Phytophthora lateralis vs Giardia lamblia Translated Blat results

Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_v1.0) 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 76. Phytophthora lateralis 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

ParameterPhytophthora lateralisGiardia 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 1,533 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora lateralis

Uncovered: 43,780,158 out of 43,981,379
Covered: 201,221 out of 43,981,379

Uncovered: 14,487,966 out of 14,663,433
Matches: 112,974 out of 14,663,433
Mismatches: 62,484 out of 14,663,433
Insertions: 9 out of 14,663,433
Identity over aligned base-pairs: 64.4%

Giardia lamblia

Uncovered: 11,051,030 out of 11,192,215
Covered: 141,185 out of 11,192,215

Uncovered: 9,182,469 out of 9,322,001
Matches: 89,345 out of 9,322,001
Mismatches: 50,172 out of 9,322,001
Insertions: 15 out of 9,322,001
Identity over aligned base-pairs: 64.0%