Rice Genome Sequencing and Variant Calling-10X Test
Short Name: Rice Genome Seq 10X
Also known as: Rice Genome Sequencing, Rice Variant Calling, 10X Rice Sequencing
Rice Genome Sequencing and Variant Calling-10X Test test available at DNA Labs India for ₹30,000. Uses Next-Generation Sequencing (NGS), 10X Genomics Linked-Read Sequencing, Bioinformatics Variant Calling on Extracted DNA samples. Results in Reports are delivered within 8 weeks from sample receipt.. Free home collection in 300+ cities across India.
🩺 Medically Reviewed By
Dr Pasupathy Arumugam
Consultant Pathologist · Reg: 21521
Last reviewed: September 7, 2026
Overview
The primary purpose of rice genome sequencing and variant calling is to identify genetic variations associated with important agronomic traits. This enables breeders to select plants with desirable characteristics more efficiently. Specific purposes include: 1) Identifying genes for yield improvement, 2) Discovering resistance genes against pests and diseases, 3) Understanding adaptation to environmental stresses (drought, salinity), 4) Improving grain quality (taste, nutrition, cooking properties), 5) Accelerating breeding cycles through genomic selection, 6) Supporting conservation of genetic diversity.
- Test Code
- 6348
- CPT Code
- 81479
- ICD Code
- Z13.9
- Price
- ₹30,000
- Sample Type
- Extracted DNA
- Result Time
- Reports are delivered within 8 weeks from sample receipt.
- Fasting Required
- No
- Method
- Next-Generation Sequencing (NGS), 10X Genomics Linked-Read Sequencing, Bioinformatics Variant Calling
Sample Collection
No specific preparation required. For leaf samples, ensure they are fresh and free from pests/diseases. If submitting extracted DNA, ensure it is of high quality (A260/280 ratio 1.8-2.0) and stored appropriately.
Method: Leaf sample collection (or extracted DNA submission)
Laboratory Analysis
Leaf samples should be collected in sterile bags or tubes. For extracted DNA, use a sterile, DNase-free tube and label clearly.
Report Delivery
Samples should be shipped to the lab within 24 hours. If delayed, store at 4°C for short-term or -20°C for long-term.
Timeline: Reports are delivered within 8 weeks from sample receipt.
Patient Instructions
About This Test
Who Should Get This Test
The primary purpose of rice genome sequencing and variant calling is to identify genetic variations associated with important agronomic traits. This enables breeders to select plants with desirable characteristics more efficiently. Specific purposes include: 1) Identifying genes for yield improvement, 2) Discovering resistance genes against pests and diseases, 3) Understanding adaptation to environmental stresses (drought, salinity), 4) Improving grain quality (taste, nutrition, cooking properties), 5) Accelerating breeding cycles through genomic selection, 6) Supporting conservation of genetic diversity.
How to Prepare
- Collect young, healthy leaf tissue (2-3 cm) from the rice plant
- Place in a sterile collection tube or zip-lock bag
- Label with sample ID, date, and variety name
- For extracted DNA, provide at least 1 µg in a volume of 20-50 µL
- Ship samples on dry ice if possible, especially in warm weather
Doctor's Notes
Reviewed by Dr Pasupathy Arumugam — MBBS, MD (Pathology) · Reg. No. 21521
"Rice genome sequencing provides critical insights for developing resilient and high-yield varieties, essential for food security."
Last medically reviewed: September 7, 2026
Test Parameters & Specifications
Sample Stability
- Sample with insufficient DNA quantity (<0.5 µg)
- Highly degraded DNA (fragments <1 kb)
- Contaminated samples (visible fungal growth or insect infestation)
- Improper labeling or missing sample information
Understanding Your Results
SNP
Action: Validate with PCR and Sanger sequencing for key candidates
Impact: May alter protein function if in coding region
Indel
Action: Associate with phenotype if known
Impact: Can cause frameshift mutations leading to loss of function
Structural Variant
Action: Use for diversity studies or marker development
Impact: May affect gene expression or gene dosage
Homozygous vs Heterozygous
Action: Consider in breeding decisions
Impact: Homozygous variants are more likely to have phenotypic effects
This test is for research and agricultural purposes. Consult a plant geneticist or agricultural scientist for interpretation and application of results. Not intended for human clinical diagnosis.
Limitations
- ⚠Variant calling may miss large structural variants or complex rearrangements
- ⚠10X coverage may not detect low-frequency variants with high confidence
- ⚠Reference genome bias may affect variant detection in non-reference accessions
- ⚠Functional interpretation of variants requires additional validation
- ⚠Results are for research purposes and not for clinical diagnosis
Risks & Considerations
- ●No physical risks as this is a laboratory test on plant samples
- ●Potential for inconclusive results if sample quality is poor
- ●Data interpretation may require expert consultation
Interfering Factors
- ●Degraded DNA samples leading to poor sequencing quality
- ●Contamination with plant pathogens or other species
- ●Insufficient DNA quantity
- ●PCR amplification errors during library preparation
- ●Bioinformatics pipeline variations affecting variant calling
Compare With Similar Tests
| Test | Rice Genome Sequencing and Variant Calling-10X | Rice Whole Genome Sequencing (30X) | Rice Exome Sequencing | Rice Genotyping by Sequencing (GBS) |
|---|---|---|---|---|
| Comparison | Rice Genome Sequencing and Variant Calling-10X |
Frequently Asked Questions
What is rice genome sequencing?
What is variant calling?
What is the cost of the test?
What type of sample is required?
How long does it take to get results?
Can this test be used for human genetic testing?
What is the coverage depth?
Do I need to fast before sample collection?
Is home sample collection available?
What kind of report will I receive?
Can this test help in developing disease-resistant rice varieties?
Are there any additional costs?
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Reference Laboratory Services
We serve as a reference laboratory for hospitals and clinics across India. Send samples from your facility with same-day pickup, priority processing, and results delivered through our online portal. Competitive institutional pricing available.
Your Data Privacy
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✓ Stored in India: All patient records are stored on servers located in India. No data is transferred outside the country.
✓ DPDP Act Compliant: Under the Digital Personal Data Protection Act 2023, you can request deletion of your records at any time by contacting support.
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