Vitis vinifera vs Aegilops tauschii LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Aegilops tauschii (Aegilops tauschii subsp. strangulata, Aet_v4.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 95. 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 viniferaAegilops tauschii
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 249,685 alignment blocks

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

Uncovered: 448,899,562 out of 486,265,422
Covered: 37,365,860 out of 486,265,422

Uncovered: 10,596,954 out of 32,794,161
Matches: 14,413,818 out of 32,794,161
Mismatches: 7,297,683 out of 32,794,161
Insertions: 485,706 out of 32,794,161
Identity over aligned base-pairs: 64.9%

Aegilops tauschii

Uncovered: 4,162,071,900 out of 4,224,915,394
Covered: 62,843,494 out of 4,224,915,394

Uncovered: 23,986,931 out of 53,210,770
Matches: 18,785,597 out of 53,210,770
Mismatches: 9,662,675 out of 53,210,770
Insertions: 775,567 out of 53,210,770
Identity over aligned base-pairs: 64.3%

Block size distribution

Size range All 249,685 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,311
6.6 kb
10 bp - 100 bp
45,875
3.2 Mb
20,151
1.4 Mb
100 bp - 1 kb
189,051
59.1 Mb
87,861
31.7 Mb
1 kb - 10 kb
13,400
20.2 Mb
26,165
48.9 Mb
10 kb - 100 kb
48
1.0 Mb
76
1.4 Mb
100 kb - 1 Mb
1
119.6 kb