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 |
|
A21 F97 I0 R1
|
51 |
42.6 |
1617048 |
90.7% |
1466662 |
142.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_000913 |
4,196,203 |
C→T |
100% |
intergenic (‑104/+129) |
thiC ← / ← rsd |
phosphomethylpyrimidine synthase/regulator of sigma D |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 4,196,203 | 0 | C | T | 98.4%
| 106.0
/ ‑6.3
| 36 | intergenic (‑104/+129) | thiC/rsd | phosphomethylpyrimidine synthase/regulator of sigma D |
| Reads supporting (aligned to +/- strand): ref base C (0/0); major base T (14/21); minor base A (0/1); total (14/22) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CGCGTTGTTCGCGGCGGGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAG > NC_000913/4196063‑4196339
|
cgcgTTGTTCGCTGCGGGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTTGc < 1:394069/143‑1 (MQ=255)
gTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTTGCAGGTATTAGCCTGATCa < 2:622718/143‑1 (MQ=255)
gttgCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTTGCAGGTATTAGCCTGATCAGGTTCcgcg < 1:79116/143‑1 (MQ=255)
gttgCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTTGCAGGTATTAGCCTGATCAGGTTCcgcg < 1:394065/143‑1 (MQ=255)
cAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTTGCAGGTATTAGCCTGATCAGGTTCCGCCGacc > 2:135686/1‑141 (MQ=255)
gACATATCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTTGCAGGTATTAGCCTGATCAGGTTCCGCGGATccc < 2:222937/143‑1 (MQ=255)
cTCATTCCACACAGTTAAGGACGTGGCTTGTCATACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTACCTCTTGTTCCCTTTGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATaaa < 1:699631/143‑1 (MQ=255)
ttCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTTGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGt < 1:478571/143‑1 (MQ=255)
aaaaaGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGCCGATCGCCGCGGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTTGCAGGTCTTCGCCTGATCAGGTTCCGCGGCTCGTGAATAAACGCTCGCa > 2:733705/1‑143 (MQ=255)
aaaaaGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTTGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACggacgca > 2:101149/1‑138 (MQ=255)
aaGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTTGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGcc < 2:271723/143‑1 (MQ=255)
aaGGACGTGGCTTGTCCGACGACGGATGAGGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTTGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTa < 2:208067/143‑1 (MQ=255)
aaGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTTGCAGGTATTAGCCGGATCAGGGTCCGCGGATCCCGAACAAACGGTCccagccaggca > 2:560005/1‑140 (MQ=255)
ggACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTTGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAg > 2:739880/1‑143 (MQ=255)
gACGTGGCCTGCCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTTGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAgg < 1:499227/143‑1 (MQ=255)
tCAGACGACGGATGCAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTTGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAACCGGTCTCAGCCAGTTAAGGCACTCCGACaa > 1:313332/1‑143 (MQ=255)
aaGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTTGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGGTCAGGCACTCCGACAAGAAATTAGCCCCGc > 1:357536/1‑143 (MQ=255)
aCGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTTGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGc < 1:398566/143‑1 (MQ=255)
aCGATAGACGCAGGCGCGATGCGATAGCAGATTCACTCTTGTTCCCTTTGCAGGGATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGc < 1:542776/143‑1 (MQ=255)
accgccgcAGGGGCGATGCCATAGCAGATTAACTCTTGTTCCCTTTGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAACCGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCAtt < 1:462499/141‑1 (MQ=255)
tgcgatAGCAGATTAACTCTTGTTCCCTTTGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCACATGGGGCATTGAATGTAAATTAcgcg > 2:570706/1‑143 (MQ=255)
tgcgatAGCAGATTAACTCTTGTTCCCTTTGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTAcgca > 2:81631/1‑142 (MQ=255)
gatAGCAGATTAACTCTTGTTCCCTTTGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCAGAATAAACGGTCTCAGCCCGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTGcgcgcga > 1:254448/1‑140 (MQ=255)
agaGCAGATTACCTCTTGTTCCCTTTGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTaa < 1:727233/141‑1 (MQ=255)
aGCAGATTAACTCGTGTTCCCTTTGCAGGTATTAGCCTGATCAGGTTCCGCTGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACa < 1:64989/143‑1 (MQ=255)
aGCAGATCAACTCTTGTTCCCTTTGCAGGAATTAGCTTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCGGCCAGTTAAGGAACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACa < 2:302525/143‑1 (MQ=255)
gCAGATTAACTCTTGTTCCCTTTGCAGGTATTAGCCTGATCAGAGTCCGCCGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAg < 2:354522/143‑1 (MQ=255)
aGATTAACTCTTGTTCCCTTTGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCACAGACAATTAGGTCGCTCCGACAAGAAATAAGCCCCGCAAATGGGGCAGTGAATGTAAATTACGCGTTAACcgcg > 2:653180/1‑143 (MQ=255)
aTTCACTCTTGTTCCCTTTGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCa < 2:806121/143‑1 (MQ=255)
aTTAACTCTTGTTCCCTTTGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCa < 1:513005/143‑1 (MQ=255)
tAACTCTTGTTCCCGTAGCAGGTATTAGCCTGAGCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGa < 1:324776/143‑1 (MQ=255)
aaCTCTTGTTCCCTTTGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGaa < 1:769199/143‑1 (MQ=255)
tctTGTTCCCTTTGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTc > 1:478683/1‑143 (MQ=255)
tGTTCCCTTTGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAg > 2:38920/1‑143 (MQ=255)
ttCCCTTTGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCa > 1:627970/1‑143 (MQ=255)
tCCCTTTGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAg < 1:256916/143‑1 (MQ=255)
|
CGCGTTGTTCGCGGCGGGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCAAGCAG > NC_000913/4196063‑4196339
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
