Hordeum vulgare vs Triticum turgidum LastZ results

Hordeum vulgare (Hordeum vulgare subsp. vulgare, IBSC_v2) and Triticum turgidum (Triticum turgidum subsp. durum, Svevo.v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 100. Hordeum vulgare 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)5000
Threshold for gapped extension (L)5000
Threshold for alignments between gapped alignment blocks (H)3000
Masking count (M)10
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

ParameterHordeum vulgareTriticum turgidum
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options

Statistics over 5,640,000 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Hordeum vulgare

Uncovered: 3,980,358,769 out of 4,834,432,680
Covered: 854,073,911 out of 4,834,432,680

Uncovered: 2,472,657 out of 44,420,163
Matches: 37,702,255 out of 44,420,163
Mismatches: 3,699,824 out of 44,420,163
Insertions: 545,427 out of 44,420,163
Identity over aligned base-pairs: 89.9%

Triticum turgidum

Uncovered: 7,830,443,914 out of 10,463,058,104
Covered: 2,632,614,190 out of 10,463,058,104

Uncovered: 5,840,858 out of 88,577,667
Matches: 73,429,752 out of 88,577,667
Mismatches: 8,528,858 out of 88,577,667
Insertions: 778,199 out of 88,577,667
Identity over aligned base-pairs: 88.8%

Block size distribution

Size range All 5,640,000 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
85,007
449.2 kb
10 bp - 100 bp
1,130,569
69.4 Mb
562,589
37.3 Mb
100 bp - 1 kb
3,501,330
1.3 Gb
1,786,000
668.7 Mb
1 kb - 10 kb
922,331
1.9 Gb
798,077
2.2 Gb
10 kb - 100 kb
763
8.4 Mb
27,196
378.3 Mb
100 kb - 1 Mb
62
9.8 Mb
1 Mb - 10 Mb
1
1.1 Mb