View source for Acidovorax JS42 Parales Project

== Objectives ==
Use whole genome sequencing to find mutations involve with the evolution of novel trains in Acidovorax JS42 (3- or 4-nitrotoluene metabolism)

== Genomes ==

454 400bp sequence unpaired
Coverage ~8x

Genomes assembled with newbler and no-split option
# Assembled the contigs against the reference genome (aka syntenic path assembly)
## Unordered: http://genomevolution.org/r/3ipl
## Ordered: http://genomevolution.org/r/3ipk
## Assembled: http://genomevolution.org/r/3ipn
# Annotated the genomes using
## Prodigal for protein coding genes
## tRNAScan-SE for tRNAs
## Don't have a solution for rRNAs
# Used the syntenic relationships from 1.c to lift over the annotations from the reference genome to the new genomes

You can find the genomes (syntenic path assembly and contig level assembly for each organism) using this link:
http://genomevolution.org/CoGe/OrganismView.pl?org_name=JS42

==Polymorphisms==

*Collective table: http://genomevolution.org/elyons/polymorphisms/JS42/JS42_polymorphisms.html
*Description of the table: http://genomevolution.org/wiki/index.php/PolyMFind

==Notes==
Google doc: https://docs.google.com/document/d/1LhKKh_i2EvkdHGq7q75h9D8rZKvhrCbdb22X2fmOAUo/edit?hl=en_US