Vitis vinifera vs Oryza longistaminata LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Oryza longistaminata (Oryza longistaminata, O_longistaminata_v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 94. 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 viniferaOryza longistaminata
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 159,489 alignment blocks

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

Uncovered: 450,047,473 out of 486,265,422
Covered: 36,217,949 out of 486,265,422

Uncovered: 11,113,719 out of 32,794,161
Matches: 13,762,446 out of 32,794,161
Mismatches: 7,478,280 out of 32,794,161
Insertions: 439,716 out of 32,794,161
Identity over aligned base-pairs: 63.5%

Oryza longistaminata

Uncovered: 292,875,989 out of 326,442,508
Covered: 33,566,519 out of 326,442,508

Uncovered: 13,852,890 out of 34,512,301
Matches: 13,533,361 out of 34,512,301
Mismatches: 6,696,082 out of 34,512,301
Insertions: 429,968 out of 34,512,301
Identity over aligned base-pairs: 65.5%

Block size distribution

Size range All 159,489 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
983
4.8 kb
10 bp - 100 bp
26,476
1.9 Mb
7,245
539.7 kb
100 bp - 1 kb
124,064
38.3 Mb
47,173
17.2 Mb
1 kb - 10 kb
7,954
12.5 Mb
16,897
34.5 Mb
10 kb - 100 kb
12
183.6 kb
48
676.2 kb