Vitis vinifera vs Glycine max LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Glycine max (Glycine max, Glycine_max_v2.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 95. Vitis vinifera was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

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

Chunking parameters

ParameterVitis viniferaGlycine max
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 367,646 alignment blocks

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

Uncovered: 423,226,514 out of 486,265,422
Covered: 63,038,908 out of 486,265,422

Uncovered: 4,518,186 out of 32,794,161
Matches: 19,725,669 out of 32,794,161
Mismatches: 7,902,447 out of 32,794,161
Insertions: 647,859 out of 32,794,161
Identity over aligned base-pairs: 69.8%

Glycine max

Uncovered: 869,355,943 out of 978,491,270
Covered: 109,135,327 out of 978,491,270

Uncovered: 10,394,780 out of 65,618,132
Matches: 39,273,133 out of 65,618,132
Mismatches: 14,911,188 out of 65,618,132
Insertions: 1,039,031 out of 65,618,132
Identity over aligned base-pairs: 71.1%

Block size distribution

Size range All 367,646 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,827
14.5 kb
10 bp - 100 bp
57,421
3.8 Mb
20,228
1.5 Mb
100 bp - 1 kb
280,975
94.5 Mb
100,501
34.5 Mb
1 kb - 10 kb
26,350
42.0 Mb
29,021
69.9 Mb
10 kb - 100 kb
73
1.3 Mb
1,174
26.0 Mb
100 kb - 1 Mb
64
9.9 Mb