Sorghum bicolor vs Zea mays LastZ Results

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Sorghum bicolor (Sorghum bicolor, Sorghum_bicolor_NCBIv3) and Zea mays (Zea mays, B73_RefGen_v4) 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: 424,040

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

Uncovered: 587,941,044 out of 708,735,318
Covered: 120,794,274 out of 708,735,318

Uncovered: 5,702,055 out of 39,785,927
Matches: 29,188,522 out of 39,785,927
Mismatches: 4,143,836 out of 39,785,927
Insertions: 751,514 out of 39,785,927

Zea mays

Uncovered: 1,996,176,118 out of 2,135,083,061
Covered: 138,906,943 out of 2,135,083,061

Uncovered: 13,778,591 out of 48,442,923
Matches: 31,282,322 out of 48,442,923
Mismatches: 2,924,734 out of 48,442,923
Insertions: 457,276 out of 48,442,923

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 Zea mays
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}