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Human vs Xenopus Translated Blat alignments

Human (Homo sapiens, GRCh37) and Xenopus (Xenopus tropicalis, JGI_4.2) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl release 62. Human 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.

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

Human Xenopus
Chunk size 1,000,000 25,000
Overlap 1,000 1,000
Group set size 100,000,000 10,000,000
Masking options {default_soft_masking => 1}

Results

Number of alignment blocks: 231,313

Genome coverage (bp) Coding exon coverage (bp)
Homo sapiens

Uncovered: 3,071,424,678 out of 3,098,825,702
Covered: 27,401,024 out of 3,098,825,702

Uncovered: 17,251,088 out of 35,313,516
Matches: 13,374,643 out of 35,313,516
Mismatches: 4,679,341 out of 35,313,516
Insertions: 8,444 out of 35,313,516

Xenopus tropicalis

Uncovered: 1,490,641,294 out of 1,511,717,716
Covered: 21,076,422 out of 1,511,717,716

Uncovered: 15,310,448 out of 30,481,746
Matches: 11,264,337 out of 30,481,746
Mismatches: 3,902,136 out of 30,481,746
Insertions: 4,825 out of 30,481,746