Vitis vinifera vs Hordeum vulgare LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Hordeum vulgare (Hordeum vulgare subsp. vulgare, IBSC_v2) 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 viniferaHordeum vulgare
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 250,538 alignment blocks

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

Uncovered: 446,621,355 out of 486,265,422
Covered: 39,644,067 out of 486,265,422

Uncovered: 10,585,218 out of 32,794,161
Matches: 14,266,418 out of 32,794,161
Mismatches: 7,478,435 out of 32,794,161
Insertions: 464,090 out of 32,794,161
Identity over aligned base-pairs: 64.2%

Hordeum vulgare

Uncovered: 4,773,954,905 out of 4,834,432,680
Covered: 60,477,775 out of 4,834,432,680

Uncovered: 18,218,495 out of 44,420,163
Matches: 16,876,048 out of 44,420,163
Mismatches: 8,673,243 out of 44,420,163
Insertions: 652,377 out of 44,420,163
Identity over aligned base-pairs: 64.4%

Block size distribution

Size range All 250,538 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,249
6.2 kb
10 bp - 100 bp
44,547
3.2 Mb
17,662
1.3 Mb
100 bp - 1 kb
191,896
58.7 Mb
92,385
32.9 Mb
1 kb - 10 kb
12,814
21.0 Mb
24,933
47.9 Mb
10 kb - 100 kb
32
544.9 kb
87
1.3 Mb