Vitis vinifera vs Manihot esculenta LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Manihot esculenta (Manihot esculenta, Manihot_esculenta_v6) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 91. 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 viniferaManihot esculenta
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 258,475 alignment blocks

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

Uncovered: 407,605,753 out of 486,265,422
Covered: 78,659,669 out of 486,265,422

Uncovered: 3,332,126 out of 32,794,161
Matches: 21,044,388 out of 32,794,161
Mismatches: 7,892,335 out of 32,794,161
Insertions: 525,312 out of 32,794,161
Identity over aligned base-pairs: 71.4%

Manihot esculenta

Uncovered: 491,763,147 out of 582,117,524
Covered: 90,354,377 out of 582,117,524

Uncovered: 3,355,332 out of 38,679,430
Matches: 25,616,380 out of 38,679,430
Mismatches: 9,050,509 out of 38,679,430
Insertions: 657,209 out of 38,679,430
Identity over aligned base-pairs: 72.5%

Block size distribution

Size range All 258,475 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,867
9.8 kb
10 bp - 100 bp
39,537
2.6 Mb
13,070
918.5 kb
100 bp - 1 kb
184,962
67.6 Mb
64,567
23.1 Mb
1 kb - 10 kb
31,919
57.1 Mb
26,463
66.2 Mb
10 kb - 100 kb
190
3.0 Mb
865
19.4 Mb
100 kb - 1 Mb
74
19.4 Mb
1 Mb - 10 Mb
1
1.2 Mb