Giardia lamblia vs Phytophthora infestans Translated Blat results

Giardia lamblia (Giardia lamblia, GL2) and Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) 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

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

ParameterGiardia lambliaPhytophthora infestans
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 1,261 alignment blocks

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

Uncovered: 11,011,630 out of 11,192,215
Covered: 180,585 out of 11,192,215

Uncovered: 9,146,467 out of 9,322,001
Matches: 113,925 out of 9,322,001
Mismatches: 61,573 out of 9,322,001
Insertions: 36 out of 9,322,001
Identity over aligned base-pairs: 64.9%

Phytophthora infestans

Uncovered: 228,380,337 out of 228,543,505
Covered: 163,168 out of 228,543,505

Uncovered: 22,263,372 out of 22,421,425
Matches: 101,834 out of 22,421,425
Mismatches: 56,213 out of 22,421,425
Insertions: 6 out of 22,421,425
Identity over aligned base-pairs: 64.4%