Table 1.
Statistics of raw reads with high quality and mapped reads ratio of M transcriptome and P transcriptome.
Figure 1.
Venn diagram of SNPs discovered using reads of the three datasets.
M represented SNPs discovered using reads from transcriptome of L.vannmei at developmental stage of mysis, P represented SNPs discovered using reads from transcriptome of L.vannmei at developmental stage of post larva. M+P represented SNPs discovered using the reads of the two transcriptomes together.
Table 2.
Statistics of transition and transversion type in the total SNPs.
Figure 2.
Statistics of read depth in each SNP in L. vannamei.
The horizontal axis represented the read depth of SNPs, the vertical axis represented the number of SNPs with the corresponding read depth. The average read depth was 44.
Figure 3.
Statistics of minor allele frequency of total discovered SNPs in L. vannamei.
SNP number with MAF below 0.2 was too small to be observed in the column diagram.
Table 3.
Classification of identified SNPs using a manual Perl script.
Figure 4.
The distribution of SNPs in unigenes.
The horizontal axis represented SNP numbers per unigene. The vertical axis represented the number of unigenes.
Figure 5.
The frequencies of SNPs in unigenes.
The frequencies of SNPs in each unigene was calculated by dividing unigene length by SNPs number per unigene. Number of unigenes with SNP frequency over 0.030 was too small to be observed in the column diagram.
Table 4.
Annotation of the top twenty unigenes with the highest SNP frequency.
Figure 6.
Gene ontology of all the annotated unigenes and unigenes with SNP frequency more than 0.014.
The blue column represented gene ontology of all unigenes containing SNPs. The red column represented gene ontology of unigenes with SNP frequency more than 0.014.
Figure 7.
The top 20 KEGG pathway classification of assigned SNPs.
The horizontal axis represented KEGG pathway annotation. The vertical axis represented the number of SNPs assigned to the corresponding KEGG pathway.