Related Experiment Video
Updated: Feb 2, 2026

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
Published on: June 17, 2012
Genomewide identification and annotation of SNPs in Bubalus bubalis
T Surya1, M R Vineeth2, Jayakumar Sivalingam3
1ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India; ICAR-National Dairy Research Institute, Karnal, Haryana, India.
Abstract:
The present study was carried out to identify and annotate the genome wide SNPs in Murrah buffalo genome. A total of 21.2 million raw reads from 4 pooled female Murrah buffalo samples were obtained using restriction enzyme digestion followed by sequencing with Illumina Hiseq 2000. After quality filtration, the reads were aligned to Murrah buffalo genome (ICAR-NBAGR) and Water buffalo genome (UMD_CASPUR_WB_2.0) which resulted in 99.37% and 99.67% of the reads aligning, respectively. A total of 130,688 high quality SNPs along with 35,110 indels were identified versus the Murrah bufffalo genome. Similarly 219,856 high quality SNPs along with 15,201 indels were identified versus the Water buffalo genome. We report 483 SNPs in 66 genes affecting Milk Production, 436 SNPs in 38 genes affecting fertility and 559 SNPs in 72 genes affecting other major traits. The average genome coverage was 13.4% and 14.8% versus the Murrah and Water buffalo genomes, respectively.
Related Concept Videos
Comparing Copy Number Variations and SNPs
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Genome Annotation and Assembly
Single Nucleotide Polymorphisms-SNPs
Methods of Classification and Identification
Peptide Identification Using Tandem Mass Spectrometry
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
Conserved Binding Sites
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

