MBKbase, Genotype

Soybean Genotype Search and Summary

Search Locus Genotype

Locus/Sources ID:			Custom Genotyping
For example: MBK Unified Locus (GmaxG00026053), Phytozomev Name (Glyma.10G021400), Phytozomev ID (Glyma.10G021400.Wm82.a2.v1),

WGS Germplasm Name:			Sample Compare Pedigree Compare
For example:

Browse SNP/InDel	Browse Locus
Reference: ALT % >= Missing % <= SNP InDel Chr: Start: End:	Reference: GT Num: ~ [ All Named Traits ] Gene Chr: Start: End:

Locus and SNP/InDel:

Annotation Venn:

Chr	Length^a		Loci^b		SNP Num.^c		InDel Num.^c
Chr	Wm82	ZH13_v1	Wm82	ZH13_v1	Wm82	ZH13_v1	Wm82	ZH13_v1
Chr1	56831624	59644097	2457	2269	847013	824689	119155	179625
Chr2	48577505	51554906	3123	2881	720687	673890	116852	164185
Chr3	45779781	47131600	2649	2438	1049748	892770	144982	203708
Chr4	52389146	53205140	2574	2327	954187	847582	130546	181980
Chr5	42234498	44072942	2491	2344	610231	568654	96011	134224
Chr6	51416486	52461415	3258	2955	1041076	858777	149005	204993
Chr7	44630646	47739153	2743	2578	730839	671829	117312	166001
Chr8	47837940	50214344	3679	3455	787748	713057	132156	182134
Chr9	50189764	51981488	2865	2612	833341	720249	127612	175412
Chr10	51566898	53404895	2989	2765	804946	733653	124580	174850
Chr11	34766867	40685020	2570	2542	512453	557597	85561	130598
Chr12	40091314	43299438	2425	2179	655815	635345	98124	143150
Chr13	45874162	46899706	3730	3456	841338	719295	145460	191358
Chr14	49042192	51865536	2245	2069	918806	864733	123146	184878
Chr15	51756343	54175411	2774	2545	1215842	955677	154883	212905
Chr16	37887014	38219656	2223	1978	922942	765728	137543	191333
Chr17	41641366	42702338	2627	2498	691976	609288	109072	150393
Chr18	58018742	60216011	3023	2692	1443516	1203732	195829	272050
Chr19	50746916	52410246	2642	2482	881815	776852	122799	174267
Chr20	47904181	52417242	2502	2331	872891	806162	121769	174375
Total	949183385	994300584	55589	51396	17337210	15399559	2552397	3592419

^aGlycine max reference genome:
(1) Wm82 (Williams82/Gmax_275), Glyma.Wm82.a2.v1
(1) ZH13_v1 (Zhong Huang No.13), Gmax_ZH13.v1

^cTotal 809 WGS samples be used for call SNP/InDel which mapped Nip and R498 reference genome respectively, SNP (AF >= 0) and InDel (AF >= 0) were used for statistics.

Locus Model for Genotyping:	Locus Statistics:
When a locus containsmore than one gene models, different annotations for the same genome can have different boundaries on the same gene. The overlapping annotations were also integrated under the same Locus ID.	There are totally 95,325 loci for both Nip and R498 genome, with an average length of 3kb. 97% of loci sequences are shorter than 10kb, and 28% shorter than 1kb.
Locus Genotyping and Show:	Genotype Statistics:
One genotype (GT) is same or differs from the reference sequence (REF), and the differs including both SNP and InDel (ALT). A Locus GT is an ALT group which located in the region of a gene locus. All GT be shown in a table, first row is reference genome position, and second row is reference base. Genotypes are encoded GT1 to GT5, and capital base means homozygous, lowercase means heterozygous, '-' means missing. In table, charts 'N' represents multiple continuous bases, which means deletion or insertion. Most cultivated rice are homozygous, so the genotype is same as the conception of haplotype and allele.	A total of 5280 WGS samples were used to call locus genotype (allele), and the genotype with sample number >=10 were summarized. For each locus, the number of genotypes can represent the number of alleles in the population.