Amborella trichopoda vs Arabidopsis thaliana Translated Blat Results

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Amborella trichopoda (Amborella trichopoda, AMTR1.0) and Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) 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: 185,044

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

Uncovered: 691,172,063 out of 706,332,640
Covered: 15,160,577 out of 706,332,640

Uncovered: 14,947,361 out of 25,807,211
Matches: 7,657,569 out of 25,807,211
Mismatches: 3,198,182 out of 25,807,211
Insertions: 4,099 out of 25,807,211

Arabidopsis thaliana

Uncovered: 104,007,840 out of 119,667,750
Covered: 15,659,910 out of 119,667,750

Uncovered: 18,966,984 out of 33,462,323
Matches: 10,259,425 out of 33,462,323
Mismatches: 4,230,969 out of 33,462,323
Insertions: 4,945 out of 33,462,323

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 Arabidopsis thaliana
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}