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 |
|
A5 F216 I0 R1
|
247 |
44.8 |
1629152 |
98.0% |
1596568 |
139.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_000913 |
1,955,176 |
Δ1 bp |
14.7% |
coding (1832/2430 nt) |
torZ ← |
trimethylamine N‑oxide reductase system III, catalytic subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,955,176 | 0 | T | . | 14.7%
| 102.2
/ 12.4
| 34 | coding (1832/2430 nt) | torZ | trimethylamine N‑oxide reductase system III, catalytic subunit |
| Reads supporting (aligned to +/- strand): ref base T (15/14); new base . (3/2); total (18/16) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.22e-01 |
TTCATCAGGAGCCAGCCAGGTTGGGTGTGCCGGGCAATCCTTATAGCCAAATTTTTCCAACGTTTTTGAATAGATTTCAATTTTGCCGCTTGGCGTACCCAGCGCATTTTTCACCGGATCGGCGCGGAAATCACCATAACGAAC‑GTACTGTTCGTTCTTCTCGCTGTGGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTGCGCACGGGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCATTTCATCTTTACCTTC > NC_000913/1955028‑1955324
|
ttCATCAGGAGCCAGCCAGGTTGGGTGTGCCGGGCAATCCTTATAGCCAAATTTTTCCAACGTTTTTGAATAGATTTCAATTTTGCCGCTTGGCGTACCCAGCGCATTTTTCACCGGATCGGCGCGGAAATCACCATAACGAAC‑GTACt > 1:160254/1‑149 (MQ=255)
caGGAGCCAGCCAGGTTGGGTGTGCCGGGCAATCCTTATAGCCAAATTTTTCCAACGTTTTTGAATAGATTTCAATTTTGCCGCTTGGCGTACCCAGCGCATTTTTCACCGGATCGGCGCGGAAATCACCATAACGAAC‑GTACTgttc < 3:329410/148‑1 (MQ=255)
ggAGCCAGCCAGGTTGGGTGTGCCGGGCAATCCTTATAGCCAAATTTTTCCAACGTTTTTGAATAGATTTCAATTTTGCCGCTTGGCGTACCCAGCGCATTTTTCACCGGATCGGCGCGGAAATCACCATAACGAAC‑GTACTgttcgtt > 2:381930/1‑149 (MQ=255)
gAGCCAGCCAGGTTGGGTGTGCCGGGCAATCCTTATAGCCAAATTTTTCCAACGTTTTTGAATAGATTTCAATTTTGCCGCTTGGCGTACCCAGCGCATTTTTCACCGGATCGGCGCGGAAATCACCATAACGAAC‑GTACTgttcgtt < 4:372187/148‑1 (MQ=255)
gccagGTTGGGTGTGCCGGGCAATCCTTATAGCCAAATTTTTCCAACGTTTTTGAATAGATTTCAATTTTGCCGCTTGGCGTACCCAGCGCATTTTTCACCGGATCGGCGCGGAAATCACCATAACGAAC‑GTACTGTTCGTTCTtctc > 3:367973/1‑148 (MQ=255)
ggTTGGGTGTGCCGGGCAATCCTTATAGCCAAATTTTTCCAACGTTTTTGAATAGATTTCAATTTTGCCGCTTGGCGTACCCAGCGCATTTTTCACCGGATCGGCGCGGAAATCACCATAACGAAC‑GTACTGTTCGTTCTTCTCGCtgt < 1:381930/149‑1 (MQ=255)
ccGGGCAATCCTTATAGCCAAATTTTTCCAACGTTTTTGAATAGATTTCAATTTTGCCGCTTGGCGTACCCAGCGCATTTTTCACCGGATCGGCGCGGAAATCACCATAACGAAC‑GTACTGTTCGTTCTTCTCGCTGTGGCGCATTTc < 3:369468/148‑1 (MQ=255)
aaTCCTTATAGCCAAATTTTTCCAACGTTTTTGAATAGATTTCAATTTTGCCGCTTGGCGTACCCAGCGCATTTTTCACCGGATCGGCGCGGAAATCACCATAACGAAC‑GTACTGTTCGTTCTTCTCGCTGTGGCGCATTTCGATCAg < 4:176617/148‑1 (MQ=255)
tCCTTATAGCCAAATTTTTCCAACGTTTTTGAATAGATTTCAATTTTGCCGCTTGGCGTACCCAGCGCATTTTTCACCGGATCGGCGCGGAAATCACCTTAACGAAC‑GTACTGTTCGTTCTTCTCGCTGTGGCGCATTTCGATCAGttt > 2:335949/1‑149 (MQ=255)
ccAAATTTTTCCAACGTTTTTGAATAGATTTCAATTTTGCCGCTTGGCGTACCCAGCGCATTTTTCACCGGATCGGCGCGGAAATCACCATAACGAAC‑GTACTGTTCGTTCTTCTCGCTGTGGCGCATTTCGATCAGTTTATTTtgctg > 1:257019/1‑149 (MQ=255)
ccAAATTTTTCCAACGTTTTTGAATAGATTTCAATTTTGCCGCTTGGCGTACCCAGCGCATTTTTCACCGGATCGGCGCGGAAATCACCATAACGAAC‑GTACTGTTCGTTCTTCTCGCTGTGGCGCATTTCGATCAGTTTATTTtgctg > 2:211906/1‑149 (MQ=255)
cAAATTTTTCCAACGTTTTTGAATAGATTTCAATTTTGCCGCTTGGCGTACCCAGCGCATTTTTCACCGGATCGGCGCGGAAATCACCATAACGAAC‑GTACTGTTCGTTCTTCTCGCTGTGGCGCATTTCGATCAGTTTATTTtgctg > 3:226229/1‑148 (MQ=255)
cAAATTTTTCCAACGTTTTTGAATAGATTTCAATTTTGCCGCTTGGCGTACCCAGCGCATTTTTCACCGGATCGGCGCGGAAATCACCATAACGAAC‑GTACTGTTCGTTCTTCTCGCTGTGGCGCATTTCGATCAGTTTATTTtgctg > 3:144788/1‑148 (MQ=255)
ttttCCAACGTTTTTGAATAGATTTCAATTTTGCCGCTTGGCGTACCCAGCGCATTTTTCACCGGATCGGCGCGGAAATCACCATAACGAAC‑GTACTGTTCGTTCTTCTCGCTGTGGCGCATTTCGATCAGTTTATTTTGCTGCCAGa < 4:75788/148‑1 (MQ=255)
ccAACGTTTTTGAATAGATTTCAATTTTGCCGCTTGGCGTACCCAGCGCATTTTTCACCGGATCGGCGCGGAAATCACCATAACGAAC‑GTACTGTTCGTTCTTCTCGCTGTGGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGc < 4:196682/148‑1 (MQ=255)
aCGTTTTTGAATAGATTTCAATTTTGCCGCTTGGCGTACCCAGCGCATTTTTCACCGGATCGGCGCGGAAATCACCATAACGAAC‑GTACTGTTCGTTCTTCTCGCTGTGGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCAtt > 3:122076/1‑148 (MQ=255)
aCGTTTTTGAATAGATTTCAATTTTGCCGCTTGGCGTACCCAGCGCATTTTTCACCGGATCGGCGCGGAAATCACCAGAACGAACAGTAc‑gttcgttatg < 4:239345/100‑4 (MQ=255)
aCGTTTTTGAATAGATTTCAATTTTGCCGCTTGGCGTACCCAGCGCATTTTTCACCGGATCGGCGCGGAAATCACCAGAACGAACAGTAc‑gttcgttatg > 3:239345/1‑97 (MQ=255)
ttGGCGTACCCAGCGCATTTTTCACCGGATCGGCGCGGAAATCACCATAACGAAC‑GTACTGTTCGTTCTTCTCTCTGTGGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTGCGCACgg < 1:407322/149‑1 (MQ=255)
aCCCAGCGCATTTTTCACCGGATCGGCGCGGAAATCACCATAACGAAC‑GTACTGTTCGTTCTTCTCGCTGTGGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTGCGCACGGGCACCt > 4:122314/1‑148 (MQ=255)
ccAGCGCATTTTTCTCCGGATCGGCGCGGAAATCACCATAACGAAC‑GTACTGTTCGTTCTTCTCGCTGTGGCGCATTTCGCTCAGTTTATTTTGCTGCCAGCAGGCATTAAACATTGGCATAGTGACGCGTTCCGCACGGGCACCTTTc > 2:15761/1‑149 (MQ=255)
ccAGCGCATTTTTCACCGGATCGGCGCGGAAATCACCATAACGAAC‑GTACTGTTCGTTCTTCTCGCTGTGGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTGCGCACGGGCACCTTTc < 2:160254/149‑1 (MQ=255)
ttttCACCGGATCGGCGCGGAAATCACCATAACGAAC‑GTACTGTTCGTTCTTCTCGCTGTGGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTGCGCACGGGCACCTTTCTGAGCGGc > 3:195596/1‑148 (MQ=255)
tCGGCGCGGAAATCACCATAACGAAC‑GTACTGTTCGTTCTTCTCGCTGTGGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTGCGCACGGGCACCTTTCTGAGCGGCATCATAGaaaa < 4:195596/148‑1 (MQ=255)
gcgcGGGAATAACCATAGCGAAC‑CTACTGTTGGTTATTCTCGCTGCGGCGCATTTCGATCTGCTGCTTTTGATGCCGGAAGCCATTAAGCATTTGCATAGTGAGGCGTTGCGCACGGGCACCGTTATGAGCGGCATCATAGAAAAAttt > 2:386455/1‑149 (MQ=255)
gcgGAAATCACCATAACGAAC‑GTACTGTTCGTTCTTCTCGCTGTGGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTGCGCACGGGCACCTTTCTGAGCGGCATCATAGAAAAATTTc < 4:226229/148‑1 (MQ=255)
cgGAAATCACCTTAACGAAC‑GTACTGTTCGTTCTTCTCGCTGTGGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTGCGCACGGGCACCTTTCTGAGCGGCATCATAGAAAAATTTCa < 3:235030/148‑1 (MQ=255)
cgGAAATCACCATAACGAAC‑GTACTGTTCGTTCTTCTCGCTGTGGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTGCGCACGGGCACCTTTCTGAGCGGCATCATAGAAAAATTTCa > 4:33690/1‑148 (MQ=255)
ggAAATCACCATAACGAAC‑GTACTGTTCGTTCTTCTCGCTGTGGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTGCGCACGGGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGc > 1:34402/1‑149 (MQ=255)
gaacgaacaGTAC‑GTTCGTTCTTCTCGCTGTGGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTGCGCACGGGCa < 2:145802/104‑1 (MQ=255)
gaacgaacaGTAC‑GTTCGTTCTTCTCGCTGTGGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTGCGCACGGGCa > 1:145802/2‑105 (MQ=255)
gaacgaacaGTAC‑GTTCGTTCTTCTCGCTGTGGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTGCGCACGGGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCATTTc > 1:328415/2‑149 (MQ=255)
aacgaacaGTAC‑GTTCGTTCTTCTCGCTGTGGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTGCGCACGGGCACCTTTc > 1:39874/1‑110 (MQ=255)
aacgaacaGTAC‑GTTCGTTCTTCTCGCTGTGGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTGCGCACGGGCACCTTTc < 2:39874/110‑1 (MQ=255)
acgaac‑gTACTGTTCGTTCTTCTCGCTGTGGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTGCGCACGGGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCATTTCa < 3:122314/148‑1 (MQ=255)
gaac‑gTACTGTTCGTTCTTCTCGCTGTGGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTGCGCACGGGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCATTTCATCt > 2:186728/1‑149 (MQ=255)
ac‑gTACTGTTCGTTCTTCTCGCTGTGGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTGCGCACGGGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCATTTCATCttt < 1:186728/149‑1 (MQ=255)
tGTTCGTTCTTCTCGCTGTGGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTGCGCACGGGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCATTTCATCTTTACCTTc > 2:55156/1‑149 (MQ=255)
|
TTCATCAGGAGCCAGCCAGGTTGGGTGTGCCGGGCAATCCTTATAGCCAAATTTTTCCAACGTTTTTGAATAGATTTCAATTTTGCCGCTTGGCGTACCCAGCGCATTTTTCACCGGATCGGCGCGGAAATCACCATAACGAAC‑GTACTGTTCGTTCTTCTCGCTGTGGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTGCGCACGGGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCATTTCATCTTTACCTTC > NC_000913/1955028‑1955324
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
