Entamoeba histolytica vs Albugo laibachii Translated Blat results

Entamoeba histolytica (Entamoeba histolytica, JCVI-ESG2-1.0) and Albugo laibachii (Albugo laibachii, ENA1) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 67. Entamoeba histolytica was used as the reference species. After running Translated Blat, the raw Translated Blat alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

Configuration parameters

Minimum score (minScore)30
Database type (t)dnax
Query type (q)dnax
Mask out repeats (mask)lower
Mask out repeats on query (qMask)lower

Chunking parameters

ParameterEntamoeba histolyticaAlbugo laibachii
Chunk size1,000,0001,000,000
Group set size100,000,000100,000,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 2,515 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Entamoeba histolytica

Uncovered: 20,434,489 out of 20,835,395
Covered: 400,906 out of 20,835,395

Uncovered: 9,857,617 out of 10,244,611
Matches: 250,158 out of 10,244,611
Mismatches: 136,811 out of 10,244,611
Insertions: 25 out of 10,244,611
Identity over aligned base-pairs: 64.6%

Albugo laibachii

Uncovered: 32,526,217 out of 32,766,811
Covered: 240,594 out of 32,766,811

Uncovered: 15,670,268 out of 15,902,867
Matches: 149,250 out of 15,902,867
Mismatches: 83,258 out of 15,902,867
Insertions: 91 out of 15,902,867
Identity over aligned base-pairs: 64.2%