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 F17 I0 R2
|
162 |
60.6 |
4616657 |
98.5% |
4547407 |
62.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,115,786 |
T→C |
7.7% |
intergenic (‑28/+55) |
msyB ← / ← mdtG |
hypothetical protein/predicted drug efflux system |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,115,786 | 0 | T | C | 7.7%
| 136.0
/ 4.3
| 52 | intergenic (‑28/+55) | msyB/mdtG | hypothetical protein/predicted drug efflux system |
| Reads supporting (aligned to +/- strand): ref base T (24/24); new base C (2/2); total (26/26) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.91e-01 |
CAGCGTCAATGGCTTCTTCAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAATCAGTTCGATAC > W3110S.gb/1115719‑1115852
|
cAGCGTCAATGGCTTCTTCAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTc < 1:4035327/71‑1 (MQ=255)
cGTCAATGGCTTCTTCAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAgg > 1:1459081/1‑71 (MQ=255)
tCAATGGCTTCTTCAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGa < 1:1778604/71‑1 (MQ=255)
aaTGGCTTCTTCAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGaa > 1:3787430/1‑70 (MQ=255)
aaTGGCTTCTTCAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGaa > 1:3792812/1‑70 (MQ=255)
aaTGGCTTCTTCAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGa > 1:548199/1‑69 (MQ=255)
gCTTCTTCAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAgg < 1:2904343/70‑1 (MQ=255)
gCTTCTTCAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGa < 1:3096625/71‑1 (MQ=255)
gCTTCTTCAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGa < 1:2136064/71‑1 (MQ=255)
tcttcAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGttt < 1:2502856/55‑1 (MQ=255)
cttcAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGtt < 1:3464478/54‑1 (MQ=255)
cttcAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAg > 1:2292741/1‑70 (MQ=255)
cttcAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGc > 1:4516084/1‑71 (MQ=255)
ttcAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAgg > 1:3793594/1‑65 (MQ=255)
cAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCt < 1:3814172/69‑1 (MQ=255)
aGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGAt > 1:1429521/1‑70 (MQ=255)
gCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCt < 1:1819074/66‑1 (MQ=255)
gTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGt < 1:1541358/45‑1 (MQ=255)
ttGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGCTTCAGGGaa < 1:2144381/53‑1 (MQ=255)
gCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGaaaa > 1:1527552/1‑53 (MQ=255)
aCATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCtttt > 1:2759500/1‑71 (MQ=255)
aCATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCtttt > 1:2016024/1‑71 (MQ=255)
aCATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCtttt > 1:3415500/1‑71 (MQ=255)
cATGGTCATCACGATTCTCCTTTTGAGTTGATGAGGTTTCAGGGAAAAGGa > 1:3345526/1‑51 (MQ=255)
cATGGTCATCACGATTCTCCTTTTGAGTTGATGAGGTTTCAGGGAAAAGGa > 1:2131627/1‑51 (MQ=255)
gTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGa > 1:13940/1‑54 (MQ=255)
gTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAg < 1:1860232/71‑1 (MQ=255)
tcaCGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAg < 1:2666891/41‑1 (MQ=255)
tcaCGATTCTCCCTTCGAGTTGATGAGGTTTCAGGGaaa < 1:4225725/39‑1 (MQ=255)
caCGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGa > 1:3089036/1‑49 (MQ=255)
aCGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGaaaa < 1:2910450/38‑1 (MQ=255)
aCGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGaa < 1:715821/71‑1 (MQ=255)
aCGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGaa < 1:158385/71‑1 (MQ=255)
aCGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGa < 1:4335714/70‑1 (MQ=255)
aCGATTCTCCCTTTGAGTTGATGAGGCTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTT‑CAAGTATGa > 1:3563783/1‑69 (MQ=255)
cGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGaaa < 1:3560077/71‑1 (MQ=255)
gATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATa > 1:4109523/1‑41 (MQ=255)
tctcCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGaaa > 1:1411322/1‑67 (MQ=255)
tcCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCg < 1:3947746/69‑1 (MQ=255)
ccTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGaa < 1:1994015/69‑1 (MQ=255)
tttGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGc < 1:4186100/51‑1 (MQ=255)
tttGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAg < 1:4128731/62‑1 (MQ=255)
tGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCtttt > 1:2535040/1‑47 (MQ=255)
gAGTTGATGAGGCTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGaaa > 1:511541/1‑58 (MQ=255)
gTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGa < 1:2751129/54‑1 (MQ=255)
gTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAATCAGtt > 1:2840679/1‑71 (MQ=255)
ttGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTcc < 1:2839896/37‑1 (MQ=255)
ttGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGc > 1:537478/1‑39 (MQ=255)
ttGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGaaaaa < 1:1134244/64‑1 (MQ=255)
ttGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGaaaa > 1:4403052/1‑63 (MQ=255)
ttGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAATCAGTTc < 1:4153071/71‑1 (MQ=255)
ttGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAATCAGTTc < 1:2930793/71‑1 (MQ=255)
gatgaGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGaaa > 1:3757353/1‑53 (MQ=255)
gaGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAATCAGTTCGATAc > 1:23513/1‑71 (MQ=255)
aGGCTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAATCAGTTCGATAc < 1:2297697/70‑1 (MQ=255)
tttCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGaaaaa < 1:3641046/55‑1 (MQ=255)
|
CAGCGTCAATGGCTTCTTCAAGCGTTGCGTACATGGTCATCACGATTCTCCCTTTGAGTTGATGAGGTTTCAGGGAAAAGGATAGCTGATTCTCCGCTTTTGCAAGTATGAAAGGCGAAAAATCAGTTCGATAC > W3110S.gb/1115719‑1115852
|
| 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
