Vitis vinifera vs Setaria viridis LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Setaria viridis (Setaria viridis, Setaria_viridis_v2.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 101. 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 viniferaSetaria viridis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 168,457 alignment blocks

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

Uncovered: 450,114,932 out of 486,265,422
Covered: 36,150,490 out of 486,265,422

Uncovered: 10,599,560 out of 32,794,161
Matches: 14,531,094 out of 32,794,161
Mismatches: 7,184,759 out of 32,794,161
Insertions: 478,748 out of 32,794,161
Identity over aligned base-pairs: 65.5%

Setaria viridis

Uncovered: 359,970,666 out of 395,731,502
Covered: 35,760,836 out of 395,731,502

Uncovered: 17,512,917 out of 41,880,594
Matches: 15,823,950 out of 41,880,594
Mismatches: 7,979,050 out of 41,880,594
Insertions: 564,677 out of 41,880,594
Identity over aligned base-pairs: 64.9%

Block size distribution

Size range All 168,457 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,291
6.1 kb
10 bp - 100 bp
28,899
2.0 Mb
8,272
603.9 kb
100 bp - 1 kb
130,159
40.0 Mb
47,163
17.3 Mb
1 kb - 10 kb
8,093
12.0 Mb
17,966
35.6 Mb
10 kb - 100 kb
15
301.9 kb
51
809.9 kb