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Vitis vinifera vs Setaria italica LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Setaria italica (Setaria italica, Setaria_italica_v2.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 93. 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)3000
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 italica
Chunk size50,000,000100,100,000
Overlap0100,000
Group set size0100,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 174,610 alignment blocks

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

Uncovered: 446,871,815 out of 486,265,422
Covered: 39,393,607 out of 486,265,422

Uncovered: 10,052,844 out of 32,794,161
Matches: 14,897,122 out of 32,794,161
Mismatches: 7,348,487 out of 32,794,161
Insertions: 495,708 out of 32,794,161
Identity over aligned base-pairs: 65.5%

Setaria italica

Uncovered: 369,279,846 out of 405,732,883
Covered: 36,453,037 out of 405,732,883

Uncovered: 15,594,245 out of 39,583,990
Matches: 15,669,643 out of 39,583,990
Mismatches: 7,764,242 out of 39,583,990
Insertions: 555,860 out of 39,583,990
Identity over aligned base-pairs: 65.3%

Block size distribution

Size range All 174,610 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,172
5.6 kb
10 bp - 100 bp
28,332
2.0 Mb
8,654
625.2 kb
100 bp - 1 kb
135,541
42.9 Mb
49,962
18.8 Mb
1 kb - 10 kb
9,565
14.0 Mb
19,720
38.8 Mb
10 kb - 100 kb
42
566.9 kb