Phytophthora kernoviae vs Giardia lamblia Translated Blat results

Phytophthora kernoviae (Phytophthora kernoviae 00238/432, PhyKer238_432v1) 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 kernoviae 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

ParameterPhytophthora kernoviaeGiardia lamblia
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 1,884 alignment blocks

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

Uncovered: 42,955,054 out of 43,208,681
Covered: 253,627 out of 43,208,681

Uncovered: 11,319,800 out of 11,508,642
Matches: 122,034 out of 11,508,642
Mismatches: 66,736 out of 11,508,642
Insertions: 72 out of 11,508,642
Identity over aligned base-pairs: 64.6%

Giardia lamblia

Uncovered: 11,021,116 out of 11,192,215
Covered: 171,099 out of 11,192,215

Uncovered: 9,153,086 out of 9,322,001
Matches: 107,624 out of 9,322,001
Mismatches: 61,255 out of 9,322,001
Insertions: 36 out of 9,322,001
Identity over aligned base-pairs: 63.7%