Accurate detections of the heterozygous SNPs with rice genomic data and prediction of de novo spontaneous mutation rate.

ABSTRACT:

Background

The use of Illumina sequencing technologies has enabled the identification and removal of mutations in various plant species. However, the Illumina sequencing method requires a considerable amount of data to ensure its integrity and quality due to the enormous number of false positives. This study aimed to explore an effective genomic data analysis for the detection of heterozygous variant (HV) in rice varieties.

Results

We compared the accuracy of four combinations of mapping tools and variant calling pipelines and selected BWA-MEM2 with GATK4.3 HaplotypeCaller. To detect heterozygous de novo polymorphisms such as HVs in the three different rice varieties (Nipponbare, Kitaake, and Hinohikari), we adopted the following cost-saving procedures; secondary references

SUBMITTER: Balimponya EG 

PROVIDER: S-EPMC12495679 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature