Zea mays vs Setaria italica LastZ Results

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Zea mays (Zea mays, AGPv4) and Setaria italica (Setaria italica, JGIv2.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 81. 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: 364,807

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

Uncovered: 1,962,298,988 out of 2,134,373,047
Covered: 172,074,059 out of 2,134,373,047

Uncovered: 3,154,867 out of 48,311,124
Matches: 38,159,553 out of 48,311,124
Mismatches: 6,140,165 out of 48,311,124
Insertions: 856,539 out of 48,311,124

Setaria italica

Uncovered: 320,194,907 out of 405,737,341
Covered: 85,542,434 out of 405,737,341

Uncovered: 11,662,726 out of 39,744,767
Matches: 24,051,813 out of 39,744,767
Mismatches: 3,516,092 out of 39,744,767
Insertions: 514,136 out of 39,744,767

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}