Triticum dicoccoides vs Hordeum vulgare LastZ results

Triticum dicoccoides (Triticum dicoccoides, WEWSeq_v.1.0) and Hordeum vulgare (Hordeum vulgare subsp. vulgare, IBSC_v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 95. Triticum dicoccoides 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)
Gap extend penalty (E)
HSP threshold (K)
Threshold for gapped extension (L)
Threshold for alignments between gapped alignment blocks (H)
Masking count (M)
Seed and Transition value (T)
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

ParameterTriticum dicoccoidesHordeum vulgare
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 3,357,299 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Triticum dicoccoides

Uncovered: 8,832,852,184 out of 10,079,039,394
Covered: 1,246,187,210 out of 10,079,039,394

Uncovered: 2,715,730 out of 81,268,905
Matches: 69,956,824 out of 81,268,905
Mismatches: 7,741,500 out of 81,268,905
Insertions: 854,851 out of 81,268,905
Identity over aligned base-pairs: 89.1%

Hordeum vulgare

Uncovered: 3,995,118,014 out of 4,834,432,680
Covered: 839,314,666 out of 4,834,432,680

Uncovered: 2,032,746 out of 44,420,163
Matches: 38,005,990 out of 44,420,163
Mismatches: 3,810,576 out of 44,420,163
Insertions: 570,851 out of 44,420,163
Identity over aligned base-pairs: 89.7%

Block size distribution

Size range All 3,357,299 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
45,877
248.2 kb
10 bp - 100 bp
608,517
37.4 Mb
246,340
16.5 Mb
100 bp - 1 kb
2,182,930
823.2 Mb
1,055,311
415.5 Mb
1 kb - 10 kb
519,801
1.0 Gb
475,605
1.2 Gb
10 kb - 100 kb
174
2.0 Mb
12,360
193.0 Mb
100 kb - 1 Mb
66
11.3 Mb