Amborella trichopoda vs Oryza sativa Japonica Translated Blat Results

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Amborella trichopoda (Amborella trichopoda, AMTR1.0) and Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Plants release 75. Amborella trichopoda 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: 256,615

Genome coverage (bp) Coding exon coverage (bp)
Amborella trichopoda

Uncovered: 684,744,466 out of 706,332,640
Covered: 21,588,174 out of 706,332,640

Uncovered: 15,604,303 out of 25,807,211
Matches: 7,192,380 out of 25,807,211
Mismatches: 3,007,568 out of 25,807,211
Insertions: 2,960 out of 25,807,211

Oryza sativa Japonica Group

Uncovered: 359,427,246 out of 374,424,240
Covered: 14,996,994 out of 374,424,240

Uncovered: 22,446,627 out of 34,124,807
Matches: 8,240,647 out of 34,124,807
Mismatches: 3,433,851 out of 34,124,807
Insertions: 3,682 out of 34,124,807

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

Amborella trichopoda Oryza sativa Japonica
Chunk size 1,000,000 25,000
Overlap 10,000 10,000
Group set size 100,000,000 10,000,000
Masking options {default_soft_masking => 1}