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 |
811,407 |
A→T |
62.0% |
A537A (GCT→GCA) |
ychM ← |
predicted transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 811,407 | 0 | A | T | 62.0%
| 32.5
/ 42.7
| 50 | A537A (GCT→GCA) | ychM | predicted transporter |
| Reads supporting (aligned to +/- strand): ref base A (9/10); new base T (22/9); total (31/19) |
| Fisher's exact test for biased strand distribution p-value = 1.35e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CCATCGCCGCGCGACGATTCGGGAAGAACGCCAGGCGTCCCGGGATCGGTTGAATGCCAGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCACGTTGCACACGCGCAGTTCACATCCCTC > minE/811349‑811469
|
ccATCGCCGCGCGACGATTCGGGAAGAACGCCAGGCGTCCCGGGATCGGTTGAATGCCAGCGCGAGCCa < 1:2706872/69‑1 (MQ=255)
ccATCGCCGCGCGACGATTCGGGAAGAACGCCAGGCGTCCCGGGATCGGTTGAATGCCAGCGCGAGCCa < 1:2505397/69‑1 (MQ=255)
ccATCGCCGCGCGACGATTCGGGAAGAACGCCAGGCGTCCCGGGATCGGTTGAATGCCAGCGCGAGCCa < 1:2225632/69‑1 (MQ=255)
ccATCGCCGCGCGACGATTCGGGAAGAACGCCAGGCGTCCCGGGATCGGTTGAATGCCAGCGCGAGCCa < 1:1816601/69‑1 (MQ=255)
gccgcGCGACGATTCGGGAAGAACGCCAGGCGTCCCGGGATCGGTTGAATGCCAGCGCGAGCCATAGTg > 1:1046398/1‑69 (MQ=255)
gccgcGCGACGATTCGGGAAGAACGCCAGGCGTCCCGGGATCGGTTGAATGCCAGCGCGAGCCATAGTg > 1:2499188/1‑69 (MQ=255)
gccgcGCGACGATTCGGGAAGAACGCCAGGCGTCCCGGGATCGGTTGAATGCCAGCGCGAGCCATAGTg > 1:764209/1‑69 (MQ=255)
gccgcGCGACGATTCGGGAAGAACGCCAGGCGTCCCGGGATCGGTTGAATGCCAGCGCGAGCCATAGTg > 1:1417023/1‑69 (MQ=255)
gccgcGCGACGATTCGGGAAGAACGCCAGGCGTCCCGGGATCGGTTGAATGCCAGCGCGAGCCATAGTg > 1:81835/1‑69 (MQ=255)
tCGGGAAGAACGCCAGGCGTCCCGGGATCGGTTGAATGCCAGCGCGAGCCATAGTGCGCAGTGGCTgg < 1:428227/68‑1 (MQ=255)
agaaCGCCAGGCGTCCCGGGATCGGTTGAATGCCAGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCa < 1:805934/69‑1 (MQ=255)
agaaCGCCAGGCGTCCCGGGATCGGTTGAATGCCAGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCa < 1:2767968/69‑1 (MQ=255)
agaaCGCCAGGCGTCCCGGGATCGGTTGAATGCCAGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCa < 1:2479799/69‑1 (MQ=255)
gaaCGCCAGGCGTCCCGGGATCGGTTGAATGCCAGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCAc > 1:1930259/1‑69 (MQ=255)
gaaCGCCAGGCGTCCCGGGATCGGTTGAATGCCAGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCAc > 1:3081778/1‑69 (MQ=255)
gTCCCGGGATCGGTTGAATGCCAGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCACGTTGCACAcg > 1:2155075/1‑68 (MQ=255)
aTCGGTTGAATGCCAGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCACGTTGCACACGCGCAGTTca < 1:2601455/69‑1 (MQ=255)
aTCGGTTGAATGCCAGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCACGTTGCACACGCGCAGTTca > 1:962138/1‑69 (MQ=255)
tGAATGCCTGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCAGGt < 1:2404616/46‑1 (MQ=39)
tGAATGCCTGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCAGGTTGCCCACGCGCAGTTCACATcct > 1:815582/1‑68 (MQ=255)
tGAATGCCTGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCAGGTTGCACACGCGCAGTTca > 1:2841273/1‑63 (MQ=255)
tGAATGCCTGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCAGGTTGCACACGCGCAGTTCACATcct > 1:3016964/1‑68 (MQ=255)
tGAATGCCTGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCAGGTTGCACACGCGCAGTTCACATcct > 1:3099434/1‑68 (MQ=255)
tGAATGCCTGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCAGGTTGCACACGCGCAGTTCACATcct > 1:1060685/1‑68 (MQ=255)
tGAATGCCTGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCAGGTTGCACACGCGCAGTTCACATcct > 1:3153909/1‑68 (MQ=255)
tGAATGCCTGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCAGGTTGCACACGCGCAGTTCACATcct > 1:428529/1‑68 (MQ=255)
tGAATGCCTGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCAGGTTGCACACGCGCAGTTCACATcct > 1:515013/1‑68 (MQ=255)
tGAATGCCTGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCAGGTTGCACACGCGCAGTTCACATcct > 1:564105/1‑68 (MQ=255)
tGAATGCCTGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCAGGTTGCACACGCGCAGTTCACATcct > 1:718547/1‑68 (MQ=255)
tGAATGCCTGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCAGGTTGCACACGCGCAGTTCACATcct > 1:733950/1‑68 (MQ=255)
tGAATGCCTGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCAGGTTGCACACGCGCAGTTCACATcct > 1:2253416/1‑68 (MQ=255)
tGAATGCCTGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCAGGTTGCACACGCGCAGTTCACATcct > 1:113520/1‑68 (MQ=255)
tGAATGCCTGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCAGGTTGCACACGCGCAGTTCACATcct > 1:1272455/1‑68 (MQ=255)
tGAATGCCTGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCAGGTTGCACACGCGCAGTTCACATcct > 1:1514455/1‑68 (MQ=255)
tGAATGCCTGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCAGGTTGCACACGCGCAGTTCACATcct > 1:1561838/1‑68 (MQ=255)
tGAATGCCTGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCAGGTTGCACACGCGCAGTTCACATcct > 1:2035798/1‑68 (MQ=255)
tGAATGCCTGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCAGGTTGCACACGCGCAGTTCACATcct > 1:215066/1‑68 (MQ=255)
tGAATGCCTGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCAGGTTGCACACGCGCAGTTCACATcct > 1:2288927/1‑68 (MQ=255)
tGAATGCCTGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCAGGTTGCACACGCGCAGTTCACATcct > 1:249905/1‑68 (MQ=255)
tGAATGCCTGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCAGGTTGCACACGCGAAGTTCACATcct > 1:3241280/1‑68 (MQ=255)
tGAATGACTGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCAGGTTGCACACGCGCAGTTCACATcct > 1:439268/1‑68 (MQ=255)
aTGCCTGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCTAGGTTGCACACGCGCAGTTCACATCCTTc < 1:130949/68‑1 (MQ=255)
aTGCCTGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCAGGTTGCACACGCGCAGTTCACATCCTTc < 1:298004/68‑1 (MQ=255)
aTGCCTGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCAGGTTGCACACGCGCAGTTCACATCCTTc < 1:2627626/68‑1 (MQ=255)
aTGCCTGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCAGGTTGCACACGCGCAGTTCACATCCTTc < 1:273654/68‑1 (MQ=255)
aTGCCTGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCAGGTTGCACACGCGCAGTTCACATCCTTc < 1:2778946/68‑1 (MQ=255)
aTGCCTGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCAGGTTGCACACGCGCAGTTCACATCCTTc < 1:2971945/68‑1 (MQ=255)
tGCCTGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCAGGTTGCACACGCGCAGTTCACATCCTTc < 1:1388054/67‑1 (MQ=255)
tGCCTGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCAGGTTGCACACGCGCAGTTCACATCCTTc < 1:907977/67‑1 (MQ=255)
ccAGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCa < 1:393103/37‑1 (MQ=255)
|
CCATCGCCGCGCGACGATTCGGGAAGAACGCCAGGCGTCCCGGGATCGGTTGAATGCCAGCGCGAGCCATAGTGCGCAGTGGCTGGAATTCCACGTTGCACACGCGCAGTTCACATCCCTC > minE/811349‑811469
|
| 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
