Pythium vexans vs Giardia lamblia Translated Blat results

Pythium vexans (Pythium vexans DAOM BR484, pve_scaffolds_v1) and Giardia lamblia (Giardia lamblia, GL2) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 75. Pythium vexans 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

ParameterValue
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

ParameterPythium vexansGiardia lamblia
Chunk size1,000,0001,000,000
Overlap10,00010,000
Group set size100,000,000100,000,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 2,051 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Pythium vexans

Uncovered: 33,587,892 out of 33,844,883
Covered: 256,991 out of 33,844,883

Uncovered: 18,370,912 out of 18,608,353
Matches: 155,355 out of 18,608,353
Mismatches: 82,048 out of 18,608,353
Insertions: 38 out of 18,608,353
Identity over aligned base-pairs: 65.4%

Giardia lamblia

Uncovered: 11,026,619 out of 11,192,215
Covered: 165,596 out of 11,192,215

Uncovered: 9,158,736 out of 9,322,001
Matches: 105,829 out of 9,322,001
Mismatches: 57,406 out of 9,322,001
Insertions: 30 out of 9,322,001
Identity over aligned base-pairs: 64.8%