Vitis vinifera vs Eragrostis curvula LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Eragrostis curvula (Eragrostis curvula, CERZOS_E.curvula1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 100. 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 viniferaEragrostis curvula
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options

Statistics over 214,780 alignment blocks

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

Uncovered: 449,904,623 out of 486,265,422
Covered: 36,360,799 out of 486,265,422

Uncovered: 10,486,925 out of 32,794,161
Matches: 14,532,049 out of 32,794,161
Mismatches: 7,275,652 out of 32,794,161
Insertions: 499,535 out of 32,794,161
Identity over aligned base-pairs: 65.1%

Eragrostis curvula

Uncovered: 551,398,286 out of 603,072,269
Covered: 51,673,983 out of 603,072,269

Uncovered: 30,953,363 out of 62,628,176
Matches: 20,535,505 out of 62,628,176
Mismatches: 10,417,499 out of 62,628,176
Insertions: 721,809 out of 62,628,176
Identity over aligned base-pairs: 64.8%

Block size distribution

Size range All 214,780 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,473
7.0 kb
10 bp - 100 bp
35,354
2.5 Mb
10,309
750.2 kb
100 bp - 1 kb
167,186
52.5 Mb
58,799
22.0 Mb
1 kb - 10 kb
10,746
15.9 Mb
24,096
47.6 Mb
10 kb - 100 kb
21
306.3 kb
64
889.8 kb