Arabidopsis thaliana vs Setaria italica LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Setaria italica (Setaria italica, Setaria_italica_v2.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . 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: 118,568

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

Uncovered: 93,296,869 out of 119,667,750
Covered: 26,370,881 out of 119,667,750

Uncovered: 14,199,221 out of 33,775,569
Matches: 12,679,009 out of 33,775,569
Mismatches: 6,498,834 out of 33,775,569
Insertions: 398,505 out of 33,775,569

Setaria italica

Uncovered: 374,798,111 out of 405,732,883
Covered: 30,934,772 out of 405,732,883

Uncovered: 18,703,830 out of 39,583,990
Matches: 13,390,184 out of 39,583,990
Mismatches: 6,991,134 out of 39,583,990
Insertions: 498,842 out of 39,583,990

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)3000
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
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)--ambiguous=iupac

Chunking parameters

Arabidopsis thaliana Setaria italica
Chunk size 50,000,000 100,100,000
Overlap 0 100,000
Group set size 0 100,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}