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 |
|
A6 F21 I0 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,789,035 |
T→C |
28.9% |
S58P (TCC→CCC) |
ygaF → |
hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,789,035 | 0 | T | C | 28.9%
| 46.4
/ 25.3
| 38 | S58P (TCC→CCC) | ygaF | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (10/17); new base C (5/6); total (15/23) |
| Fisher's exact test for biased strand distribution p-value = 7.22e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.85e-01 |
AGTCCGCCCCGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGTCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGAAACCGCGCCACCAAAGCCTTTTGCGATC > minE/1788967‑1789098
|
agTCCGCCCCGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGccc < 1:1775817/71‑1 (MQ=255)
cGCCCCGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGTGTCTATTACACGTCCGGCa < 1:2379323/71‑1 (MQ=255)
cGCCCCGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGCCCGGCa < 1:1966601/71‑1 (MQ=255)
ccccGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGTCCGGCAGc > 1:501068/1‑71 (MQ=255)
ccGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGCCCGGCAGCCt > 1:2976618/1‑71 (MQ=255)
cGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGTCCGGc > 1:2133773/1‑65 (MQ=255)
gCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGCCCGGCAGCCTg > 1:1249125/1‑69 (MQ=255)
ccTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGCCCGGCAGCCTGAAg < 1:2389998/71‑1 (MQ=255)
tCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGTCCg < 1:3822041/56‑1 (MQ=255)
tCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGTCCGGCAGCCTGAAGgc < 1:1275994/69‑1 (MQ=255)
cACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGTCCGGCAGCCTGAAGgcg > 1:3477365/1‑69 (MQ=255)
ccAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGTCCGGCAGCCTGAAGGCGCAGt < 1:1857796/71‑1 (MQ=255)
cAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGTCCGGGAGCCTGAAGGCGCAGtt < 1:818801/71‑1 (MQ=255)
cAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGCCCGGCAGCCTGAAGGCGCAGtt > 1:3594740/1‑71 (MQ=255)
aGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGTCCGGCAGCCTGAAGGCGCAGttt > 1:3054022/1‑71 (MQ=255)
gACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGTCCGGCAGCCTGAAGGCGCAGtttt < 1:1501073/71‑1 (MQ=255)
gACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGCCCGGCAGCCTGAAGGCGCAGtttt > 1:137683/1‑71 (MQ=255)
aCGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGTCCGGCAGCCTGAAGGCGCAGtttt < 1:1075776/70‑1 (MQ=255)
ggCCACAACAGCGGCGT‑ATCCATGCCGGGGTCTATTACACGTCCGGCAGCCTGAAGGCGCAGTTTTGCCTg < 1:2734702/71‑1 (MQ=255)
cacaACAGCGGCGTGATCCATGCCGGTGTCTATTACACGTCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGc < 1:3563961/71‑1 (MQ=255)
cacaACAGCGGCGTGATCCATGCCGGGGTCTATTACACGCCCGGCAGCCTGAAGGCGCAGTTTTGCCt < 1:1532171/68‑1 (MQ=255)
acaGCGGCGTGATCCATGCCGGGGTCTATTACACGTCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGa < 1:3670669/71‑1 (MQ=255)
acaGCGGCGTGATCCATGCCGGGGTCTATTACACGTCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGa < 1:2909275/71‑1 (MQ=255)
cggcgTGATCCATGCCGGGGTCTATTACACGTCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGAAAcc < 1:2172304/71‑1 (MQ=255)
cggcgTGATCCATGCCGGGGTCTATTACACGTCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGAAAcc < 1:1809943/71‑1 (MQ=255)
ggcgTGATCCATGCCGGGGTCTATTACACGCCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGAAAcc < 1:3296986/70‑1 (MQ=255)
gTGATCCATGCCGGGGTCTATTACACGTCCGGCAGCCTGAAGGCGCAGtttt < 1:2525183/52‑1 (MQ=255)
tGATCCATGCCGGGGTCTATTACACGTCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCg > 1:501719/1‑59 (MQ=255)
tCCATGCCGGGGTCTATTACACGCCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGAAACCGCGccacc < 1:641796/71‑1 (MQ=255)
ccGGGGTCTATTACACGTCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGAAACCGCGCCACCAAAGcc > 1:2724958/1‑71 (MQ=255)
gggTCTATTACACGTCCGGCAGCCTGAAGGCGCAGttt < 1:3067325/38‑1 (MQ=255)
gggTCTATTACACGCCCGGCAGCCTGAAGGCGCCGt < 1:1693940/36‑1 (MQ=37)
tATTACACGTCCGGCAGCCTGAAGTCGCAGTTTTGc < 1:237955/36‑1 (MQ=255)
tATTACACGCCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGAAACCGCGCCTCCAAAGCCTTTTGCGa > 1:1610200/1‑71 (MQ=255)
aTTACACGTCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGAAACCGCGCCACCAAAGCCTTTTGCGAt > 1:3245868/1‑71 (MQ=255)
ttACACGTCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGAAACCGCGCCACCAAAGCCTTTTGCGAt > 1:2583252/1‑70 (MQ=255)
ttACACGTCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGAAACCGCGCCACCAAAGCCTTTTGCGAt > 1:2578652/1‑70 (MQ=255)
ttACACGTCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGAAACCGCGCCACCAAAGCCTTTTGCGATc < 1:3253006/71‑1 (MQ=255)
tACACGTCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGAAACCGCGCCACCAAAGCCttt > 1:2172152/1‑63 (MQ=255)
tCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGAAAcc < 1:1024160/40‑1 (MQ=255)
|
AGTCCGCCCCGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGTCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGAAACCGCGCCACCAAAGCCTTTTGCGATC > minE/1788967‑1789098
|
| 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
