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 |
|
A3 F1 I1 R1
|
781 |
46.9 |
2231650 |
93.5% |
2086592 |
109.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
850,389 |
T→C |
intergenic (‑292/‑61) |
rhtA ← / → ompX |
threonine and homoserine efflux system/outer membrane protein X |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 850,389 | 0 | T | C | 95.8%
| 154.5
/ ‑2.6
| 48 | intergenic (‑292/‑61) | rhtA/ompX | threonine and homoserine efflux system/outer membrane protein X |
| Reads supporting (aligned to +/- strand): ref base T (1/1); new base C (23/23); total (24/24) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.29e-01 |
ATGACAGGGAAAACATGCGTAATACTTACGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTTCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCAGG > NC_000913/850258‑850505
|
atgaCAGGGAAAACATGCGTAATACTTACGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTa > 2:896510/1‑139 (MQ=255)
atgaCAGGGAAAACATGCGTAATACTTACGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTa > 2:962213/1‑139 (MQ=255)
aaaaCATGCGTAATACTTACGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGat < 1:962213/139‑1 (MQ=255)
aaaaCATGCGTAATACTTACGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGat < 1:32654/139‑1 (MQ=255)
aCGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGAc > 2:808170/1‑139 (MQ=255)
cGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACt > 2:1095591/1‑139 (MQ=255)
gTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTAtt > 2:137978/1‑139 (MQ=255)
gTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTAtt > 2:114156/1‑139 (MQ=255)
ttCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCAt < 2:199374/104‑1 (MQ=255)
ttCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCAt > 1:199374/1‑104 (MQ=255)
tctGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTa < 1:439143/119‑1 (MQ=255)
tctGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTa > 2:439143/1‑119 (MQ=255)
ctGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAATTGGCCCGTTAGACATCACAAATCGCGAAGAGTCCCCCATTAATTTTTGATATATGTAAAACTTAGGACGTATTTGaag < 2:1109396/139‑2 (MQ=255)
ctGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAAt < 1:896510/139‑1 (MQ=255)
gATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAg < 1:808170/139‑1 (MQ=255)
aTTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAAt < 2:82097/128‑1 (MQ=255)
aTTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAAt > 1:82097/1‑128 (MQ=255)
aTTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAgg < 1:759313/139‑1 (MQ=255)
aTTTAAATTTAGATGGATAGCGGTGTATAGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAgg < 1:1087244/139‑1 (MQ=255)
gtgtATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAAt < 2:1089464/106‑1 (MQ=255)
gtgtATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAAt > 1:1089464/1‑106 (MQ=255)
tATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCAt > 1:795660/1‑64 (MQ=255)
tATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCAt < 2:795660/64‑1 (MQ=255)
tATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAAt < 1:918117/103‑1 (MQ=255)
tATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAAt > 2:918117/1‑103 (MQ=255)
tATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAG‑TTCCCATTAATTTTTGATATATTTAAAACTTAGGa > 1:981520/1‑91 (MQ=255)
tATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAG‑TTCCCATTAATTTTTGATATATTTAAAACTTAGGa < 2:981520/91‑1 (MQ=255)
tGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCttt < 1:114156/139‑1 (MQ=255)
aaaCGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAg < 1:913746/108‑1 (MQ=255)
aaaCGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAg > 2:913746/1‑108 (MQ=255)
aCGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAAt < 2:994554/61‑1 (MQ=255)
aCGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAAt > 1:994554/1‑61 (MQ=255)
cGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCa > 2:204714/1‑126 (MQ=255)
cGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCa < 1:204714/126‑1 (MQ=255)
ttCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAAt < 1:648549/93‑1 (MQ=255)
ttCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATg > 2:40365/1‑126 (MQ=255)
ttCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATg < 1:40365/126‑1 (MQ=255)
ttCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTg > 1:681903/1‑139 (MQ=255)
ttCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTg > 1:651140/1‑139 (MQ=255)
ttCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATCTAAAACTTAGGACTTATTTGAAt > 2:648549/1‑93 (MQ=255)
cTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGc > 2:516568/1‑139 (MQ=255)
ttACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTa > 2:469297/1‑67 (MQ=255)
ttACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTa < 1:469297/67‑1 (MQ=255)
tGGCCCGTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCt > 1:595118/1‑139 (MQ=255)
gTTAGACATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCAcc < 2:595118/139‑1 (MQ=255)
aCATCACAAATCGCGAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCAgg < 1:137978/139‑1 (MQ=255)
cgAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCa > 1:689120/1‑97 (MQ=255)
cgAAGAGTTCCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCa < 2:689120/97‑1 (MQ=255)
|
ATGACAGGGAAAACATGCGTAATACTTACGCAGTTCTCTGAAAAAGTGATTTAAATTTAGATGGATAGCGGTGTATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTTCCCATTAATTTTTGATATATTTAAAACTTAGGACTTATTTGAATCACATTTGAGGTGGTTATGAAAAAAATTGCATGTCTTTCAGCACTGGCCGCAGTTCTGGCTTTCACCGCAGG > NC_000913/850258‑850505
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
