Arabidopsis thaliana vs Setaria italica LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Setaria italica (Setaria italica, JGIv2.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. Arabidopsis thaliana was used as the reference species. After running LastZ, the raw LastZ 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: 79,329

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 92,935,350 out of 119,667,750
Covered: 26,732,400 out of 119,667,750

Uncovered: 13,476,769 out of 33,462,323
Matches: 13,033,714 out of 33,462,323
Mismatches: 6,574,752 out of 33,462,323
Insertions: 377,088 out of 33,462,323

Setaria italica

Uncovered: 386,558,423 out of 405,737,341
Covered: 19,178,918 out of 405,737,341

Uncovered: 26,369,061 out of 39,744,767
Matches: 8,681,334 out of 39,744,767
Mismatches: 4,375,991 out of 39,744,767
Insertions: 318,381 out of 39,744,767

Configuration parameters

ParameterValue
Gap open penalty (O)
Gap extend penalty (E)
HSP threshold (K)
Threshold for gapped extension (L)
Threshold for alignments between gapped alignment blocks (H)
Masking count (M)
Seed and Transition value (T)
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91
Other parameters (other)