Zea mays vs Sorghum bicolor LastZ Results

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Zea mays (Zea mays, AGPv3) and Sorghum bicolor (Sorghum bicolor, Sorbi1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. 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: 464,518

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

Uncovered: 1,869,951,707 out of 2,067,864,162
Covered: 197,912,455 out of 2,067,864,162

Uncovered: 3,732,002 out of 44,177,667
Matches: 36,365,767 out of 44,177,667
Mismatches: 3,514,913 out of 44,177,667
Insertions: 564,985 out of 44,177,667

Sorghum bicolor

Uncovered: 634,317,379 out of 738,540,932
Covered: 104,223,553 out of 738,540,932

Uncovered: 12,100,648 out of 40,003,363
Matches: 25,188,317 out of 40,003,363
Mismatches: 2,224,542 out of 40,003,363
Insertions: 489,856 out of 40,003,363

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

Zea mays Sorghum bicolor
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}