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Mutant Information

Mutant Name	FN2090-S [Download]
Generation	M2
Genus Species	Oryza Sativa
Cultivar	Kitaake
Alignment File (BAM File)	Download FN2090-S Alignment File
Seed Availability	Yes [Order Seeds]
Phenotype	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: 8

Variant Type	Chromosome	Position	Change	Genotype	Effect	Gene Affected
SBS	Chr10	5459556	A-G	HET
SBS	Chr10	8959811	G-A	HET	NON_SYNONYMOUS_CODING	LOC_Os10g17724
SBS	Chr4	15901993	G-A	Homo
SBS	Chr4	15968511	G-A	Homo
SBS	Chr5	16056849	C-A	HET
SBS	Chr5	19335557	A-G	HET
SBS	Chr6	20607861	G-A	HET
SBS	Chr6	3652652	G-A	HET

Deletions: 102

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Deletion	Chr11	190001	219000	28999	4
Deletion	Chr10	470001	484000	13999	4
Deletion	Chr5	577001	596000	18999	3
Deletion	Chr6	705001	738000	32999	2
Deletion	Chr11	749001	786000	36999	6
Deletion	Chr9	1557001	1596000	38999	8
Deletion	Chr8	1693001	1712000	18999	LOC_Os08g03620
Deletion	Chr8	1765001	1796000	30999	7
Deletion	Chr3	1986001	2007000	20999	3
Deletion	Chr6	2101001	2136000	34999	4
Deletion	Chr5	2106001	2159000	52999	4
Deletion	Chr5	2281001	2301000	19999	LOC_Os05g04810
Deletion	Chr11	2390001	2418000	27999	2
Deletion	Chr7	2765001	2786000	20999	4
Deletion	Chr7	2820001	2893000	72999	10
Deletion	Chr12	3373001	3386000	12999	2
Deletion	Chr12	3551001	3573000	21999	5
Deletion	Chr3	3598001	3628000	29999	6
Deletion	Chr11	3763001	3782000	18999
Deletion	Chr3	3883001	3915000	31999	7
Deletion	Chr8	4216001	4262000	45999	7
Deletion	Chr12	4572001	4629000	56999	5
Deletion	Chr2	5353001	5375000	21999	5
Deletion	Chr8	5760001	5806000	45999	5
Deletion	Chr7	5981001	5996000	14999	2
Deletion	Chr6	6283001	6301000	17999	LOC_Os06g11850
Deletion	Chr9	6347001	6368000	20999	3
Deletion	Chr1	6833001	6866000	32999	5
Deletion	Chr10	7247001	7273000	25999	5
Deletion	Chr9	8175001	8193000	17999	3
Deletion	Chr9	8954001	8966000	11999	LOC_Os09g14950
Deletion	Chr12	9270001	9295000	24999	5
Deletion	Chr11	9417705	9417709	4	LOC_Os11g16990
Deletion	Chr9	9904001	9924000	19999	5
Deletion	Chr1	10765001	10789000	23999	5
Deletion	Chr11	10817001	10857000	39999	7
Deletion	Chr4	11035001	11051000	15999	3
Deletion	Chr1	11115001	11137000	21999	2
Deletion	Chr1	11535001	11583000	47999	5
Deletion	Chr11	11574001	11595000	20999	2
Deletion	Chr9	12681001	12704000	22999	6
Deletion	Chr11	13223001	13254000	30999	5
Deletion	Chr4	13259001	13296000	36999	6
Deletion	Chr12	13495001	13561000	65999	9
Deletion	Chr2	13509001	13523000	13999	2
Deletion	Chr8	14332001	14348000	15999	2
Deletion	Chr9	15176001	15202000	25999	3
Deletion	Chr11	15281001	15303000	21999	5
Deletion	Chr10	15525001	15547000	21999	6
Deletion	Chr9	16092001	16224000	131999	13
Deletion	Chr3	16139001	16166000	26999	4
Deletion	Chr7	16732001	16770000	37999	8
Deletion	Chr9	17707001	17734000	26999	2
Deletion	Chr10	17826001	17847000	20999	LOC_Os10g33750
Deletion	Chr12	17852001	17903000	50999	8
Deletion	Chr4	18332001	18371000	38999	5
Deletion	Chr7	19028001	19082000	53999	12
Deletion	Chr2	19110001	19154000	43999	4
Deletion	Chr11	19227001	19284000	56999	8
Deletion	Chr4	19458001	19541000	82999	4
Deletion	Chr12	19969001	19998000	28999	3
Deletion	Chr5	20445001	20546000	100999	17
Deletion	Chr5	20680001	20720000	39999	4
Deletion	Chr10	20899001	20932000	32999	3
Deletion	Chr11	21352001	21362000	9999	2
Deletion	Chr12	21505001	21524000	18999	3
Deletion	Chr2	21615001	21634000	18999	3
Deletion	Chr8	21639001	21697000	57999	6
Deletion	Chr7	21827001	21866000	38999	7
Deletion	Chr1	21904691	21904692	1
Deletion	Chr12	22560001	22576000	15999	2
Deletion	Chr12	22604001	22651000	46999	6
Deletion	Chr12	22829315	22829316	1
Deletion	Chr12	23739001	23765000	25999	5
Deletion	Chr12	23855001	23874000	18999	3
Deletion	Chr2	23882001	23905000	22999	5
Deletion	Chr2	23951001	23963000	11999	LOC_Os02g39660
Deletion	Chr3	24118001	24135000	16999	3
Deletion	Chr3	24642001	24692000	49999	5
Deletion	Chr12	24666001	24681000	14999	LOC_Os12g39920
Deletion	Chr12	24785001	24838000	52999	7
Deletion	Chr12	24882001	24905000	22999	4
Deletion	Chr12	25140001	25163000	22999	LOC_Os12g40630
Deletion	Chr11	26145001	26162000	16999	2
Deletion	Chr1	26421326	26421339	13	LOC_Os01g46430
Deletion	Chr2	26805001	26837000	31999	5
Deletion	Chr8	27184001	27284000	99999	13
Deletion	Chr3	27316001	27348000	31999	5
Deletion	Chr2	28565001	28660000	94999	16
Deletion	Chr4	28747001	28769000	21999	3
Deletion	Chr6	29622001	29655000	32999	2
Deletion	Chr3	30425001	30476000	50999	8
Deletion	Chr6	30963001	30994000	30999	5
Deletion	Chr1	32366001	32394000	27999	7
Deletion	Chr1	33260001	33363000	102999	13
Deletion	Chr3	33412093	33412094	1
Deletion	Chr2	34067001	34187000	119999	17
Deletion	Chr1	35128911	35128912	1
Deletion	Chr1	36501001	36536000	34999	4
Deletion	Chr1	37338001	37353000	14999	3
Deletion	Chr1	39355706	39355707	1
Deletion	Chr1	40419001	40437000	17999

Insertions: 10

Variant Type	Chromosome	Start	End	Size (bp)	Number of Genes
Insertion	Chr10	22281218	22281219	2
Insertion	Chr12	14044985	14044985	1
Insertion	Chr2	10627343	10627347	5
Insertion	Chr2	8031873	8031873	1
Insertion	Chr4	31914422	31914423	2
Insertion	Chr6	16242922	16242922	1
Insertion	Chr6	5718466	5718472	7
Insertion	Chr8	18376583	18376584	2
Insertion	Chr8	28191559	28191559	1	LOC_Os08g44890
Insertion	Chr9	19095800	19095819	20

Inversions: 55

Variant Type	Chromosome	Position 1	Position 2	Number of Genes
Inversion	Chr7	639343	639635
Inversion	Chr6	643073	643415
Inversion	Chr7	1078855	1079028
Inversion	Chr1	2226620	2226794	LOC_Os01g04840
Inversion	Chr12	2323019	2323316
Inversion	Chr5	2907342	2907740	LOC_Os05g05810
Inversion	Chr3	3206209	3206558	LOC_Os03g06410
Inversion	Chr3	3272948	3273306	LOC_Os03g06520
Inversion	Chr8	4903507	4903717
Inversion	Chr1	5116269	5116654	LOC_Os01g09860
Inversion	Chr7	5856381	5856493	LOC_Os07g10770
Inversion	Chr11	5997263	5997491	LOC_Os11g10870
Inversion	Chr2	6469458	6469778	LOC_Os02g12400
Inversion	Chr1	6733617	6733760	LOC_Os01g12330
Inversion	Chr5	7679311	7679544
Inversion	Chr6	11395434	11395599	LOC_Os06g19920
Inversion	Chr11	11761999	11762203
Inversion	Chr8	13368836	13368982
Inversion	Chr4	13587794	13588052	LOC_Os04g23760
Inversion	Chr10	15261709	15262156	2
Inversion	Chr3	15395021	15395146
Inversion	Chr9	15610412	15610571
Inversion	Chr1	16769281	16776548
Inversion	Chr3	17438779	17439018	LOC_Os03g30550
Inversion	Chr6	17444113	17444307
Inversion	Chr5	18308171	18308615
Inversion	Chr10	18627906	18628149	LOC_Os10g34890
Inversion	Chr10	19029246	19029436	LOC_Os10g35570
Inversion	Chr11	19587183	19587295
Inversion	Chr4	20758512	20758634	LOC_Os04g34270
Inversion	Chr9	20934204	20934692	LOC_Os09g36270
Inversion	Chr5	21693048	21693442	LOC_Os05g37120
Inversion	Chr9	21707700	21707942	2
Inversion	Chr3	21742206	21742444
Inversion	Chr9	21780725	21780929	LOC_Os09g37800
Inversion	Chr8	21953733	21953991	LOC_Os08g34879
Inversion	Chr3	22167056	22167168	LOC_Os03g39860
Inversion	Chr5	22486934	22487180
Inversion	Chr1	23922685	23923112	LOC_Os01g42220
Inversion	Chr2	25459920	25460355	LOC_Os02g42330
Inversion	Chr3	25463879	25464073	LOC_Os03g45120
Inversion	Chr2	26024818	26025140
Inversion	Chr3	26620708	26620913
Inversion	Chr8	27211725	27211870	LOC_Os08g43060
Inversion	Chr8	28311476	28311720	LOC_Os08g45090
Inversion	Chr3	28432216	28432375
Inversion	Chr6	29979547	29979736	LOC_Os06g49500
Inversion	Chr6	30036645	30036747	LOC_Os06g49640
Inversion	Chr2	30042692	30042888
Inversion	Chr1	30255014	30255127
Inversion	Chr1	33779914	33780122
Inversion	Chr3	34895531	34896105	LOC_Os03g61530
Inversion	Chr1	35984515	35984658	LOC_Os01g62160
Inversion	Chr3	36292701	36293001	LOC_Os03g64230
Inversion	Chr1	38027083	38027387	LOC_Os01g65520

Translocations: 8

Variant Type	Chromosome	Position 1	Chromosome	Position 2	Number of Genes
Translocation	Chr11	3290075	Chr1	1398457
Translocation	Chr10	3842500	Chr9	17291579
Translocation	Chr11	5074004	Chr7	420971	LOC_Os11g09460
Translocation	Chr5	5767540	Chr1	6544940
Translocation	Chr8	10058150	Chr6	15131928
Translocation	Chr10	16098183	Chr7	4798226	LOC_Os10g30870
Translocation	Chr8	16481338	Chr6	15183919
Translocation	Chr12	20135618	Chr8	11589499	2

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