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Arabidopsis thaliana vs Pistacia vera LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Pistacia vera (Pistacia vera, PisVer_v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 100. Arabidopsis thaliana 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

ParameterArabidopsis thalianaPistacia vera
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options

Statistics over 195,980 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 81,437,206 out of 119,667,750
Covered: 38,230,544 out of 119,667,750

Uncovered: 7,313,153 out of 33,775,569
Matches: 18,105,469 out of 33,775,569
Mismatches: 7,749,801 out of 33,775,569
Insertions: 607,146 out of 33,775,569
Identity over aligned base-pairs: 68.4%

Pistacia vera

Uncovered: 605,107,907 out of 671,152,441
Covered: 66,044,534 out of 671,152,441

Uncovered: 7,936,046 out of 38,113,229
Matches: 20,478,210 out of 38,113,229
Mismatches: 8,903,582 out of 38,113,229
Insertions: 795,391 out of 38,113,229
Identity over aligned base-pairs: 67.9%

Block size distribution

Size range All 195,980 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,667
9.5 kb
10 bp - 100 bp
27,867
1.8 Mb
7,939
560.9 kb
100 bp - 1 kb
149,303
53.8 Mb
46,019
18.2 Mb
1 kb - 10 kb
17,137
25.9 Mb
24,858
56.7 Mb
10 kb - 100 kb
6
69.0 kb
408
6.1 Mb