LpbbsSNPDB: SNP Database of Lanping black-boned Sheep

Lanping black-boned sheep was first discovered in the 1950s in Lanping county of China and characterized by black pigmentation on skin and internal organs. Due to the novel and unique trait, the genetic background of Lanping black-boned sheep is of great interest. The rapid development of high-throughput sequencing technology and the decrease in sequencing costs provide valuable resources and great opportunities for researchers to investigate genomic variations. However, the management and exploration of these large-scale genomic variations, such as single-nucleotide polymorphism(SNP) heavily rely on programming and command-line environments, which are challenging and time-consuming for most experimental biologists and sheep breeders. We present a SNP database of the Lanping black-boned Sheep (LpbbsSNPDB), which is an interactive web portal with a user-friendly interface that provides multiple analysis modules for retrieving, analyzing, and visualizing SNPs among 150 accessions, including 100 Lanping black-boned sheeps and 50 Lanping norm sheeps. This database is essential for accelerating studies on the functional genomics and screening of the molecular markers of molecular-assisted breeding in the Lanping black-boned sheep.

Analysis Modules

We here present 5 modules to retrieve and analyze the SNP dataset. Within each module, the user can select different parameters to retrieve and analyze the SNP dataset.

LDheatmap

This module provides a pipeline to retrieve SNPs and display pairwise linkage disequilibria between SNPs and allows the user select different parameters.

SNP Distribution

This module compares the conserved SNPs specific to different groups of Lanping black-boned sheep.

Phylogenetic

This module implements the functionality to perform phylogenetic analysis in user-specified genomic regions.

Diversity

This module provides the functionality to calculate nucleotide diversity among groups of Lanping black-boned sheep accessions in user-specified genomic regions.

Extraction

This module allows user to extract the detail informations of SNPs, annotation of genes and essential information on the 150 accessions used in the LpbbsSNPDB.

LDheatmap:

Download LDheatmap


SNP Informations:

ref: reference allele - The reference allele is whatever is found in the reference genome.
alt: alternative allele - The alternative allele is the allele found in the sample.
major: major allele, is the common allele with high frequency.
minor: minor allele, is the less common allele with lower frequency.
Download SNP Data



SNPdistribution:

Download SNPdistribution


SNP Informations:

ref: reference allele - The reference allele is whatever is found in the reference genome.
alt: alternative allele - The alternative allele is the allele found in the sample.
major: major allele, is the common allele with high frequency.
minor: minor allele, is the less common allele with lower frequency.
Download SNP Data



Phylogenetic Tree:

Download Phylogenetics tree


SNP Informations:

ref: reference allele - The reference allele is whatever is found in the reference genome.
alt: alternative allele - The alternative allele is the allele found in the sample.
major: major allele, is the common allele with high frequency.
minor: minorr allele, is the less common allele with lower frequency.
Download SNP Data



Diversity Plot:


Download Diversity Plot


Allele Informations (Major/Minor):

ref: reference allele - The reference allele is whatever is found in the reference genome.
alt: alternative allele - The alternative allele is the allele found in the sample.
major: major allele, is the common allele with high frequency.
minor: monir allele, is the less common allele with lower frequency.
Download Allele Data



SNP data:

ref: reference allele - The reference allele is whatever is found in the reference genome.
alt: alternative allele - The alternative allele is the allele found in the sample.
major: major allele, is the common allele with high frequency.
minor: minor allele, is the less common allele with lower frequency.
Download SNP Data

Gene Info:


Download Genes Informations



Accession Info:


Download Accession Informations