hetero	INTERGENIC
SBS	Chr4	16494332	C-A	Hetero	INTRON
SBS	Chr5	5843708	G-T	Hetero	INTERGENIC
SBS	Chr5	16531046	C-A	Homo	NON_SYNONYMOUS_CODING	OsKitaake05g126400
SBS	Chr5	21317067	G-A	Hetero	INTERGENIC
SBS	Chr7	5736072	C-T	Hetero	INTERGENIC
SBS	Chr7	9975232	A-G	Hetero	INTERGENIC
SBS	Chr7	12902247	C-T	Hetero	INTERGENIC
SBS	Chr7	15024253	C-T	Hetero	INTERGENIC
SBS	Chr7	28733423	C-T	Hetero	INTERGENIC
SBS	Chr8	9331923	C-T	Hetero	INTERGENIC
SBS	Chr8	13101510	C-A	Hetero	INTERGENIC
SBS	Chr8	13247444	G-C	Hetero	INTERGENIC
SBS	Chr8	13268419	C-A	Hetero	INTRON
SBS	Chr8	17639987	G-T	Hetero	INTERGENIC
SBS	Chr8	18810422	A-T	Hetero	INTERGENIC
SBS	Chr8	27509278	T-C	Homo	INTERGENIC
SBS	Chr8	27761250	A-G	Homo	INTRON
SBS	Chr9	15606879	C-T	Hetero	INTERGENIC
SBS	Chr9	15670153	C-G	Hetero	INTERGENIC
SBS	Chr10	759033	T-A	Hetero	INTERGENIC
SBS	Chr11	17329228	C-T	Homo	INTERGENIC
SBS	Chr11	23303435	T-C	Hetero	NON_SYNONYMOUS_CODING	OsKitaake11g185600
SBS	Chr11	29419607	G-A	Hetero	INTERGENIC
SBS	Chr12	1845881	C-A	Hetero	INTERGENIC
SBS	Chr12	9008677	A-T	Homo	INTERGENIC
SBS	Chr12	12881336	C-T	Hetero	INTERGENIC
SBS	Chr12	19090294	T-C	Hetero	INTERGENIC

Variant Type	Chromosome	Start	End	Size(bp)	Number of Genes
Deletion	Chr6	85068	85076	8
Deletion	Chr5	164001	190000	25999	7
Deletion	Chr10	345001	355000	9999	2
Deletion	Chr2	591001	612000	20999	2
Deletion	Chr5	1121001	1138000	16999	3
Deletion	Chr10	1377344	1377345	1
Deletion	Chr2	1708001	1741000	32999	4
Deletion	Chr3	1844001	1860000	15999	2
Deletion	Chr2	2304015	2304024	9
Deletion	Chr4	3356001	3373000	16999	OsKitaake04g017201
Deletion	Chr9	3712001	3728000	15999
Deletion	Chr10	4043001	4053000	9999	OsKitaake10g030600
Deletion	Chr10	4143001	4173000	29999	2
Deletion	Chr7	4459001	4476000	16999	2
Deletion	Chr8	5296001	5309000	12999	3
Deletion	Chr2	5458001	5467000	8999	2
Deletion	Chr7	5988001	6002000	13999	OsKitaake07g072200
Deletion	Chr5	6194001	6212000	17999	OsKitaake05g064100
Deletion	Chr7	6224001	6232000	7999	OsKitaake07g073800
Deletion	Chr8	6264001	6279000	14999	OsKitaake08g067400
Deletion	Chr2	7436001	7453000	16999
Deletion	Chr6	7610001	7624000	13999
Deletion	Chr9	7829001	7854000	24999	4
Deletion	Chr2	8387001	8399000	11999	OsKitaake02g106600
Deletion	Chr9	8750001	8777000	26999	OsKitaake09g051400
Deletion	Chr4	8930001	8950000	19999	OsKitaake04g046100
Deletion	Chr7	9015001	9026000	10999	2
Deletion	Chr2	9029001	9049000	19999	OsKitaake02g113050
Deletion	Chr11	9276001	9286000	9999	3
Deletion	Chr2	9327001	9343000	15999	OsKitaake02g116000
Deletion	Chr1	9650001	9660000	9999	OsKitaake01g123400
Deletion	Chr6	9765001	9777000	11999	OsKitaake06g114000
Deletion	Chr6	9915001	9933000	17999	OsKitaake06g115100
Deletion	Chr10	10114848	10114850	2
Deletion	Chr4	10192001	10218000	25999
Deletion	Chr10	10309001	10329000	19999	3
Deletion	Chr2	10502001	10532000	29999	3
Deletion	Chr2	10580001	10591000	10999	2
Deletion	Chr7	10728001	10746000	17999	3
Deletion	Chr6	10916001	10927000	10999	OsKitaake06g121600
Deletion	Chr11	10993001	11007000	13999
Deletion	Chr7	11244001	11259000	14999	OsKitaake07g105700
Deletion	Chr12	11444001	11460000	15999
Deletion	Chr12	11648001	11656000	7999
Deletion	Chr11	11665001	11855000	189999	13
Deletion	Chr4	12019001	12033000	13999
Deletion	Chr11	12132001	12141000	8999	OsKitaake11g112400
Deletion	Chr2	12495001	12510000	14999	3
Deletion	Chr9	12606001	12621000	14999
Deletion	Chr5	13039001	13053000	13999	OsKitaake05g101400
Deletion	Chr5	13070001	13080000	9999	OsKitaake05g101700
Deletion	Chr3	13106001	13124000	17999	2
Deletion	Chr10	13295285	13295287	2
Deletion	Chr5	13807633	13807635	2
Deletion	Chr4	13953001	13969000	15999	OsKitaake04g067000
Deletion	Chr1	13996001	14010000	13999	2
Deletion	Chr3	14101001	14112000	10999	OsKitaake03g184300
Deletion	Chr3	14506001	14517000	10999	OsKitaake03g189000
Deletion	Chr10	14598001	14612000	13999	OsKitaake10g091900
Deletion	Chr10	14623001	14637000	13999	2
Deletion	Chr9	14860235	14860237	2
Deletion	Chr9	14992001	15005000	12999
Deletion	Chr11	15024001	15037000	12999	OsKitaake11g123300
Deletion	Chr6	15222001	15233000	10999
Deletion	Chr8	15244001	15259000	14999	OsKitaake08g119000
Deletion	Chr2	15368001	15378000	9999
Deletion	Chr11	15545001	15589000	43999
Deletion	Chr3	15546001	15584000	37999
Deletion	Chr2	16304001	16321000	16999	OsKitaake02g167700
Deletion	Chr7	16382001	16409000	26999
Deletion	Chr8	16565001	16581000	15999	OsKitaake08g127300
Deletion	Chr5	16860001	16881000	20999	2
Deletion	Chr12	17377001	17401000	23999	3
Deletion	Chr1	17464001	17491000	26999	OsKitaake01g179300
Deletion	Chr6	17733001	17758000	24999	OsKitaake06g163600
Deletion	Chr8	18074001	18111000	36999	2
Deletion	Chr7	18216001	18228000	11999	2
Deletion	Chr1	18816001	18826000	9999	3
Deletion	Chr10	19010001	19019000	8999	OsKitaake10g136000
Deletion	Chr5	19092001	19113000	20999	2
Deletion	Chr8	19690001	19706000	15999	OsKitaake08g144800
Deletion	Chr3	20273001	20289000	15999
Deletion	Chr4	20584001	20603000	18999	OsKitaake04g110900
Deletion	Chr1	20688001	20703000	14999	OsKitaake01g202700
Deletion	Chr8	20942001	20954000	11999	3
Deletion	Chr1	21044001	21053000	8999	2
Deletion	Chr1	21242001	21253000	10999
Deletion	Chr9	21306001	21332000	25999	3
Deletion	Chr1	21547001	21575000	27999
Deletion	Chr2	22553001	22570000	16999	3
Deletion	Chr4	22742001	22752000	9999	3
Deletion	Chr1	23752001	23776000	23999	OsKitaake01g228000
Deletion	Chr12	23796001	23821000	24999	3
Deletion	Chr12	23830001	23864000	33999	5
Deletion	Chr10	24020001	24035000	14999	4
Deletion	Chr6	24031001	24047000	15999
Deletion	Chr12	24381001	24405000	23999	4
Deletion	Chr1	24582001	24602000	19999	2
Deletion	Chr8	24966001	24992000	25999	OsKitaake08g194166
Deletion	Chr12	25021001	25035000	13999	OsKitaake12g202800
Deletion	Chr11	25110001	25125000	14999	2
Deletion	Chr12	25395001	25415000	19999	7
Deletion	Chr8	25757001	25770000	12999
Deletion	Chr3	25804001	25813000	8999	OsKitaake03g272200
Deletion	Chr1	26055001	26067000	11999
Deletion	Chr3	26450649	26450654	5
Deletion	Chr7	26841001	26861000	19999	2
Deletion	Chr8	27058001	27071000	12999	2
Deletion	Chr3	27428001	27443000	14999	3
Deletion	Chr8	27761150	27761176	26
Deletion	Chr8	27889001	27905000	15999	2
Deletion	Chr5	28109001	28124000	14999	2
Deletion	Chr1	28149001	28159000	9999	3
Deletion	Chr3	28181001	28203000	21999	OsKitaake03g291400
Deletion	Chr5	28978830	28978831	1
Deletion	Chr4	29083001	29098000	14999	OsKitaake04g219900
Deletion	Chr6	29196001	29206000	9999	2
Deletion	Chr2	29996068	29996081	13	OsKitaake02g304500
Deletion	Chr6	30573001	30601000	27999	4
Deletion	Chr6	30826001	30833000	6999	OsKitaake06g291700
Deletion	Chr3	31016001	31031000	14999	OsKitaake03g325700
Deletion	Chr3	37293024	37293026	2
Deletion	Chr3	37706001	37720000	13999	OsKitaake03g423700
Deletion	Chr1	41444001	41451000	6999	2
Deletion	Chr1	41460001	41481000	20999
Deletion	Chr1	44224001	44238000	13999	2

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr9	947745	971123	2
Inversion	Chr9	947791	971122	OsKitaake09g006112
Inversion	Chr12	7672644	7673831
Inversion	Chr1	42622212	42772206
Inversion	Chr1	42772209	43171184

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Variant Type

Chromosome

Position

Change

Genotype

Effect

Gene Affected

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Variant Type

Chromosome

Start

End

Size(bp)

Number of Genes

Variant Type

Chromosome

Position 1

Position 2

Number of Genes

Variant Type

Chromosome

Position 1

Chromosome

Position 2

Number of Genes