Pythium aphanidermatum vs Giardia lamblia Translated Blat Results

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Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_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 74. Pythium aphanidermatum was used as the reference species. After running Translated Blat, the raw Translated Blat alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 1,934

Genome coverage (bp) Coding exon coverage (bp)
Pythium aphanidermatum DAOM BR444

Uncovered: 35,624,368 out of 35,876,849
Covered: 252,481 out of 35,876,849

Uncovered: 17,784,270 out of 18,015,574
Matches: 149,111 out of 18,015,574
Mismatches: 82,144 out of 18,015,574
Insertions: 49 out of 18,015,574

Giardia lamblia

Uncovered: 11,028,232 out of 11,192,215
Covered: 163,983 out of 11,192,215

Uncovered: 9,159,286 out of 9,322,001
Matches: 104,057 out of 9,322,001
Mismatches: 58,637 out of 9,322,001
Insertions: 21 out of 9,322,001

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

Pythium aphanidermatum Giardia lamblia
Chunk size 1,000,000 1,000,000
Overlap 10,000 10,000
Group set size 100,000,000 100,000,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}