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 |
927,449 |
C→T |
36.8% |
R82H (CGC→CAC) |
narZ ← |
nitrate reductase 2 (NRZ), alpha subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 927,449 | 0 | C | T | 36.8%
| 27.4
/ 24.7
| 46 | R82H (CGC→CAC) | narZ | nitrate reductase 2 (NRZ), alpha subunit |
| Reads supporting (aligned to +/- strand): ref base C (16/13); new base T (9/8); total (25/21) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.81e-01 |
GTAAAGATACCAGGAGTAACTTGCGCCACGCGGGCAGCCGCGAGGTTCATGATTGGGCAGGTCAGGGCGAGTGCGCGGGTAGTCGGTCTGTTGGATTTCCCAGGTCACCAGACCATTTTTAACGTAGATTTTCCA > minE/927382‑927516
|
gTAAAGATACCAGGAGTAACTTGCGCCACGCGGGCAGCCGCGAGGTTCATGATTGGGCAGGTCAGGGCg < 1:2576449/69‑1 (MQ=255)
tAACTTGCGCCACGCGGGCAGCCGCGAGGTTCATGATTGGGCAGGTCAGGGCg < 1:1994553/53‑1 (MQ=255)
aaCTTGCGCCACGCGGGCAGCCGCGAGGTTCATGATTGGGCAGGTCAGGGCGAGTGCGCGGGTTGTCgg > 1:474636/1‑69 (MQ=255)
aaCTTGCGCCACGCGGGCAGCCGCGAGGTTCATGATTGGGCAGGTCAGGGCGAGTGCGCGGGTAGTc > 1:1702398/1‑67 (MQ=255)
aaCTTGCGCCACGCGGGCAGCCGCGAGGTTCATGATTGGGCAGGTCAGGGCGAGTGCGCGGGTAGTCgg > 1:2508594/1‑69 (MQ=255)
aaCTTGCGCCACGCGGGCAGCCGCGAGGTTCATGATTGGGCAGGTCAGGGCGAGTGCGCGGGTAGTCgg > 1:275540/1‑69 (MQ=255)
aCTTGCGCCACGCGGGCAGCCGCGAGGTTCATGATTGGGCAGGTCAGGGCGAGTGCGCGGGTAGTCGGt > 1:3196737/1‑69 (MQ=255)
ttGCGCCACGCGGGCAGCCGCGAGGTTCGTGATTTGGCAGGTCAGTGTGAGTGCGCGGGTAGTCGGTCt < 1:3076884/69‑1 (MQ=25)
ttGCGCCACGCGGGCAGCCGCGAGGTTCGTGATTTGGCAGGTCAGGGTGAGTGCGCGGGTAGTCGGTCt < 1:1083143/69‑1 (MQ=25)
ttGCGCCACGCGGGCAGCCGCGAGGTTCGTGATTTGGCAGGTCAGGGTGAGTGCGCGGGTAGTCGGTCt < 1:1032255/69‑1 (MQ=25)
ttGCGCCACGCGGGCAGCCGCGAGGTTCGTGATTTGGCAGGTCAGGGTGAGTGCGCGGGTAGTCGGTCt < 1:2928509/69‑1 (MQ=25)
ttGCGCCACGCGGGCAGCCGCGAGGTTCGTGATTTGGCAGGTCAGGGTGAGTGCGCGGGTAGTCGGTCt < 1:2203989/69‑1 (MQ=25)
ttGCGCCACGCGGGCAGCCGCGAGGTTCGTGATTTGGCAGGTCAGGGTGAGTGCGCGGGTAGTCGGTCt < 1:649833/69‑1 (MQ=25)
ttGCGCCACGCGGGCAGCCGCGAGGTTCGTGATTTGGCAGGTCAGGGTGAGTGCGCGGGTAGTCGGTCt < 1:110838/69‑1 (MQ=25)
cctcgcgGGCAGCCGCGAGGTTCATGATTGGGCAGGTCAGGGCGAGTGCGCGGGTAGTCGGTCTGTTgg < 1:1564724/66‑1 (MQ=255)
ccACGCGGGCAGCCGCGAGGTTCATGATTGGGCAGGTCAGGGCGAGTGCGCGGGTAGTCGGTCTGTTgg < 1:3358463/69‑1 (MQ=255)
ccACGCGGGCAGCCGCGAGGTTCATGATTGGGCAGGTCAGGGCGAGTGCGCGGGTAGTCGGTCTGTTgg < 1:3385800/69‑1 (MQ=255)
ccACGCGGGCAGCCGCGAGGTTCATGATTGGGCAGGTCAGGGCGAGTGCGCGGGTAGTCGGTCTGTTgg < 1:3435093/69‑1 (MQ=255)
ccACGCGGGCAGCCGCGAGGTTCATGATTGGGCAGGTCAGGGCGAGTGCGCGGGTAGTCGGTCTGTTgg < 1:2802396/69‑1 (MQ=255)
ccACGCGGGCAGCCGCGAGGTTCATGATTGGGCAGGTCAGGGCGAGTGCGCGGGTAGTCGGTCTGTTgg < 1:80634/69‑1 (MQ=255)
ccACGCGGGCAGCCGCGAGGTTCATGATTGGGCAGGTCAGGGCGAGTGCGCGGGTAGTCGGTCTGTTgg < 1:2671696/69‑1 (MQ=255)
ccACGCGGGCAGCCGCGAGGTTCATGATTGGGCAGGTCAGGGCGAGTGCGCGGGTAGTCGGTCTGTTgg < 1:2405931/69‑1 (MQ=255)
ccGCGAGGTTCGTGATTTGGCAGGTCAGGGTGAGTGCGCGGGTAGTCGGTCt < 1:3358355/52‑1 (MQ=255)
gcgAGGTTCATGATTGGGCAGGTCAGGGCGAGTGCGCGGGTAGTCGGTCTGTTGGATTTCCCAGGTCAc < 1:541029/69‑1 (MQ=255)
cATGATTGGGCAGGTCAGGGCGAGTGCGCGGGTAGTCGGTCTGTTGGATTTCCCAGGTCAc < 1:89129/61‑1 (MQ=255)
aGGTCAGGGCGAGTGCGCGGGTAGTCGGTCTGTTgg < 1:1905219/36‑1 (MQ=255)
gTCAGGGTGAGTGCGCGGGTAGTCGGTCTGTTGGATTTCCCa > 1:2545392/1‑42 (MQ=255)
gTCAGGGTGAGTGCGCGGGTAGTCGGTCTGTTGGATTTCCCAGGTCACCAGACCATTTTTAACGTAGAt > 1:2539939/1‑69 (MQ=255)
gTCAGGGTGAGTGCGCGGGTAGTCGGTCTGTTGGATTTCCCAGGTCACCAGACCATTTTTAACGTAGAt > 1:2435118/1‑69 (MQ=255)
gTCAGGGTGAGTGCGCGGGTAGTCGGTCTGTTGGATTTCCCAGGTCACCAGACCATTTTTAACGTAGAt > 1:2327604/1‑69 (MQ=255)
gTCAGGGTGAGTGCGCGGGTAGTCGGTCTGTTGGATTTCCCAGGTCACCAGACCATTTTTAACGTAGAt > 1:2822957/1‑69 (MQ=255)
gTCAGGGTGAGTGCGCGGGTAGTCGGTCTGTTGGATTTCCCAGGTCACCAGACCATTTTTAACGTAGAt > 1:783958/1‑69 (MQ=255)
gTCAGGGTGAGTGCGCGGGTAGTCGGTCTGTTGGATTTCCCAGGTCACCAGACCATTTTTAACGTAGAt > 1:3039055/1‑69 (MQ=255)
gTCAGGGTGAGTGCGCGGGTAGTCGGTCTGTTGGATTTCCCAGGTCACCAGACCATTTTTAACGTAGAt > 1:1558/1‑69 (MQ=255)
gTCAGGGTGAGTGCGCGGGTAGTCGGTCTGTTGGATTTCCCAGGTCACCAGACCATTTTTAACGTAGAt > 1:353498/1‑69 (MQ=255)
tCAGGGCGAGTGCGCGGGTAGTCGGTCTGTTGGATTTCCCAGGTCACCAGACCATTTTTaa > 1:1769446/1‑61 (MQ=255)
tCAGGGCGAGTGCGCGGGTAGTCGGTCTGTTGGATTTCCCAGGTCACCAGACCATTTTTAACGTAGAtt > 1:1563295/1‑69 (MQ=255)
tCAGGGCGAGTGCGCGGGTAGTCGGTCTGTTGGATTTCCCAGGTCACCAGACCATTTTTAACGTAGAtt > 1:1391767/1‑69 (MQ=255)
tCAGGGCGAGTGCGCGGGTAGTCGGTCTGTTGGATTTCCCAGGTCACCAGACCATTTTTAACGTAGAtt > 1:931171/1‑69 (MQ=255)
tCAGGGCGAGTGCGCGGGTAGTCGGTCTGTTGGATTTCCCAGGTCACCAGACCATTTTTAACGTAGAt > 1:767716/1‑68 (MQ=255)
cAGGGCGAGTGCGCGGGTAGTCGGTCTGTTGGATTTCCCAGGTCACCAGACCATTTTTAACGTAGAttt > 1:1650189/1‑69 (MQ=255)
cAGGGCGAGTGCGCGGGTAGTCGGTCTGTTGGATTTCCCAGGTCACCAGACCATTTTTAACGTAGAttt > 1:1793217/1‑69 (MQ=255)
cAGGGCGAGTGCGCGGGTAGTCGGTCTGTTGGATTTCCCAGGTCACCAGACCATTTTTAACGTAGAttt > 1:645125/1‑69 (MQ=255)
cAGGGCGAGTGCGCGGGTAGTCGGTCTGTTGGATTTCCCAGGTCACCAGACCATTTTTAACGTAGAttt > 1:2263206/1‑69 (MQ=255)
cAGGGCGAGTGCGCGGGTAGTCGGTCTGTTGGATTTCCCAGGTCACCAGACCATTTTTAACGTAGAttt > 1:2923156/1‑69 (MQ=255)
gCGAGTGCGCGGGTAGTCGGTCTGTTGGATTTCCCAGGTCACCAGACCATTTTTAACGTAGATTTTCCa > 1:1371616/1‑69 (MQ=255)
|
GTAAAGATACCAGGAGTAACTTGCGCCACGCGGGCAGCCGCGAGGTTCATGATTGGGCAGGTCAGGGCGAGTGCGCGGGTAGTCGGTCTGTTGGATTTCCCAGGTCACCAGACCATTTTTAACGTAGATTTTCCA > minE/927382‑927516
|
| 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
