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 |
2,628,259 |
T→C |
100% |
T243T (ACT→ACC) |
livJ → |
leucine/isoleucine/valine transporter subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,628,259 | 0 | T | C | 79.2%
| 51.1
/ 8.1
| 43 | T243T (ACT→ACC) | livJ | leucine/isoleucine/valine transporter subunit |
| Reads supporting (aligned to +/- strand): ref base T (8/1); new base C (23/11); total (31/12) |
| Fisher's exact test for biased strand distribution p-value = 4.05e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.95e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
GGAAATGGGGCAAATCCTGCGTCAGGCACGCGCGGCAGGGCTGAAAACTCAGTTTATGGGGCCGGAAGGTGTGGCTAACGTTTCGCTGTCTAACATTGCGGGCGAATCAGCGGA > minE/2628211‑2628324
|
ggAAATGGGGCAGATCCTGCGTCAGGCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAgg > 1:1196847/1‑69 (MQ=17)
ggAAATGGGGCAGATCCTGCGTCAGGCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAgg > 1:1952095/1‑69 (MQ=17)
ggAAATGGGGCAGATCCTGCGTCAGGCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAgg > 1:1894214/1‑69 (MQ=17)
ggAAATGGGGCAGATCCTGCGTCAGGCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAgg > 1:2752678/1‑69 (MQ=17)
ggAAATGGGGCAGATCCTGCGTCAGGCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAgg > 1:2787974/1‑69 (MQ=17)
ggAAATGGGGCAGATCCTGCGTCAGGCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAgg > 1:2824865/1‑69 (MQ=17)
ggAAATGGGGCAGATCCTGCGTCAGGCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAgg > 1:1643612/1‑69 (MQ=17)
ggAAATGGGGCAGATCCTGCGTCAGGCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAgg > 1:1538043/1‑69 (MQ=17)
ggAAATGGGGCAGATCCTGCGTCAGGCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAgg > 1:3397208/1‑69 (MQ=17)
ggAAATGGGGCAGATCCTGCGTCAGGCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAgg > 1:1221141/1‑69 (MQ=17)
aaTCCTGCGTCAGGCACGCGCGGCAGGGCTGAAAACTCAGTTTATGGGGCCGGAAGGTGTGGCTAACGt < 1:2847762/69‑1 (MQ=255)
cAGGCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCt < 1:3034606/69‑1 (MQ=25)
cAGGCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCt < 1:329331/69‑1 (MQ=25)
cAGGCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCt < 1:2840951/69‑1 (MQ=25)
cAGGCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCt < 1:3325578/69‑1 (MQ=25)
cAGGCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCt < 1:473343/69‑1 (MQ=25)
cAGGCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCt < 1:203066/69‑1 (MQ=25)
cAGGCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCt < 1:927996/69‑1 (MQ=25)
cAGGCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCt < 1:1836526/69‑1 (MQ=25)
cAGGCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCt < 1:151484/69‑1 (MQ=25)
cAGGCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCt < 1:1359807/69‑1 (MQ=25)
gCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCTaag > 1:3142369/1‑68 (MQ=21)
gCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCTAAc > 1:2092205/1‑69 (MQ=21)
gCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCTAAc > 1:59129/1‑69 (MQ=21)
gCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCTAAc > 1:1221242/1‑69 (MQ=21)
gCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCTAAc > 1:2769484/1‑69 (MQ=21)
gCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCTAAc > 1:1816423/1‑69 (MQ=21)
gCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCTAAc > 1:1765653/1‑69 (MQ=21)
gCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCTAAc > 1:1346686/1‑69 (MQ=21)
gCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCTAAc > 1:3396672/1‑69 (MQ=21)
gCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCTAAc > 1:2864417/1‑69 (MQ=21)
gCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCTAAc > 1:1414155/1‑69 (MQ=21)
gCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCGCGCTGTCTAAc > 1:3104365/1‑69 (MQ=21)
gCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGACTCGCTGTCTAAc > 1:1191590/1‑69 (MQ=21)
cACGCGCGGCAGGGCTGAAAACTCAGTTTATGGGGCCGGAAGgtgt > 1:540329/1‑46 (MQ=255)
cACGCGCGGCAGGGCTGAAAACTCAGTTTATGGGGCCGGAAGGTGTGGCTAACGTTTCGCTGTCTAACa > 1:325848/1‑69 (MQ=255)
cACGCGCGGCAGGGCTGAAAACTCAGTTTATGGGGCCGGAAGGTGTGGCTAACGTTTCGCTGTCTAACa > 1:1904070/1‑69 (MQ=255)
cACGCGCGGCAGGGCTGAAAACTCAGTTTATGGGGCCGGAAGGTGTGGCTAACGTTTCGCTGTCTAACa > 1:1692091/1‑69 (MQ=255)
cACGCGCGGCAGGGCTGAAAACTCAGTTTATGGGGCCGGAAGGTGTGGCTAACGTTTCGCTGTCTAACa > 1:2147406/1‑69 (MQ=255)
cgGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGGGGCTAACGTCTCGCTGTCt < 1:87247/59‑1 (MQ=21)
aaaCTCAGTTTATGGGGCCGGAAGGTGTGGCTAACGTTTCGCTGTCTAACATTGCGGGCGAATCAGc > 1:1830383/1‑67 (MQ=255)
aaaCTCAGTTTATGGGGCCGGAAGGTGTGGCTAACGTTTCGCTGTCTAACATTGCGGGCGAATCAGc > 1:492646/1‑67 (MQ=255)
aaCTCAGTTTATGGGGCCGGAAGGTGTGGCTAACGTTTCGCTGTCTAACATTGCGGGCGAATCAGCGGa > 1:1591918/1‑69 (MQ=255)
|
GGAAATGGGGCAAATCCTGCGTCAGGCACGCGCGGCAGGGCTGAAAACTCAGTTTATGGGGCCGGAAGGTGTGGCTAACGTTTCGCTGTCTAACATTGCGGGCGAATCAGCGGA > minE/2628211‑2628324
|
| 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
