Zea mays vs Setaria italica LastZ Results

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Zea mays (Zea mays, B73_RefGen_v4) and Setaria italica (Setaria italica, Setaria_italica_v2.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Zea mays 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: 367,182

Genome coverage (bp) Coding exon coverage (bp)
Zea mays

Uncovered: 2,018,470,650 out of 2,135,083,061
Covered: 116,612,411 out of 2,135,083,061

Uncovered: 14,422,182 out of 48,442,923
Matches: 28,933,198 out of 48,442,923
Mismatches: 4,438,145 out of 48,442,923
Insertions: 649,398 out of 48,442,923

Setaria italica

Uncovered: 293,108,768 out of 405,732,883
Covered: 112,624,115 out of 405,732,883

Uncovered: 5,946,301 out of 39,583,990
Matches: 27,524,063 out of 39,583,990
Mismatches: 5,401,424 out of 39,583,990
Insertions: 712,202 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

Zea mays 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}