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 I207 R1
|
218 |
45.0 |
2482936 |
97.1% |
2410930 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,972,691 |
A→G |
intergenic (‑237/‑543) |
flhD ← / → uspC |
flagellar transcriptional regulator FlhD/universal stress protein UspC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,972,691 | 0 | A | G | 100.0%
| 115.4
/ NA
| 34 | intergenic (‑237/‑543) | flhD/uspC | flagellar transcriptional regulator FlhD/universal stress protein UspC |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (19/15); total (19/15) |
TACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTG > NZ_CP009273/1972605‑1972776
|
tACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACgggggg > 2:307530/1‑90 (MQ=255)
aaTAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGc > 2:929208/1‑90 (MQ=255)
aGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGc < 1:1019889/90‑1 (MQ=255)
gAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCg > 2:426382/1‑90 (MQ=255)
aaaTGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGa < 2:655713/90‑1 (MQ=255)
gTCTTTACCCTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCa > 2:721035/1‑90 (MQ=255)
ttACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCaataa > 2:459884/1‑90 (MQ=255)
ttACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCaataa > 2:440195/1‑90 (MQ=255)
ttACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCaataa < 1:144566/90‑1 (MQ=255)
cTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGt < 2:805819/90‑1 (MQ=255)
cTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGt < 1:340050/90‑1 (MQ=255)
cTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGt > 2:1075233/1‑90 (MQ=255)
ttATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGAttt < 1:657632/77‑1 (MQ=255)
ttATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGAttt > 2:657632/1‑77 (MQ=255)
ttATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTg > 1:175877/1‑90 (MQ=255)
tATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGa > 1:1232848/1‑90 (MQ=255)
tATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGCGa > 1:941663/1‑90 (MQ=255)
gATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGAt < 1:721035/90‑1 (MQ=255)
gATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGAt < 1:765930/90‑1 (MQ=255)
aaaTCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAac < 1:511872/90‑1 (MQ=255)
aaaTCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAac > 2:562898/1‑90 (MQ=255)
aTCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAacac < 1:134198/90‑1 (MQ=255)
gCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAAtt < 2:646259/90‑1 (MQ=255)
cGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaag > 1:619055‑M1/1‑85 (MQ=255)
cGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaag > 1:998918‑M1/1‑85 (MQ=255)
gTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaagg < 2:131052‑M1/90‑7 (MQ=255)
cTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcg < 1:982982‑M1/90‑11 (MQ=255)
acGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaaca < 1:1206182‑M1/90‑15 (MQ=255)
cGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaa > 2:652626‑M1/1‑75 (MQ=255)
cacaTACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagt > 2:575297‑M1/1‑73 (MQ=255)
cacaTACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagt > 1:244949‑M1/1‑73 (MQ=255)
aTACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccc < 1:432758‑M1/90‑21 (MQ=255)
aTACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccc > 1:1064739‑M1/1‑70 (MQ=255)
cAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctga > 2:178790‑M1/1‑67 (MQ=255)
aCGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgata > 1:557861‑M1/1‑65 (MQ=255)
|
TACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTG > NZ_CP009273/1972605‑1972776
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ 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
TAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACA‑ACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGT > NZ_CP009273/1972594‑1972784
|
TAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACA‑ACGGGGG < SRR3722089.892377/100‑1 (MQ=60)
TAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACA‑ACGGGGG < SRR3722089.164756/100‑1 (MQ=60)
AGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACA‑ACGGGGGGGGGCTGCGATTTTCAAT < SRR3722089.1035086/100‑1 (MQ=60)
caGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACA‑ACGGGGGGGGGCTGCGATTTTCAATAATGC < SRR3722089.666103/98‑1 (MQ=60)
GTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACA‑ACGGGGGGGGGCTGCGATTTTCAATAATGCGTG > SRR3722089.178077/1‑100 (MQ=60)
TCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACA‑ACGGGGGGGGGCTGCGATTTTCAATAATGCGTGA > SRR3722089.1251588/1‑100 (MQ=60)
TCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACA‑ACGGGGGGGGGCTGCGATTTTCAATAATGCGCGA > SRR3722089.955456/1‑100 (MQ=60)
TTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACA‑ACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGC < SRR3722089.146356/100‑1 (MQ=60)
CTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACA‑ACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATC < SRR3722089.344285/100‑1 (MQ=60)
GATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACA‑ACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAAC < SRR3722089.776228/100‑1 (MQ=60)
GATTTTTCCTAAACCGACGCAACTGTACTCGTCACTACACGCACATACA‑ACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAAC < SRR3722089.730417/100‑1 (MQ=60)
AAATCGACGCAACTGTACTCGTCACTACACGCACATACA‑ACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTAC < SRR3722089.517899/100‑1 (MQ=60)
ATCGACGCAACTGTACTCGTCACTACACGCACATACA‑ACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTT < SRR3722089.135824/100‑1 (MQ=60)
nnnnnntgnnntagnnnnnnnACGCACATACA‑ACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAgga < SRR3722089.171198/79‑4 (MQ=60)
CAACTGTACTCGTCACTACACGCACATACA‑ACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaag > SRR3722089.1013768/1‑95 (MQ=60)
CAACTGTACTCGTCACTACACGCACATACA‑ACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaag > SRR3722089.626824/1‑95 (MQ=60)
TCACTACACGCACATACA‑ACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagt > SRR3722089.248069/1‑83 (MQ=60)
CTACACGCACATACA‑ACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccc < SRR3722089.997554/100‑21 (MQ=60)
CTACACGCACATACA‑ACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccc > SRR3722089.1080724/1‑80 (MQ=60)
agacagCATACA‑ACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctga < SRR3722089.1082963/94‑24 (MQ=60)
ACGCACATACA‑ACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgat < SRR3722089.1224523/100‑25 (MQ=60)
CGCACATACA‑ACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgata > SRR3722089.564342/1‑75 (MQ=60)
CATACA‑ACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgag > SRR3722089.383553/1‑71 (MQ=60)
CATACA‑ACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgag > SRR3722089.794857/1‑71 (MQ=60)
ATACA‑ACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgaga < SRR3722089.604975/100‑31 (MQ=60)
ATACA‑ACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgaga < SRR3722089.437963/100‑31 (MQ=60)
TACA‑ACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagat > SRR3722089.413808/1‑69 (MQ=60)
ACAGACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagat < SRR3722089.494693/100‑32 (MQ=60)
CA‑ACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagactg > SRR3722089.765806/1‑67 (MQ=60)
|
TAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACA‑ACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGT > NZ_CP009273/1972594‑1972784
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
