In this section

Phytophthora ramorum vs Bigelowiella natans LastZ results

Phytophthora ramorum (Phytophthora ramorum, ASM14973v1) and Bigelowiella natans (Bigelowiella natans CCMP2755, Bigna1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Phytophthora ramorum 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

ParameterPhytophthora ramorumBigelowiella natans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 8,048 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora ramorum

Uncovered: 64,891,709 out of 66,652,401
Covered: 1,760,692 out of 66,652,401

Uncovered: 20,792,753 out of 22,377,278
Matches: 966,246 out of 22,377,278
Mismatches: 567,450 out of 22,377,278
Insertions: 50,829 out of 22,377,278
Identity over aligned base-pairs: 61.0%

Bigelowiella natans

Uncovered: 93,228,800 out of 94,701,163
Covered: 1,472,363 out of 94,701,163

Uncovered: 27,510,622 out of 28,817,508
Matches: 797,768 out of 28,817,508
Mismatches: 471,629 out of 28,817,508
Insertions: 37,489 out of 28,817,508
Identity over aligned base-pairs: 61.0%

Block size distribution

Size range All 8,048 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
35
195.0 bp
10 bp - 100 bp
2,765
192.6 kb
576
40.1 kb
100 bp - 1 kb
4,879
1.3 Mb
2,492
977.0 kb
1 kb - 10 kb
368
606.4 kb
565
1.1 Mb
10 kb - 100 kb
1
11.4 kb
8
91.3 kb