FishSNP currently collects ~ 17 million non-redundant SNPs from 12 farmed fish species. In graph 1, SNPs are classified to three types according to the results of population test, by default, stacked column plot is used to show the proportion of SNPs of three types in each species. In graph 2, SNPs are classified to two sets according to the population type (family or random population), and stacked column plot is also used by default to show the proportional number of SNPs of two sets of each species. The graphs can be switched to different display modes.
Note: the chart is plotted by species on the horizontal axis and SNP numbers on the vertical. 'Pass' represent alleles passed population test, which means P-value of SNPs is greater than 1e-3, 'Deviation' represent alleles failed population test, which presents when P-value of SNPs is between 1e-6 and 1e-3. 'Untested' means SNPs not be tested by the author of article for SNPs from file attachments or SNPs from EVA, 'Sum' means the sum of three types of SNPs.
Note: the chart is plotted by species on the horizontal axis and SNP numbers on the vertical. Population types inclued family population and random population for each species. 'FAM_data' means SNPs statisticed from data of family population and 'Popu_data' means SNPs statisticed from data of random population.
FishSNP currently collects 72 articles about high-throughput SNP discovery, 14 papers provide detailed SNP information, 12 papers provide original sequencing data, and a total of 26 articles can obtain valid data sets, accounting for 36.1%. In graph 3, we classified all used papers to ‘Useless’ and ‘Useful’ according to the data of papers are useful or not. In graph 4, We divided all useful data resources into useful SNP attachment and useful bioproject, and we can get SNPs directly from SNP attachment or download raw sequencing data from bioproject. Four population test types were classified according to population types and test situation for file attachment resources, while three types for bioproject resources. In graph 4.1, all SNP attachments can be classified as useful and useless ones, and we divided useless attachments into three different types which can explain reasons. In graph 4.2, all bioproject can be classified as useful and useless ones, and we divided useless bioprojects into six different types which can explain reasons.
Note: the chart was plotted by species on the horizontal axis and paper numbers on the vertical. 'Useful' means that SNPs could be retrived from SNP attachment or raw sequencing data and 'Useless' represent we can not get SNPs from these papers.
Note: the pie chart shows the proportion of four SNP attachment types and explanation of usless data.
Note: the core of the sunburst chart shows the proportion of attachments and bioprojects which can be subdivided to different parts dispayed on the outer layer.
Note: the pie chart shows the proportion of seven SNP bioproject types and explanation of usless data.
In graph 5, four sequence types used in useful papers and each part of the pie chart shows paper numbers of each type. Graph6 shows the statisticed SNP numbers of each sequence type.
Note: the pie chart shows the proportion of useful papers in four sequencing types.Array( Genotyping By Array ), GBS( Genotyping By Sequencing ), RAD( restriction site associated DNA sequencing ), WGS( Whole Genome Sequencing )
Note: the bar chart shows the SNP numbers of four sequencing types.Array( Genotyping By Array ), GBS( Genotyping By Sequencing ), RAD( restriction site associated DNA sequencing ), WGS( Whole Genome Sequencing )
The populations are divided into four types according to whether the population was tested or not and the gpopulation type, namely, the family population with test, the family population without tested, the random group with tested, and the random group without tested. Graphs 7.1 and 7.2 show the population numbers and sample sizes in the four different population types respectively. Graph 8.1 counts the population number of random groups and family populations and graph 8.2 counts the sample size of random groups and family populations for each species.
Note: the bar chart shows population numbers in four different population test types, and plotted by popultion test type on the horizontal axis and population number on the vertical.RG test(Random group with test),RG(Random group without test),FD test(family data with test),FD(family data without test)
Note: the chart shows sample numbers in four different population test types, and plotted by popultion test type on the horizontal axis and sample number on the vertical.RG test(Random group with test),RG(Random group without test),FD test(family data with test),FD(family data without test)
Note: the chart is plotted by species on the horizontal axis and Population number on the vertical. ‘Random group num’ represnts the population number of random groups of each species and ‘Family num’ represnts the population number of family population of each species.
Note: the chart is plotted by species on the horizontal axis and sample number on the vertical. ‘Random group size’ represnts the sample size of random groups of each species and ‘Family size’ represnts the sample size of family population of each species.