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 |
2,479,184 |
G→A |
27.3% |
P123P (CCG→CCA) |
phoU → |
DNA‑binding transcriptional regulator |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,479,184 | 0 | G | A | 27.3%
| 68.5
/ 22.8
| 62 | P123P (CCG→CCA) | phoU | DNA‑binding transcriptional regulator |
| Reads supporting (aligned to +/- strand): ref base G (9/36); new base A (5/12); total (14/48) |
| Fisher's exact test for biased strand distribution p-value = 5.02e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GTATTGGCGACGTGGCGGACAAAATCTGCCGTACTGCGCTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGCTGGTAAGTCTGGAGTCGCTGGGCCGTCATACCATCCAGATGCTGCACGACGTGCTGGACGCGTT > minE/2479117‑2479252
|
gTATTGGCGACGTGGCGGACAAAATCTGCCGTACTGCGCTGGAGAAATTCTCCCAGCAGCATCAGCCGt < 1:3350322/69‑1 (MQ=255)
ggCGACGTTGCGGACAAAATCTGCCGTACTGCGCTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGCTg < 1:2234054/69‑1 (MQ=255)
ggCGACGTGGCGGACAAAATCTGCCGTACTGCGCTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGc > 1:387198/1‑67 (MQ=255)
ggCGACGTGGCGGACAAAATCTGCCGTACTGCGCTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGCt > 1:770540/1‑68 (MQ=255)
ggCGACGTGGCGGACAAAATCTGCCGTACTGCGCTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGCt > 1:2322971/1‑68 (MQ=255)
ggCGACGTGGCGGACAAAATCTGCCGTACTGCGCTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGCt > 1:3300391/1‑68 (MQ=255)
ggCGACGTGGCGGACAAAATCTGCCGTACTGCGCTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGCt > 1:1450014/1‑68 (MQ=255)
ggCGACGTGGCGGACAAAATCTGCCGTACTGCGCTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGCt > 1:1352993/1‑68 (MQ=255)
ggCGACGTGGCGGACAAAATCTGCCGTACTGCGCTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGCTg < 1:3436101/69‑1 (MQ=255)
ggCGACGTGGCGGACAAAATCTGCCGTACTGCGCTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGCTg < 1:582551/69‑1 (MQ=255)
cGTGGCGGACAAAATCTGCCGTACTGCGCTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGCTGGTAAg < 1:2833099/69‑1 (MQ=255)
cGTGGCGGACAAAATCTGCCGTACTGCGCTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGCTGGTAAg < 1:1621491/69‑1 (MQ=255)
cGTGGCGGACAAAATCTGCCGTACTGCGCTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGCTGGTAAg < 1:56639/69‑1 (MQ=255)
cGTGGCGGACAAAATCTGCCGTACTGCGCTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGCTGGTAAg < 1:2111993/69‑1 (MQ=255)
gTGGCGGACAAAATCTGCCGTACTGCGCTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGCTGGTAAg < 1:2884828/68‑1 (MQ=255)
gTGGCGGACAAAATCTGCCGTACTGCGCTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGCTGGTAAg < 1:2702495/68‑1 (MQ=255)
aCAAAATCTGCCGTACTGCACTGGAGAAATTCTCCCAGCAGCATCAGCCATTGCTGGTAAGTCTGGAg > 1:1894821/1‑68 (MQ=255)
aCAAAATCTGCCGTACTGCACTGGAGAAATTCTCCCAGCAGCATCAGCCATTGCTGGTAAGTCTGGAGt > 1:1899125/1‑69 (MQ=255)
aCAAAATCTGCCGTACTGCACTGGAGAAATTCTCCCAGCAGCATCAGCCATTGCTGGTAAGTCTGGAGt > 1:2615109/1‑69 (MQ=255)
aCAAAATCTGCCGTACTGCACTGGAGAAATTCTCCCAGCAGCATCAGCCATTGCTGGTAAGTCTGGAGt > 1:679757/1‑69 (MQ=255)
aCAAAATCTGCCGTACTGCACTGGAGAAATTCTCCCAGCAGCATCAGCCATTGCTGGTAAGTCTGGAGt > 1:1627013/1‑69 (MQ=255)
cAAAATCTGCCGTACTGCGCTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGCTGGTAAGTCTGGAGTc < 1:624877/69‑1 (MQ=255)
cAAAATCTGCCGTACTGCGCTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGCTGGTAAGTCTGGAGTc < 1:3005602/69‑1 (MQ=255)
cAAAATCTGCCGTACTGCGCTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGCTGGTAAGTCTGGAGTc < 1:1414510/69‑1 (MQ=255)
cAAAATCTGCCGTACTGCGCTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGCTGGTAAGTCTGGAGTc < 1:1815126/69‑1 (MQ=255)
cTGCCGTACTCCGCTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGCTg < 1:2530073/49‑1 (MQ=255)
gTACTGCGCTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGCTGGTAAGTCTGGAGTCGCTGGGc < 1:1169420/65‑1 (MQ=255)
tACTGCGCTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGCTTGTAAg < 1:2924973/48‑1 (MQ=255)
cTGCGCTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGCTGGTAAGTCTg < 1:1202794/50‑1 (MQ=255)
cTGCGCTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGCTGGTAAGTCTg < 1:558626/50‑1 (MQ=255)
cTGCGCTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGCTGGTAAGTCTg < 1:2379838/50‑1 (MQ=255)
cTGCGCTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGCTGGTAAGTCTg < 1:2188515/50‑1 (MQ=255)
cTGCGCTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGCTGGTAAGTCTg < 1:861149/50‑1 (MQ=255)
cTGCGCTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGCTGGTAAGTCTg < 1:1643648/50‑1 (MQ=255)
cTGCGCTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGCTGGTAAGTCTg < 1:1231437/50‑1 (MQ=255)
cTGCGCTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGCTGGTAAGTCTg < 1:3350696/50‑1 (MQ=255)
cTGCGCTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGCTGGTAAGTCTg < 1:1376668/50‑1 (MQ=255)
cTGCGCTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGCTGGTAAGTCTGGAGTCGCTGGGCCGTCAt > 1:3421268/1‑68 (MQ=255)
cTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGCTGGTAAGTCTGGAGTCGCTGGGCCGTCATACCa < 1:1008898/67‑1 (MQ=255)
cTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGCTGGTAAGTCTGGAGTCGCTGGGCCGTCATACCa < 1:1746646/67‑1 (MQ=255)
cagcaTCAGCCGTTGCTGGTAAGTCTGGAGTCGCTGGGCCGTCATACCATCCAGATGCTGCACGACGTg < 1:2854598/69‑1 (MQ=255)
cagcaTCAGCCGTTGCTGGTAAGTCTGGAGTCGCTGGGCCGTCATACCATCCAGATGCTGCACGACGTg < 1:2645672/69‑1 (MQ=255)
cagcaTCAGCCGTTGCTGGTAAGTCTGGAGTCGCTGGGCCGTCATACCATCCAGATGCTGCACGACGTg < 1:2395702/69‑1 (MQ=255)
cagcaTCAGCCGTTGCTGGTAAGTCTGGAGTCGCTGGGCCGTCATACCATCCAGATGCTGCACGACGTg < 1:2190338/69‑1 (MQ=255)
gcaTCAGCCATTGCTGGTAAGTCTGGAGTCGCTGGGCCGTCATACCATCCAAATGCTGCACGACGTGCt < 1:527087/69‑1 (MQ=255)
gcaTCAGCCATTGCTGGTAAGTCTGGAGTCGCTGGGCCGTCATACCATCCAAATGCTGCACGACGTGCt < 1:416150/69‑1 (MQ=255)
gcaTCAGCCATTGCTGGTAAGTCTGGAGTCGCTGGGCCGTCATACCATCCAAATGCTGCACGACGTGCt < 1:3332290/69‑1 (MQ=255)
gcaTCAGCCATTGCTGGTAAGTCTGGAGTCGCTGGGCCGTCATACCATCCAAATGCTGCACGACGTGCt < 1:2752855/69‑1 (MQ=255)
gcaTCAGCCATTGCTGGTAAGTCTGGAGTCGCTGGGCCGTCATACCATCCAAATGCTGCACGACGTGCt < 1:237557/69‑1 (MQ=255)
gcaTCAGCCATTGCTGGTAAGTCTGGAGTCGCTGGGCCGTCATACCATCCAAATGCTGCACGACGTGCt < 1:162985/69‑1 (MQ=255)
gcaTCAGCCATTGCTGGTAAGTCTGGAGTCGCTGGGCCGTCATACCATCCAAATGCTGCACGACGTGCt < 1:793074/69‑1 (MQ=255)
caTCAGCCGTTGCTGGTAAGTCTGGAGTCGCTGGGCCGTCATACCATCCAGATGCTGCACGACGTGCTg < 1:11596/69‑1 (MQ=255)
caTCAGCCGTTGCTGGTAAGTCTGGAGTCGCTGGGCCGTCATACCATCCAGATGCTGCACGACGTGCTg < 1:3271735/69‑1 (MQ=255)
caTCAGCCGTTGCTGGTAAGTCTGGAGTCGCTGGGCCGTCATACCATCCAGATGCTGCACGACGTGCTg < 1:2701163/69‑1 (MQ=255)
caTCAGCCGTTGCTGGTAAGTCTGGAGGCGCTGGGCCGTCATACCATCCAGATGCTGCACGACGTGCTg < 1:398649/69‑1 (MQ=255)
caTCAGCCATTGCTGGTAAGTCTGGAGTCGCTGGGCCGTCATACCATCCAAATGCTGCACGACGTGCt < 1:2824743/68‑1 (MQ=255)
caTCAGCCATTGCTGGTAAGTCTGGAGTCGCTGGGCCGTCATACCATCCAAATGCTGCACGACGTGCt < 1:1418075/68‑1 (MQ=255)
caTCAGCCATTGCTGGTAAGTCTGGAGTCGCTGGGCCGTCATACCATCCAAATGCTGCACGACGTGCt < 1:92207/68‑1 (MQ=255)
aTCAGCCATTGCTGGTAAGTCTGGAGTCGCTGGGCCGTCATACCATCCAAATGCTGCACGACGTGCt < 1:3122561/67‑1 (MQ=255)
aTCAGCCATTGCTGGTAAGTCTGGAGTCGCTGGGCCGTCATACCATCCAAATGCTGCACGACGTGCt < 1:1208512/67‑1 (MQ=255)
aGCCGTTGCTGGTAAGTCTGGAGTCGCTGGGCCGTCATACCATCCAGATGCTGCACGACGTGCTGGAcg > 1:735870/1‑69 (MQ=255)
aGCCGTTGCTGGTAAGTCTGGAGTCGCTGGGCCGTCATACCATCCAGATGCTGCACGACGTGCTGGAcg > 1:1999399/1‑69 (MQ=255)
gTTGCTGGTAAGTCTGGAGTCGCTGGGCCGTCATACCATCCAGATGCTGCACGACGTGCTGGACGCGtt < 1:2024967/69‑1 (MQ=255)
|
GTATTGGCGACGTGGCGGACAAAATCTGCCGTACTGCGCTGGAGAAATTCTCCCAGCAGCATCAGCCGTTGCTGGTAAGTCTGGAGTCGCTGGGCCGTCATACCATCCAGATGCTGCACGACGTGCTGGACGCGTT > minE/2479117‑2479252
|
| 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
