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Vitis vinifera vs Nicotiana attenuata LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Nicotiana attenuata (Nicotiana attenuata, NIATTr2) 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 viniferaNicotiana attenuata
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 218,979 alignment blocks

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

Uncovered: 438,569,948 out of 486,265,422
Covered: 47,695,474 out of 486,265,422

Uncovered: 9,277,381 out of 32,794,161
Matches: 16,143,415 out of 32,794,161
Mismatches: 6,897,612 out of 32,794,161
Insertions: 475,753 out of 32,794,161
Identity over aligned base-pairs: 68.6%

Nicotiana attenuata

Uncovered: 1,435,622,376 out of 1,492,146,380
Covered: 56,524,004 out of 1,492,146,380

Uncovered: 4,791,913 out of 23,314,391
Matches: 13,037,905 out of 23,314,391
Mismatches: 5,140,177 out of 23,314,391
Insertions: 344,396 out of 23,314,391
Identity over aligned base-pairs: 70.4%

Block size distribution

Size range All 218,979 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,305
7.0 kb
1
5.0 bp
10 bp - 100 bp
37,440
2.6 Mb
17,231
1.2 Mb
100 bp - 1 kb
164,603
54.6 Mb
75,221
25.6 Mb
1 kb - 10 kb
15,566
25.5 Mb
24,252
54.0 Mb
10 kb - 100 kb
64
1.3 Mb
191
2.8 Mb
100 kb - 1 Mb
1
139.4 kb
3
469.3 kb