Sorghum bicolor vs Musa acuminata LastZ Results

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Sorghum bicolor (Sorghum bicolor, Sorghum_bicolor_NCBIv3) and Musa acuminata (Musa acuminata subsp. malaccensis, MA1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Sorghum bicolor 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: 182,750

Genome coverage (bp) Coding exon coverage (bp)
Sorghum bicolor

Uncovered: 665,553,026 out of 708,735,318
Covered: 43,182,292 out of 708,735,318

Uncovered: 11,835,157 out of 39,785,927
Matches: 18,633,783 out of 39,785,927
Mismatches: 8,475,805 out of 39,785,927
Insertions: 841,182 out of 39,785,927

Musa acuminata subsp. malaccensis

Uncovered: 422,816,787 out of 472,960,417
Covered: 50,143,630 out of 472,960,417

Uncovered: 6,635,613 out of 37,920,568
Matches: 21,559,381 out of 37,920,568
Mismatches: 9,025,422 out of 37,920,568
Insertions: 700,152 out of 37,920,568

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
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

Sorghum bicolor Musa acuminata
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}