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Human vs Anole lizard Translated Blat alignments

Human (Homo sapiens, GRCh37) and Anole lizard (Anolis carolinensis, AnoCar2.0) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl release 61. 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 Anole lizard
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}

Results

Number of alignment blocks: 310,701

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

Uncovered: 3,063,352,911 out of 3,098,825,702
Covered: 35,472,791 out of 3,098,825,702

Uncovered: 15,371,370 out of 35,313,516
Matches: 15,287,839 out of 35,313,516
Mismatches: 4,644,352 out of 35,313,516
Insertions: 9,955 out of 35,313,516

Anolis carolinensis

Uncovered: 1,787,419,310 out of 1,799,126,364
Covered: 11,707,054 out of 1,799,126,364

Uncovered: 10,357,774 out of 27,370,256
Matches: 13,080,816 out of 27,370,256
Mismatches: 3,922,320 out of 27,370,256
Insertions: 9,346 out of 27,370,256