# 2. Search Genotypes

Note that our QTL/trait of interest is in this region:
**<u>Chr4:4662701-4670717</u>**

You can begin by searching for SNPS that lie within this region using the 3k rice dataset. There are 4 SNP Sets available:

- **<u>3K All</u>:** 32 million full 3K RG SNPs Dataset

  This SNP Set contains the full set of 32 million biallelic & multiallelic SNP.

  Total SNPs: 32,064,217

  Samples : 3024

- **<u>3kbase</u>:** 18 million base SNP

  The Base SNP set of ~18 million SNPs was created from the ~29 million biallelic SNPs subset from the 32M full SNP set by removing SNPs with excess of heterozygous calls.

- **<u>3K core</u>**: 404k CoreSNP dataset

  The Core SNP set was obtained from the filtered SNP set by applying two-step LD pruning procedure as follows:

  1.  LD pruning with window size 10kb, step 1 SNP, R2 threshold 0.8

  2.  LD pruning with window size 50 SNPs, step 1 SNP, R2 threshold 0.8

- **<u>3k filtered</u>:** 4.8million filtered SNP dataset

  The filtered SNP set was obtained from the Base SNP set by applying the following filtering criteria:

  1.  alternative allele frequency at least 0.01

  2.  proportion of missing calls per SNP at most 0.2

You may use different SNP sets but for this hands-on, we will use the **"3Kbase" SNP set.**

In the Chromosome, put **"Chr4"**, in Start use **"4662701"** and end **"4670717".**

Click **"Search"** to retrieve the positions within this region within the 3KRG accessions.

```{image} /_static/image2.png
:alt: Search Genotype
:width: 600px
:class: zoomable
:align: center
```
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Knowledge Check: How many SNPs were retrieved within the given region?