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 F3 I122 R1
|
193 |
20.9 |
1228102 |
94.7% |
1163012 |
84.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,791,182 |
A→C |
Y292S (TAC→TCC) |
waaL → |
O‑antigen ligase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,791,182 | 0 | A | C | 100.0%
| 93.9
/ NA
| 26 | Y292S (TAC→TCC) | waaL | O‑antigen ligase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (18/8); total (18/8) |
GCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTACGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGTT > NZ_CP009273/3791101‑3791263
|
gCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTg > 2:385884/1‑90 (MQ=255)
gTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCttttt > 1:29487/1‑90 (MQ=255)
tataCCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCa > 1:601996/1‑90 (MQ=255)
aaTGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGa > 2:483696/1‑90 (MQ=255)
aaTGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGa < 1:483696/90‑1 (MQ=255)
aaTGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGa > 2:190721/1‑90 (MQ=255)
tAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATcagc > 1:279141/1‑90 (MQ=255)
aaTAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAatat > 2:526859/1‑56 (MQ=255)
aaTAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAatat < 1:526859/56‑1 (MQ=255)
gtTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAatat < 1:338392/50‑1 (MQ=255)
gtTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAatat > 2:338392/1‑50 (MQ=255)
gtTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAGGTCACCTTTTTCATTTAGATCAGCAGAGTCa > 2:424430/1‑90 (MQ=255)
gtTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGa > 1:21060/1‑78 (MQ=255)
gtTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGa < 2:21060/78‑1 (MQ=255)
gtTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCa > 2:158298/1‑90 (MQ=255)
gtTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCa > 1:94651/1‑90 (MQ=255)
gtTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCa > 2:469862/1‑90 (MQ=255)
ttCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACgcgc < 2:606588/90‑1 (MQ=255)
ccTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGa > 1:393730/1‑90 (MQ=255)
cTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGaa < 2:499620/90‑1 (MQ=255)
cTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGaa < 2:510421/90‑1 (MQ=255)
tAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGaaa > 1:113743/1‑90 (MQ=255)
aGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAg > 2:250742/1‑90 (MQ=255)
cTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTg < 2:94651/90‑1 (MQ=255)
ggCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGtt > 2:209508/1‑90 (MQ=255)
ggCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGtt > 2:201871/1‑90 (MQ=255)
|
GCTATAATGAAGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTACGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGTT > NZ_CP009273/3791101‑3791263
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTACGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGTTAGTTGCAGAACACAATAG > NZ_CP009273/3791111‑3791281
|
tcggcagcgtcagatgtgtataagagacagTGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAG < SRR3721989.344861/70‑1 (MQ=60)
gcgtcagatgtgtataagagacagTACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAG < SRR3721989.538128/76‑1 (MQ=60)
GACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTT > SRR3721989.30003/1‑100 (MQ=60)
CTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCA > SRR3721989.615076/1‑100 (MQ=60)
ATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGC > SRR3721989.284229/1‑100 (MQ=60)
AATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGT < SRR3721989.493907/100‑1 (MQ=60)
TGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCT > SRR3721989.21427/1‑100 (MQ=60)
TGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCA > SRR3721989.96370/1‑100 (MQ=60)
GTGTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGA > SRR3721989.401703/1‑100 (MQ=60)
GTTACTTCCCTAGGTGCAAGACTGGCAATGTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAA > SRR3721989.115822/1‑100 (MQ=60)
GTCCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGTTAGTTGCAGAACACAAT < SRR3721989.393647/100‑1 (MQ=60)
CCGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGTTAGTTGCAGAACACAATAG < SRR3721989.205548/100‑1 (MQ=60)
|
AGCATTAAATGACTTAAACAGTTATACCAATGCTAATAGTGTTACTTCCCTAGGTGCAAGACTGGCAATGTACGAAATTGGTTTAAATATATTCATAAAGTCACCTTTTTCATTTAGATCAGCAGAGTCACGCGCTGAAAGTATGAATTTGTTAGTTGCAGAACACAATAG > NZ_CP009273/3791111‑3791281
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
