Zea mays vs Musa acuminata LastZ Results

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Zea mays (Zea mays, AGPv4) and Musa acuminata (Musa acuminata subsp. malaccensis, MA1) 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: 199,091

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

Uncovered: 2,073,344,131 out of 2,134,373,047
Covered: 61,028,916 out of 2,134,373,047

Uncovered: 13,288,329 out of 48,311,124
Matches: 23,886,509 out of 48,311,124
Mismatches: 10,142,420 out of 48,311,124
Insertions: 993,866 out of 48,311,124

Musa acuminata subsp. malaccensis

Uncovered: 443,110,997 out of 472,960,417
Covered: 29,849,420 out of 472,960,417

Uncovered: 18,823,516 out of 37,920,568
Matches: 13,148,630 out of 37,920,568
Mismatches: 5,477,906 out of 37,920,568
Insertions: 470,516 out of 37,920,568

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 Musa acuminata
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}