Giardia lamblia vs Phytophthora ramorum Translated Blat results

Giardia lamblia (Giardia lamblia, GL2) and Phytophthora ramorum (Phytophthora ramorum, ASM14973v1) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 70. Giardia lamblia 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

ParameterGiardia lambliaPhytophthora ramorum
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 1,314 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Giardia lamblia

Uncovered: 11,007,808 out of 11,192,215
Covered: 184,407 out of 11,192,215

Uncovered: 9,142,056 out of 9,322,001
Matches: 117,208 out of 9,322,001
Mismatches: 62,698 out of 9,322,001
Insertions: 39 out of 9,322,001
Identity over aligned base-pairs: 65.1%

Phytophthora ramorum

Uncovered: 66,488,134 out of 66,652,401
Covered: 164,267 out of 66,652,401

Uncovered: 22,216,242 out of 22,377,278
Matches: 104,196 out of 22,377,278
Mismatches: 56,837 out of 22,377,278
Insertions: 3 out of 22,377,278
Identity over aligned base-pairs: 64.7%