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Arabidopsis thaliana vs Cucumis sativus LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Cucumis sativus (Cucumis sativus, ASM407v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 91. 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 thalianaCucumis sativus
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 111,212 alignment blocks

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

Uncovered: 86,090,083 out of 119,667,750
Covered: 33,577,667 out of 119,667,750

Uncovered: 9,673,734 out of 33,775,569
Matches: 16,280,672 out of 33,775,569
Mismatches: 7,315,063 out of 33,775,569
Insertions: 506,100 out of 33,775,569
Identity over aligned base-pairs: 67.5%

Cucumis sativus

Uncovered: 163,352,304 out of 193,829,320
Covered: 30,477,016 out of 193,829,320

Uncovered: 6,191,625 out of 26,192,424
Matches: 13,428,071 out of 26,192,424
Mismatches: 6,043,108 out of 26,192,424
Insertions: 529,620 out of 26,192,424
Identity over aligned base-pairs: 67.1%

Block size distribution

Size range All 111,212 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,038
5.7 kb
10 bp - 100 bp
16,323
1.1 Mb
3,374
232.7 kb
100 bp - 1 kb
85,542
29.9 Mb
17,423
7.0 Mb
1 kb - 10 kb
8,309
12.4 Mb
13,052
31.4 Mb
10 kb - 100 kb
281
4.8 Mb