Sorghum bicolor vs Setaria italica LastZ Results

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Sorghum bicolor (Sorghum bicolor, Sorghum_bicolor_NCBIv3) and Setaria italica (Setaria italica, JGIv2.0) 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: 408,331

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

Uncovered: 574,802,777 out of 708,735,318
Covered: 133,932,541 out of 708,735,318

Uncovered: 2,630,869 out of 39,785,927
Matches: 31,272,586 out of 39,785,927
Mismatches: 5,021,795 out of 39,785,927
Insertions: 860,677 out of 39,785,927

Setaria italica

Uncovered: 251,975,155 out of 405,737,341
Covered: 153,762,186 out of 405,737,341

Uncovered: 2,517,314 out of 39,744,767
Matches: 31,381,958 out of 39,744,767
Mismatches: 5,216,425 out of 39,744,767
Insertions: 629,070 out of 39,744,767

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 Setaria italica
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}