Vitis vinifera vs Sorghum bicolor LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Sorghum bicolor (Sorghum bicolor, Sorghum_bicolor_NCBIv3) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Vitis vinifera 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: 159,715

Genome coverage (bp) Coding exon coverage (bp)
Vitis vinifera

Uncovered: 450,821,342 out of 486,265,422
Covered: 35,444,080 out of 486,265,422

Uncovered: 10,713,456 out of 32,794,161
Matches: 14,434,862 out of 32,794,161
Mismatches: 7,176,111 out of 32,794,161
Insertions: 469,732 out of 32,794,161

Sorghum bicolor

Uncovered: 675,686,366 out of 708,735,318
Covered: 33,048,952 out of 708,735,318

Uncovered: 15,951,722 out of 39,785,927
Matches: 15,485,370 out of 39,785,927
Mismatches: 7,778,123 out of 39,785,927
Insertions: 570,712 out of 39,785,927

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

Vitis vinifera Sorghum bicolor
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}