Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate |
Predicted Mutations |
Mean Coverage |
Total Reads |
Percent Mapped |
Mapped Reads |
Average Read Length |
|
A1 F2 I75 R1
|
71 |
32.8 |
2150506 |
93.3% |
2006422 |
83.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,087,432 |
A→G |
intergenic (‑82/‑232) |
rhaD ← / → rhaS |
rhamnulose‑1‑phosphate aldolase/HTH‑type transcriptional activator RhaS |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,087,432 | 0 | A | G | 100.0%
| 189.6
/ NA
| 53 | intergenic (‑82/‑232) | rhaD/rhaS | rhamnulose‑1‑phosphate aldolase/HTH‑type transcriptional activator RhaS |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (30/23); total (30/23) |
CATGCGGATCCTCTAGAGTCGACATATGGTGATCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGACCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGTGATGATGTTCACAATTTGCTGAATT > NZ_CP009273/4087352‑4087512
|
cATGCGGATCCTCTAGAGTCGACATATGGTGATCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGt < 2:4287/90‑1 (MQ=255)
ggATCCTCTAGAGTCGACATATGGTGATCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTg < 1:977036/90‑1 (MQ=255)
ccTCTAGAGTCGACATATGGTGATCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAg > 2:861879/1‑90 (MQ=255)
agTCGACATATGGTGATCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATg > 2:716741/1‑90 (MQ=255)
tCGACATATGGTGATCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATggg > 2:852106/1‑90 (MQ=255)
cGACATATGGTGATCCTGCTGAATTTCATTACGGCCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACa > 1:107165/1‑79 (MQ=255)
cGACATATGGTGATCCTGCTGAATTTCATTACGGCCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACa < 2:107165/79‑1 (MQ=255)
cGACATATGGTGATCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGc > 2:842469/1‑90 (MQ=255)
gACATATGGTGATCCTGCTGAATTTCATTACGACCAGTCT‑AAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCa > 2:1003720/1‑90 (MQ=255)
cATATGGTGATCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCAt > 1:769654/1‑90 (MQ=255)
tatGGTGATCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTg > 1:311739/1‑90 (MQ=255)
atGGTGATCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTgg > 2:203524/1‑90 (MQ=255)
ggTGATCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCa > 2:849418/1‑90 (MQ=255)
ggTGATCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCa > 2:688852/1‑90 (MQ=255)
tGATCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAAc > 2:377319/1‑90 (MQ=255)
tGATCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAAc > 1:771573/1‑90 (MQ=255)
aTCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCa > 2:135981/1‑90 (MQ=255)
aTCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCa < 2:31676/90‑1 (MQ=255)
aTCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCAGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCa > 2:300316/1‑90 (MQ=255)
tCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAAcc < 1:922518/88‑1 (MQ=255)
tCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAAcc > 2:922518/1‑88 (MQ=255)
ctgctgAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGt > 2:982437/1‑56 (MQ=255)
ctgctgAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGt < 1:982437/56‑1 (MQ=255)
ctgctgAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAggg > 2:491946/1‑90 (MQ=255)
ttctgAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGa > 1:227241/3‑90 (MQ=255)
tgctgAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGa > 2:900733/1‑90 (MQ=255)
gctgAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTAc > 2:452506/1‑57 (MQ=255)
gctgAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTAc < 1:452506/57‑1 (MQ=255)
tgAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAg > 2:849523/1‑90 (MQ=255)
tttCATTACGACCAGTCT‑AAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGaa < 1:1003720/90‑1 (MQ=255)
tCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGCTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAAc < 2:97324/90‑1 (MQ=255)
aCGACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGtgat > 1:330541/1‑90 (MQ=255)
gACCAGTCTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGtgatga < 1:159798/90‑1 (MQ=255)
cTAAAAAGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGTGATGATGTTcac < 1:32645/90‑1 (MQ=255)
aaaaaGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGTGATGATGTTCACaa < 1:280668/90‑1 (MQ=255)
aaaGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGTGATGATGTTCACAAtt < 1:849418/90‑1 (MQ=255)
aaaGCGCCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGTGATGATGTTCACAAtt < 1:688852/90‑1 (MQ=255)
gcgcCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGTGATGATGTTCACAATTTGc < 2:878793/90‑1 (MQ=255)
cgcCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAAt > 1:441627/1‑39 (MQ=39)
cgcCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAAt < 2:441627/39‑1 (MQ=39)
cgcCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGa > 2:466098/1‑63 (MQ=255)
cgcCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGa < 1:466098/63‑1 (MQ=255)
cgcCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGtgatga < 1:1035664/75‑1 (MQ=255)
cgcCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGtgatga > 2:1035664/1‑75 (MQ=255)
cgcCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGTGATGATGTTCACAATTTGCt > 1:1014745/1‑90 (MQ=255)
cgcCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGTGATGATGTTCACAATTTGCt > 2:967791/1‑90 (MQ=255)
cgcCTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGTGATGATGTTCACAATTTGCt > 2:277640/1‑90 (MQ=255)
ccTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGtga > 1:169961/1‑70 (MQ=255)
ccTGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGtga < 2:169961/70‑1 (MQ=255)
tGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGTGATGATGTTCACAATTTGCTGAAt < 2:588833/90‑1 (MQ=255)
tGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGTGATGATGTTCACAATTTGCTGAAt < 1:552245/90‑1 (MQ=255)
tGAATTCGCGGCCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGTGATGATGTTCACAATTTGCTGAAt < 1:102044/90‑1 (MQ=255)
gAATTCGCGGGCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGTGATGATGTTCACAATTTGCTGAAtt < 2:769654/90‑1 (MQ=255)
|
CATGCGGATCCTCTAGAGTCGACATATGGTGATCCTGCTGAATTTCATTACGACCAGTCTAAAAAGCGCCTGAATTCGCGACCTTCTCGTTACTGACAGGAAAATGGGCCATTGGCAACCAGGGAAAGATGAACGTGATGATGTTCACAATTTGCTGAATT > NZ_CP009273/4087352‑4087512
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TTTCTATATCCTCAAGAATATGCTTTGCCTTATTGCCTGTGACTTTCTGAGATTCAATTATAGTATCGTTAAATTCTAATGTTAAAGAGAACTCTTTTTTCCGCTTTGTGTAAGTTTAACCTTATATTGATTACCAATATCAAATAAAAAGGTCCTGTAATGAGAATAATCACCTTTAACCTCCTCGGCAAAAC > NZ_CP009273/4258492‑4258685
|
TTTCTATATCCTCAAGAATATGCTTTGCCTTATTGCCTGTGACTTTCTGAGATTCAATTATAGTATCGTTAAATTCTAATGTTAAAGAGAACTCTTTTTC > SRR3722213.976377/1‑100 (MQ=60)
TCTATATCCTCAAGAATATGCTTTGCCTTATTGCCTGTGACTTTCTGAGATTCAATTATAGTATCGTTAAATTCTAATGTTAAAGAGAACTC‑TTTTTCCG > SRR3722213.163703/1‑100 (MQ=60)
tcgtgggctcggagatgtgtataagagacagGCCTGTGACTTTCTGAGATTCAATTATAGTATCGTTAAATTCTAATGTTAAAGAGAACTC‑TTTTTCCGC < SRR3722213.533527/69‑1 (MQ=60)
ATCCTCAAGAATATGCTTTGCCTTATTGCCTGTGACTTTCTGAGATTCAATTATAGTATCGTTAAATTCTAATGTTAAAGAGAACTC‑TTTTTCCGCTTTG > SRR3722213.315318/1‑100 (MQ=60)
AGAATATGCTTTGCCTTATTGCCTGTGACTTTCTGAGATTCAATTATAGTATCGTTAAATTCTAATGTTAAAGAGAACTC‑TTTTTCCGCTTTGTGTAAGT > SRR3722213.666814/1‑100 (MQ=60)
AGAATATGCTTTGCCTTATTGCCTGTGACTTTCTGAGATTCAATTATAGTATCGTTAAATTCTAATGTTAAAGAGAACTC‑TTTTTCCGCTTTGTGTAAGT > SRR3722213.241321/1‑100 (MQ=60)
AGAATATGCTTTGCCTTATTGCCTGTGACTTTCTGAGATTCAATTATAGTATCGTTAAATTCTAATGTTAAAGAGAACTC‑TTTTTCCGCTTTGTGTAAGT > SRR3722213.294209/1‑100 (MQ=60)
AGAATATGCTTTGCCTTATTGCCTGTGACTTTCTGAGATTCAATTATAGTATCGTTAAATTCTAATGTTAAAGAGAACTC‑TTTTTCCGCTTTGTGTAAGT > SRR3722213.445447/1‑100 (MQ=60)
AGAATATGCTTTGCCTTATTGCCTGTGACTTTCTGAGATTCAATTATAGTATCGTTAAATTCTAATGTTAAAGAGAACTC‑TTTTTCCGCTTTGTGTAAGT > SRR3722213.38315/1‑100 (MQ=60)
gtctcgtgggctcggagatgtgtataagagacagCAATTATAGTATCGTTAAATTCTAATGTTAAAGAGAACTC‑TTTTTCCGCTTTGTGTAAGTTTAACC < SRR3722213.940805/66‑1 (MQ=60)
GCTTTGCCTTATTGCCTGTGACTTTCTGAGATTCAATTATAGTATCGTTAAATTCTAATGTTAAAGAGAACTC‑TTTTTCCGCTTTGTGTAAGTTTAACCT < SRR3722213.997998/100‑1 (MQ=60)
GCCTTATTGCCTGTGACTTTCTGAGATTCAATTATAGTATCGTTAAATTCTAATGTTAAAGGGAACTC‑TTTTTCCGCTTTGTGTAAGTTTAACCTTATAT > SRR3722213.593172/1‑100 (MQ=60)
GCCTTATTGCCTGTGACTTTCTGAGATTCAATTATAGTATCGTTAAATTCTAATGTTAAAGAGAACTC‑TTTTTCCGCTTTGTGTAAGTTTAACCTTATAT > SRR3722213.40913/1‑100 (MQ=60)
GCCTTATTGCCTGTGACTTTCTGAGATTCAATTATAGTATCGTTAAATTCTAATGTTAAAGAGAACTC‑TTTTTCCGCTTTGTGTAAGTTTAACCTTATAT > SRR3722213.462777/1‑100 (MQ=60)
GCCTTATTGCCTGTGACTTTCTGAGATTCAATTATAGTATCGTTAAATTCTAATGTTAAAGAGAACTC‑TTTTTCCGCTTTGTGTAAGTTTAACCTTATAT < SRR3722213.914982/100‑1 (MQ=60)
GCCTGTGACTTTCTGAGATTCAATTATAGTATCGTTAAATTCTAATGTTAAAGAGAACTC‑TTTTTCCGCTTTGTGTAAGTTTAACCTTATATTGATTACC > SRR3722213.363773/1‑100 (MQ=60)
CTGTGACTTTCTGAGATTCAATTATAGTATCGTTAAATTCTAATGTTAAAGAGAACTC‑TTTTTCCGCTTTGTGTAAGTTTAACCTTATATTGATTACCAA < SRR3722213.125714/100‑1 (MQ=60)
TTCTGAGATTCAATTATAGTATCGTTAAATTCTAATGTTAAAGAGAACTC‑TTTTTCCGCTTTGTGTAAGTTTAACCTTATATTGATTACCAATATCAAAT > SRR3722213.731925/1‑100 (MQ=60)
CTGAGATTCAATTATAGTATCGTTAAATTCTAATGTTAAAGAGAACTC‑TTTTTCCGCTTTGTGTAAGTTTAACCTTATATTGATTACCAATATCAAATAA < SRR3722213.994645/100‑1 (MQ=60)
TTCAATTATAGTATCGTTAAATTCTAATGTTAAAGAGAACTC‑TTTTTCCGCTTTGTGTAAGTTTAACCTTATATTGATTACCAATATCAAATAAAAAGGT < SRR3722213.173788/100‑1 (MQ=60)
CAATTATAGTATCGTTAAATTCTAATGTTAAAGAGAACTC‑TTTTTCCGCTTTGTGTAAGTTTAACCTTATATTGATTACCAATATCAAATAAAAAGGTCC > SRR3722213.453881/1‑100 (MQ=60)
AGTATCGTTAAATTCTAATGTTAAAGAGAACTC‑TTTTTCCGCTTTGTGTAAGTTTAACCTTATATTGATTACCAATATCAAATAAAAAGGTCCTGTAATG < SRR3722213.202603/100‑1 (MQ=60)
GTTAAATTCTAATGTTAAAGAGAACTC‑TTTTTCCGCTTTGTGTAAGTTTAACCTTATATTGATTACCAATATCAAATAAAAAGGTCCTGTAATGAGAATA > SRR3722213.1052481/1‑100 (MQ=60)
GTTAAAGAGAACTC‑TTTTTCCGCTTTGTGTAAGTTTAACCTTATATTGATTACCAATATCAAATAAAAAGGTCCTGTAATGAGAATAATCACCTTTAACC < SRR3722213.707816/100‑1 (MQ=60)
GTTAAAGAGAACTC‑TTTTTCCGCTTTGTGTAAGTTTAACCTTATATTGATTACCAATATCAAATAAAAAGGTCCTGTAATGAGAATAATCACCTTTAACC < SRR3722213.642554/100‑1 (MQ=60)
GTTAAAGAGAACTC‑TTTTTCCGCTTTGTGTAAGTTTAACCTTATATTGATTACCAATATCAAATAAAAAGGTCCTGTAATGAGAATAATCACCTTTAACC < SRR3722213.264132/100‑1 (MQ=60)
GTTAAAGAGAACTC‑TTTTTCCGCTTTGTGTAAGTTTAACCTTATATTGATTACCAATATCAAATAAAAAGGTCCTGTAATGAGAATAATCACCTTTAACC < SRR3722213.372615/100‑1 (MQ=60)
gtataagagacagcTTTTTCCGCTTTGTGTAAGTTTAACCTTATATTGATTACCAATATCAAATAAAAAGGTCCTGTAATGAGAATAATCACCTTTAACC < SRR3722213.39402/86‑1 (MQ=60)
CTTTTTCCGCTTTGTGTAAGTTTAACCTTATATTGATTACCAATATCAAATAAAAAGGTCCTGTAATGAGAATAATCACCTTTAACCTCCTCGGCAAAAC > SRR3722213.720077/1‑100 (MQ=60)
|
TTTCTATATCCTCAAGAATATGCTTTGCCTTATTGCCTGTGACTTTCTGAGATTCAATTATAGTATCGTTAAATTCTAATGTTAAAGAGAACTCTTTTTTCCGCTTTGTGTAAGTTTAACCTTATATTGATTACCAATATCAAATAAAAAGGTCCTGTAATGAGAATAATCACCTTTAACCTCCTCGGCAAAAC > NZ_CP009273/4258492‑4258685
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
