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 |
2,586,227 |
T→G |
77.7% |
L350L (CTA→CTC) |
mdtF ← |
multidrug transporter, RpoS‑dependent |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,586,227 | 0 | T | G | 77.7%
| 115.0
/ 23.7
| 67 | L350L (CTA→CTC) | mdtF | multidrug transporter, RpoS‑dependent |
| Reads supporting (aligned to +/- strand): ref base T (7/8); new base G (15/37); total (22/45) |
| Fisher's exact test for biased strand distribution p-value = 2.23e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TACGGCAATCGTCGGGATGATTGTGGCACGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACTAGGATGATAGCCTCAACCAGTGTTTTGAAAACTTCCTGAATAGAAATT > minE/2586161‑2586275
|
tACGGCAATCGTCGGGATGATTGTGGCGCGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACGAg < 1:2727892/69‑1 (MQ=255)
tACGGCAATCGTCGGGATGATTGTGGCGCGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACGAg < 1:1862465/69‑1 (MQ=255)
tACGGCAATCGTCGGGATGATTGTGGCGCGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACGAg < 1:1990729/69‑1 (MQ=255)
tACGGCAATCGTCGGGATGATTGTGGCGCGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACGAg < 1:2254348/69‑1 (MQ=255)
tACGGCAATCGTCGGGATGATTGTGGCGCGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACGAg < 1:2283692/69‑1 (MQ=255)
tACGGCAATCGTCGGGATGATTGTGGCGCGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACGAg < 1:2823665/69‑1 (MQ=255)
tACGGCAATCGTCGGGATGATTGTGGCGCGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACGAg < 1:2910425/69‑1 (MQ=255)
tACGGCAATCGTCGGGATGATTGTGGCGCGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACGAg < 1:2949683/69‑1 (MQ=255)
tACGGCAATCGTCGGGATGATTGTGGCGCGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACGAg < 1:1441596/69‑1 (MQ=255)
tACGGCAATCGTCGGGATGATTGTGGCGCGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACGAg < 1:3418716/69‑1 (MQ=255)
tACGGCAATCGTCGGGATGATTGTGGCGCGGAAATCCTGCAAAAACAGATACATGACCAGGAAGACGAg < 1:2703085/69‑1 (MQ=25)
aCGGCAATCGTCGGGATGATTGTGGCGCGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACGAg < 1:434355/68‑1 (MQ=255)
aCGGCAATCGTCGGGATGATTGTGGCGCGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACGAg < 1:1872878/68‑1 (MQ=255)
aCGGCAATCGTCGGGATGATTGTGGCGCGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACGAg < 1:2124525/68‑1 (MQ=255)
aCGGCAATCGTCGGGAGGATTGTGGCGCGGAAATTCTGCAAAAACAGATACATGACCAGGACGACGAg < 1:2203873/68‑1 (MQ=25)
tcAATCGTCGGGATGATTGTGGCGCGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACGAGgatg < 1:1798888/68‑1 (MQ=255)
gCAATCGTCGGGATGATTGTGGCGCGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACGAGgatg < 1:797271/69‑1 (MQ=255)
gCAATCGTCGGGATGATTGTGGCGCGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACGAGgatg < 1:1946519/69‑1 (MQ=255)
gCAATCGTCGGGATGATTGTGGCGCGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACGAGgatg < 1:747324/69‑1 (MQ=255)
gCAATCGTCGGGATGATTGTGGCGCGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACGAGgatg < 1:208474/69‑1 (MQ=255)
gCAATCGTCGGGATGATTGTGGCGCGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACGAGgatg < 1:2096483/69‑1 (MQ=255)
gCAATCGTCGGGATGATTGTGGCGCGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACGAGgatg < 1:605808/69‑1 (MQ=255)
gCAATCGTCGGGATGATTGTGGCGCGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACGAGgatg < 1:477549/69‑1 (MQ=255)
gCAATCGTCGGGATGATTGTGGCGCGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACGAGgatg < 1:1069155/69‑1 (MQ=255)
gCAATCGTCGGGATGATTGTGGCGCGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACGAGgatg < 1:3126074/69‑1 (MQ=255)
gCAATCGTCGGGATGATTGTGGCGCGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACGAGgatg < 1:1663899/69‑1 (MQ=255)
gCAATCGTCGGGATGATTGTGGCGCGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACGAGgatg < 1:1414165/69‑1 (MQ=255)
gCAATCGTCGGGATGATTGTGGCACGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACTAGgat > 1:398961/1‑68 (MQ=255)
gCAATCGTCGGGAAGATTGTGGCGCGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACGAGgatg < 1:1704617/69‑1 (MQ=255)
cgtcgGGATGATTGTGGCACGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACTAGGATGATAGc > 1:1774417/1‑69 (MQ=255)
cgtcgGGATGATTGTGGCACGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACTAGGATGATAGc > 1:2984725/1‑69 (MQ=255)
cgtcgGGATGATTGTGGCACGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACTAGGATGATAGc > 1:1341704/1‑69 (MQ=255)
cgtcgGGATGATTGTGGCACGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACTAGGATGATAGc > 1:1331141/1‑69 (MQ=255)
cgtcgGGATGATTGTGGCACGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACTAGGATGATAGc > 1:755554/1‑69 (MQ=255)
gtcgGGATGATTGTGGCACGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACt > 1:3196166/1‑57 (MQ=255)
gtcgGGATGATTGTGGCACGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACt > 1:174583/1‑57 (MQ=255)
gtcgGGATGATTGTGGCACGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACt > 1:3150062/1‑57 (MQ=255)
gtcgGGATGATTGTGGCACGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACt > 1:1523261/1‑57 (MQ=255)
gtcgGGATGATTGTGGCACGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACt > 1:2786893/1‑57 (MQ=255)
gtcgGGATGATTGTGGCACGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACt > 1:1900434/1‑57 (MQ=255)
gtgGCACGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACTAGgat > 1:179641/1‑50 (MQ=255)
gcGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACGAGGATGATAGCCTCAACCAGCGTTTTGaa < 1:2921638/68‑1 (MQ=18)
gcGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACGAGGATGATAGCCTCAACCAGCGTTTTGaa < 1:409547/68‑1 (MQ=18)
gcGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACGAGGATGATAGCCTCAACCAGCGTTTTGaa < 1:2735621/68‑1 (MQ=18)
gcGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACGAGGATGATAGCCTCAACCAGCGTTTTGaa < 1:1698671/68‑1 (MQ=18)
gcGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACGAGGATGATAGCCTCAACCAGCGTTTTGaa < 1:2458647/68‑1 (MQ=18)
gAAATTCTGCAAAAACAGATACATGACCTGGAAGACGAGgatg < 1:1825886/43‑1 (MQ=38)
gAAATTCTGCAAAAACAGATACATGACCAGGAAGACGAg < 1:2217260/39‑1 (MQ=255)
tCTGCAAAAACAGATACATGACCAGGAAGACGAGgatg < 1:696259/38‑1 (MQ=255)
aaaCAGATACATGACCAGGAAGACGAGGATGATATcc > 1:3341357/1‑37 (MQ=17)
aaaCAGATACATGACCAGGAAGACGAGGATGATAGCCTCAACCAGCGTTTTGAAAACTTCCTGAATAg > 1:521153/1‑68 (MQ=255)
aaaCAGATACATGACCAGGAAGACGAGGATGATAGCCTCAACCAGCGTTTTGAAAACTTCCTGAATAg > 1:3070/1‑68 (MQ=255)
aaaCAGATACATGACCAGGAAGACGAGGATGATAGCCTCAACCAGCGTTTTGAAAACTTCCTGAATAGa > 1:1332896/1‑69 (MQ=255)
aaaCAGATACATGACCAGGAAGACGAGGATGATAGCCTCAACCAGCGTTTTGAAAACTTCCTGAATAGa > 1:1975862/1‑69 (MQ=255)
aaaCAGATACATGACCAGGAAGACGAGGATGATAGCCTCAACCAGCGTTTTGAAAACTTCCTGAATAGa > 1:711075/1‑69 (MQ=255)
aaaCAGATACATGACCAGGAAGACGAGGATGATAGCCTCAACCAGCGTTTTGAAAACTTCCTGAATAGa > 1:1792700/1‑69 (MQ=255)
aaaCAGATACATGACCAGGAAGACGAGGATGATAGCCTCAACCAGCGTTTTGAAAACTTCCTGAATAGa > 1:1143074/1‑69 (MQ=255)
aaaCAGATACATGACCAGGAAGACGAGGATGATAGCCTCAACCAGCGTTTTGAAAACTTCCTGAATAGa > 1:1720448/1‑69 (MQ=255)
aaaCAGATACATGACCAGGAAGACGAGGATGATAGCCTCAACCAGCGTTTTGAAAACTTCCTGAATAGa > 1:1705871/1‑69 (MQ=255)
aaaCAGATACATGACCAGGAAGACGAGGATGATAGCCTCAACCAGCGTTTTGAAAACTTCCTGAATAGa > 1:750595/1‑69 (MQ=255)
aaaCAGATACATGACCAGGAAGACGAGGATGATAGCCTCAACCAGCGTTTTGAAAACTTCCTGAATAGa > 1:1058496/1‑69 (MQ=255)
aaaCAGATACATGACCAGGAAGACGAGGATGATAGCCTCAACCAGCGTTTTGAAAACTTCCTGAATAGa > 1:2530450/1‑69 (MQ=255)
aaaCAGATACATGACCAGGAAGACGAGGATGATAGCCTCAACCAGCGTTTTGAAAACTTACTGAATAGa > 1:2648902/1‑69 (MQ=255)
aaaCAGATACATGACCAGAAAGGCGAGGATGATAGCCTCAACCAGCGTTTTGAAAACTTCCTGAATAGa > 1:1523810/1‑69 (MQ=255)
aGATACATGACCAGGAAGACTAGGATGATAGCCTCAACCAGTGTTTTGAAAACTTCCTGAATAGAAAtt < 1:19643/69‑1 (MQ=255)
aGATACATGACCAGGAAGACTAGGATGATAGCCTCAACCAGTGTTTTGAAAACTTCCTGAATAGAAAtt < 1:608564/69‑1 (MQ=255)
aGATACATGACCAGGAAGACTAGGATGATAGCCTCAACCAGTGTTTTGAAAACTTCCTGAATAGAAAtt < 1:615388/69‑1 (MQ=255)
aGATACATGACCAGGAAGACTAGGATGATAGCCTCAACCAGTGTTTTGAAAACTTCCTGAATAGAAAtt < 1:2021312/69‑1 (MQ=255)
aGATACATGACCAGGAAGACTAGGATGATAGCCTCAACCAGTGTTTTGAAAACTTCCTGAATAGAAAtt < 1:3430073/69‑1 (MQ=255)
aGATACATGACCAGGAAGACTAGGATGATAGCCTCAACCAGTGTTTTGAAAACTTCCTGAATAGAAAtt < 1:1789365/69‑1 (MQ=255)
aGATACATGACCAGGAAGACTAGGATGATAGCCTCAACCAGTGTTTTGAAAACTTCCTGAATAGAAAtt < 1:2438821/69‑1 (MQ=255)
aGATACATGACCAGGAAGACTAGGATGATAGCCTCAACCAGTGTTTTGAAAACTTCCTGAATAGAAAtt < 1:1848019/69‑1 (MQ=255)
gATACATGACCAGGAAGACGAGGATGATAGCCTCAAGCAGCGTTTTGaa < 1:1333247/49‑1 (MQ=255)
|
TACGGCAATCGTCGGGATGATTGTGGCACGGAAATTCTGCAAAAACAGATACATGACCAGGAAGACTAGGATGATAGCCTCAACCAGTGTTTTGAAAACTTCCTGAATAGAAATT > minE/2586161‑2586275
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
