Index of /arthropods/data/polymorphism

 Name                                        Last modified       Size  Description

 Parent Directory                            05-Dec-2009 18:17      -  
 acyr1_aug5.genes.mblastdupsc-pi80.genes     22-Sep-2008 00:31   148k  
 acyr1_gnomon.genes.mblastdupsc-pi80.genes   23-Sep-2008 19:26   200k  
 acyrgeno-smallsc-mblastdupsc-pi80.ids       22-Sep-2008 00:25    89k  
 acyrgeno-smallsc.mblast.stats               22-Sep-2008 15:03   951k  
 arp-acyr1_gnomon-pi80dupgene.tab            23-Sep-2008 20:39    11k  
 dpulex1_gnomon.genes.mblastdupsc-pi80.genes 22-Sep-2008 00:29    15k  
 dpulexgeno-smallsc-mblastdupsc-pi80.ids     22-Sep-2008 00:26     4k  
 dpulexgeno-smallsc.mblast.stats             22-Sep-2008 14:58   246k  
 nasoniageno-smallsc-mblastdupsc-pi80.genes  23-Sep-2008 19:20    20k  
 nasoniageno-smallsc-mblastdupsc-pi80.ids    23-Sep-2008 19:20    11k  
 nasoniageno-smallsc.mblast.stats            23-Sep-2008 19:06   160k  

Estimate of polymorphic (spurious) scaffolds in new genome assemblies.
Re http://insects.eugenes.org/arthropods/data/polymorphism/
2008 Sept 23, D. Gilbert

Method:
  1. Select subset of scaffolds under 10Kb, as these are often ones with partial coverage,
     inability to assemble due to redundancy with existing larger scaffolds. For Daphnia
     with scaffold read coverage stats, these are almost all < 4x (many 1x) of the 8x coverage.
  2. Megablast match small scaf to full genome assembly
  3. Combine HSP/scaffold and select those small scaf with > 80% overall identity to larger scaffold
     (other criteria could be used).

Genomes tested: Acyr. pisum, Nasonia vit., Daphnia pulex,

Results:
Files *smallsc.mblast.stats summarize megablast results as
small (querysc) x large (targetsc) with query length, blast align, mismatch, gap, and % identity
-------- dpulexgeno-smallsc.mblast.stats ----- 
querysc  	targs    c	qlen	align	mismat	gaps	ident	%ident	targloc
scaffold_764	scaffold_65	9938	2770	45	23	2698	27	17302-18434,...
scaffold_821	scaffold_257	9208	3273	46	13	3206	34	77559-80732,38245-38162,
scaffold_872	scaffold_65	8340	8145	15	6	8123	97	101197-98515,....
--------
Files *smallsc-mblastdupsc-pi80.ids list scaffold ids with >80% identity to larger scaffold
In the above case, Daphnia scaffold_872 is highly identical to part of scaffold_65
Files *gnomon.genes.mblastdupsc-pi80.genes list genes on these pi80 scaffolds.

Scaffold counts of putative spurious (polymorphic) scaffolds
  6197 acyr1-geno-smallsc-mblastdupsc-pi80.ids
   821 nasonia1-geno-smallsc-mblastdupsc-pi80.ids
   233 dpulex1-geno-smallsc-mblastdupsc-pi80.ids

Gene counts on putative spurious (polymorphic) scaffolds
  1866 acyr1_gnomon.genes.mblastdupsc-pi80.genes  
   208 nasonia1_gnomon.genes.mblastdupsc-pi80.genes
    89 dpulex1_gnomon.genes.mblastdupsc-pi80.genes

These are likely underestimates: criteria selected <10kb scaffold size (as most likely
partial-coverage heterozygous assemblies), and >80% total scaffold identity (where
high identity on part of scaffold may indicate a heterozygous contig).