Sorghum bicolor vs Brachypodium distachyon LastZ Results

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Sorghum bicolor (Sorghum bicolor, Sorghum_bicolor_NCBIv3) and Brachypodium distachyon (Brachypodium distachyon, v1.0) 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: 177,673

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

Uncovered: 635,269,724 out of 708,735,318
Covered: 73,465,594 out of 708,735,318

Uncovered: 4,845,040 out of 39,785,927
Matches: 26,810,138 out of 39,785,927
Mismatches: 7,115,454 out of 39,785,927
Insertions: 1,015,295 out of 39,785,927

Brachypodium distachyon

Uncovered: 201,030,041 out of 271,923,306
Covered: 70,893,265 out of 271,923,306

Uncovered: 2,843,651 out of 34,177,820
Matches: 24,423,189 out of 34,177,820
Mismatches: 6,216,926 out of 34,177,820
Insertions: 694,054 out of 34,177,820

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 Brachypodium distachyon
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}