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 I228 R1
|
214 |
26.5 |
1448192 |
97.1% |
1406194 |
86.4 |
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 | 93.1%
| 80.2
/ ‑0.5
| 30 | intergenic (‑237/‑543) | flhD/uspC | flagellar transcriptional regulator FlhD/universal stress protein UspC |
| Reads supporting (aligned to +/- strand): ref base A (1/1); new base G (11/16); total (13/17) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.00e-01 |
AGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTG > NZ_CP009273/1972612‑1972776
|
aGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGc < 2:357672/90‑1 (MQ=255)
aTGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGAtt < 2:398416/90‑1 (MQ=255)
gggTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGGCTGCGAttt < 2:705487/90‑1 (MQ=255)
tttACACTTATCTAAGATTTTTCCTAAATCGACGCAACGGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCaata > 1:419344/1‑90 (MQ=255)
ttATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTg > 2:628714/1‑90 (MQ=255)
cTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGc < 2:438012/90‑1 (MQ=255)
ttttCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATcac > 1:205024/1‑90 (MQ=255)
tttCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATcaca > 2:464697/1‑90 (MQ=255)
tttCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATcaca > 1:713330/1‑90 (MQ=255)
tttCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGAGGGGGGCTGCGa > 1:322390/1‑62 (MQ=255)
tttCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGAGGGGGGCTGCGa < 2:322390/62‑1 (MQ=255)
tttCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GG‑GGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATcacac > 1:262928/1‑90 (MQ=255)
ccTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACaa < 2:506931/90‑1 (MQ=255)
cTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACaaa < 1:208707/90‑1 (MQ=255)
aaaTCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAac < 2:400948/90‑1 (MQ=255)
aTCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAacac < 1:561565/90‑1 (MQ=255)
aTCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAacac < 1:481717/90‑1 (MQ=255)
gACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCa > 2:397069/1‑90 (MQ=255)
cGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAAt < 2:713330/90‑1 (MQ=255)
gCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAAtt < 1:316904/90‑1 (MQ=255)
gTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACAC‑AAACCCTCCATTACtttag > 1:432717/1‑87 (MQ=255)
cTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAgga < 2:23964‑M1/90‑4 (MQ=255)
tCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggt > 2:536742‑M1/1‑83 (MQ=255)
cACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtg < 1:570898‑M1/90‑9 (MQ=255)
cacGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaac < 2:497693‑M1/90‑14 (MQ=255)
cGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaa < 2:205024‑M1/90‑16 (MQ=255)
cacaTACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagt > 2:225463‑M1/1‑73 (MQ=255)
aC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgata < 2:504100‑M1/90‑26 (MQ=255)
aC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgata > 2:622219‑M1/1‑65 (MQ=255)
aC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgata > 2:704323‑M1/1‑65 (MQ=255)
|
AGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTG > NZ_CP009273/1972612‑1972776
|
| 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
TAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTAT > NZ_CP009273/1972594‑1972788
|
TAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGG < SRR3722112.187476/100‑1 (MQ=60)
attcgtcggcagcgtcagatgtgtataagagacagATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGG < SRR3722112.146179/65‑1 (MQ=60)
tcgtcggcagcgtcagatgtgtataagagacagATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGC < SRR3722112.83732/67‑1 (MQ=60)
GAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACGGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATA > SRR3722112.424899/1‑100 (MQ=60)
TATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCAC > SRR3722112.207509/1‑100 (MQ=60)
ATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACA > SRR3722112.724478/1‑100 (MQ=60)
ATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAActgtctcttatacacatc > SRR3722112.326191/1‑82 (MQ=60)
ATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGG‑GGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACAC > SRR3722112.266018/1‑100 (MQ=60)
CTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATT < SRR3722112.211234/100‑1 (MQ=60)
ATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTT < SRR3722112.488621/100‑1 (MQ=60)
ATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTT < SRR3722112.570084/100‑1 (MQ=60)
CGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAccctccattactttag > SRR3722112.438617/1‑84 (MQ=60)
GCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaa < SRR3722112.320578/100‑5 (MQ=60)
CACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtc < SRR3722112.579594/100‑19 (MQ=60)
CATACAACGGGGGGGGGCTTCGATTTTCAATAATGCGTGATGCAGATCAAACAAAACGCTCAATTACTTAAggaaggtgcgaacaaatccctgatatgag > SRR3722112.206750/1‑71 (MQ=60)
GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtt > SRR3722112.707956/1‑63 (MQ=60)
|
TAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTAT > NZ_CP009273/1972594‑1972788
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
