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 |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,547,147 |
A→G |
68.3% |
A114A (GCT→GCC) |
rfaD ← |
ADP‑L‑glycero‑D‑mannoheptose‑6‑epimerase, NAD(P)‑binding |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,547,147 | 0 | A | G | 68.3%
| 36.2
/ 18.6
| 44 | A114A (GCT→GCC) | rfaD | ADP‑L‑glycero‑D‑mannoheptose‑6‑epimerase, NAD(P)‑binding |
| Reads supporting (aligned to +/- strand): ref base A (2/12); new base G (15/15); total (17/27) |
| Fisher's exact test for biased strand distribution p-value = 4.41e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.66e-01 |
GGTTTTTCGTACTCGCGGGATTCAATAAAGTCGGAGGTGCGTCCGCCGTAGGTGGCTGCGGAAGAAGCGTACAGGAACGGGATTTCACGCTCCAGGCAGTAGTGCAGCAGCTCCTTGGAGTATTGATAGTTGTT > minE/2547082‑2547215
|
ggTTTTTCGTACTCGCGGGATTCAATAAAGTCGGAGGTGCGTCCGCCGTAGGTGGCTGCGGAAGAAGCg < 1:1563662/69‑1 (MQ=255)
ggTTTTTCGTACTCGCGGGATTCAATAAAGTCGGAGGTGCGTCCGCCGTAGGTGGCTGCGGAAGAAGCg < 1:302697/69‑1 (MQ=255)
gggATTCAATAAAGTCGGAGGTGCGTCCGCCGTAGGTGGCTGCGGAAGAAGCGTACAGGAACGGGAttt < 1:2718336/69‑1 (MQ=255)
gggATTCAATAAAGTCGGAGGTGCGTCCGCCGTAGGTGGCTGCGGAAGAAGCGTACAGGAACGGGAttt > 1:1051303/1‑69 (MQ=255)
gggATTCAATAAAGTCGGAGGTGCGTCCGCCGTAGGTGGCTGCGGAAGAAGCGTACAGGAACGGGAttt < 1:1656967/69‑1 (MQ=255)
gggATTCAATAAAGTCGGAGGTGCGTCCGCCGTAGGTGGCTGCGGAAGAAGCGTACAGGAACGGGAttt < 1:1709050/69‑1 (MQ=255)
gggATTCAATAAAGTCGGAGGTGCGTCCGCCGTAGGTGGCTGCGGAAGAAGCGTACAGGAACGGGAttt < 1:2080875/69‑1 (MQ=255)
gggATTCAATAAAGTCGGAGGTGCGTCCGCCGTAGGTGGCTGCGGAAGAAGCGTACAGGAACGGGAttt > 1:1816744/1‑69 (MQ=255)
ggATTCAATAAAGTCGGAGGTGCGTCCGCCGTAGGTGGCTGCGGAAGAAGCGTACAGGAACGGGAttt < 1:858717/68‑1 (MQ=255)
tCGGAGGTGCGTCCACCGTAAGTGGCTGCGGAAGAGTCATACAGGAACGGGATTTCGCGCTCCAGACag < 1:2491031/69‑1 (MQ=255)
tCGGAGGTGCGTCCACCGTAAGTGGCTGCGGAAGAGGCATACAGGAACGGGATTTCGCGCTCCAGACag < 1:2832122/69‑1 (MQ=255)
tCGGAGGTGCGTCCACCGTAAGTGGCTGCGGAAGAGGCATACAGGAACGGGATTTCGCGCTCCAGACag < 1:2424628/69‑1 (MQ=255)
tCGGAGGTGCGTCCACCGTAAGTGGCTGCGGAAGAGGCATACAGGAACGGGATTTCGCGCTCCAGACag < 1:2940758/69‑1 (MQ=255)
tCGGAGGTGCGTCCACCGTAAGTGGCTGCGGAAGAGGCATACAGGAACGGGATTTCGCGCTCCAGACag < 1:2158555/69‑1 (MQ=255)
tCGGAGGTGCGTCCACCGTAAGTGGCTGCGGAAGAGGCATACAGGAACGGGATTTCGCGCTCCAGACag < 1:1952763/69‑1 (MQ=255)
tCGGAGGTGCGTCCACCGTAAGTGGCTGCGGAAGAGGCATACAGGAACGGGATTTCGCGCTCCAGACag < 1:3140906/69‑1 (MQ=255)
tCGGAGGTGCGTCCACCGTAAGTGGCTGCGGAAGAGGCATACAGGAACGGGATTTCGCGCTCCAGACag < 1:3221200/69‑1 (MQ=255)
tCGGAGGTGCGTCCACCGTAAGTGGCTGCGGAAGAGGCATACAGGAACGGGATTTCGCGCTCCAGACag < 1:1761505/69‑1 (MQ=255)
tCGGAGGTGCGTCCACCGTAAGTGGCTGCGGAAGAGGCATACAGGAACGGGATTTCGCGCTCCAGACag < 1:3244287/69‑1 (MQ=255)
tCGGAGGTGCGTCCACCGTAAGTGGCTGCGGAAGAGGCATACAGGAACGGGATTTCGCGCTCCAGACag < 1:1720512/69‑1 (MQ=255)
tCGGAGGTGCGTCCACCGTAAGTGGCTGCGGAAGAGGCATACAGGAACGGGATTTCGCGCTCCAGACag < 1:165400/69‑1 (MQ=255)
tCGGAGGTGCGTCCACCGTAAGTGGCTGCGGAAGAGGCATACAGGAACGGGATTTCGCGCTCCAGACag < 1:436099/69‑1 (MQ=255)
tCGGAGGTGCGTCCACCGTAAGTGGCTGCGGAAGAGGCATACAGGAACGGGATTTCGCGCTCCAGACag < 1:1240843/69‑1 (MQ=255)
cGGAGGTGCGTCCGCCGTAGGTGGCTGCGGAAGAAGCGTACAGGAACGGGATTTCACGCTCCAGGCagt < 1:184404/69‑1 (MQ=255)
cGGAGGTGCGTCCGCCGTAGGTGGCTGCGGAAGAAGCGTACAGGAACGGGATTTCACGCTCCAGGCagt < 1:2874552/69‑1 (MQ=255)
cgTAAGTGGCTGCGGAAGAGGCATACAGGAACGGGATTTCGCGCTCCAGACAGTAGTGCAGCAGCt > 1:2390114/1‑66 (MQ=255)
cgTAAGTGGCTGCGGAAGAGGCATACAGGAACGGGATTTCGCGCTCCAGACAGTAGTGCAGCAGCTctt > 1:3385141/1‑67 (MQ=255)
cgTAAGTGGCTGCGGAAGAGGCATACAGGAACGGGATTTCGCGCTCCAGACAGTAGTGCAGCAGCTctt > 1:2854941/1‑67 (MQ=255)
cgTAAGTGGCTGCGGAAGAGGCATACAGGAACGGGATTTCGCGCTCCAGACAGTAGTGCAGCAGCTctt > 1:2836277/1‑67 (MQ=255)
cgTAAGTGGCTGCGGAAGAGGCATACAGGAACGGGATTTCGCGCTCCAGACAGTAGTGCAGCAGCTctt > 1:845923/1‑67 (MQ=255)
cgTAAGTGGCTGCGGAAGAGGCATACAGGAACGGGATTTCGCGCTCCAGACAGTAGTGCAGCAGCTctt > 1:2366116/1‑67 (MQ=255)
cgTAAGTGGCTGCGGAAGAGGCATACAGGAACGGGATTTCGCGCTCCAGACAGTAGTGCAGCAGCTctt > 1:2369348/1‑67 (MQ=255)
cgTAAGTGGCTGCGGAAGAGGCATACAGGAACGGGATTTCGCGCTCCAGACAGTAGTGCAGCAGCTctt > 1:2272925/1‑67 (MQ=255)
cgTAAGTGGCTGCGGAAGAGGCATACAGGAACGGGATTTCGCGCTCCAGACAGTAGTGCAGCAGCTctt > 1:193739/1‑67 (MQ=255)
cgTAAGTGGCTGCGGAAGAGGCATACAGGAACGGGATTTCGCGCTCCAGACAGTAGTGCAGCAGCTctt > 1:1877340/1‑67 (MQ=255)
cgTAAGTGGCTGCGGAAGAGGCATACAGGAACGGGATTTCGCGCTCCAGACAGTAGTGCAGCAGCTctt > 1:1758513/1‑67 (MQ=255)
cgTAAGTGGCTGCGGAAGAGGCATACAGGAACGGGATTTCGCGCTCCAGACAGTAGTGCAGCAGCTctt > 1:1591206/1‑67 (MQ=255)
cgTAAGTGGCTGCGGAAGAGGCATACAGGAACGGGATTTCGCGCTCCAGACAGTAGTGCAGCAGCTctt > 1:1451928/1‑67 (MQ=255)
cgTAAGTGGCTGCGGAAGAGGCATACAGGAACGGGATTTCGCGCTCCAGACAGTAGTGCAGCAGCTctt > 1:1261791/1‑67 (MQ=255)
cgTAAGTGGCTGCGGAAGAGGCATACAGGAACGGGATTTCGCGCTCCAGACAGTAGTGCAGCAGCTctt > 1:1093009/1‑67 (MQ=255)
gTAAGTGGCTGCGGAAGAGGCATACAGGAACGGGATTTCGCGCTCCAGACag < 1:3080084/52‑1 (MQ=255)
tGGCTGCGGAAGAAGCGTACAGGAACGGGATTTCACGCTCCAGGCAGTAGTGCAGCAGCTCCTTGGAg < 1:2836113/68‑1 (MQ=255)
tGGCTGCGGAAGAAGCGTACAGGAACGGGATTTCACGCTCCAGGCAGTAGTGCAGCAGCTCCTTGGAg < 1:1990076/68‑1 (MQ=255)
tGGCTGCGGAAGAAGCGTACAGGAACGGGATTTCACGCTCCAGGCAGTAGTGCAGCAGCTCCTTGGAg < 1:633679/68‑1 (MQ=255)
aagCGTACAGGAACGGGATTTCACGCTCCAGGCAGTAGTGCAGCAGCTCCTTGGAGTATTGATAgttgt < 1:2366955/69‑1 (MQ=255)
aagCGTACAGGAACGGGATTTCACGCTCCAGGCAGTAGTGCAGCAGCTCCTTGGAGTATTGATAgttgt < 1:2225749/69‑1 (MQ=255)
agCGTACAGGAACGGGATTTCACGCTCCAGGCAGTAGTGCAGCAGCTCCTTGGAGTATTGTTAgttgtt > 1:2856605/1‑69 (MQ=255)
|
GGTTTTTCGTACTCGCGGGATTCAATAAAGTCGGAGGTGCGTCCGCCGTAGGTGGCTGCGGAAGAAGCGTACAGGAACGGGATTTCACGCTCCAGGCAGTAGTGCAGCAGCTCCTTGGAGTATTGATAGTTGTT > minE/2547082‑2547215
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
