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 F1 I0 R1
|
2892 |
75.3 |
5698161 |
66.1% |
3766484 |
59.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,816,759:1 |
+G |
48.1% |
coding (417/441 nt) |
soxR → |
DNA‑binding transcriptional dual regulator, Fe‑S center for redox‑sensing |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,816,759 | 1 | . | G | 48.1%
| 38.1
/ 68.2
| 27 | coding (417/441 nt) | soxR | DNA‑binding transcriptional dual regulator, Fe‑S center for redox‑sensing |
| Reads supporting (aligned to +/- strand): ref base . (11/3); new base G (7/6); total (18/9) |
| Fisher's exact test for biased strand distribution p-value = 2.36e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.34e-01 |
GACGGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTA‑GAGAAGAAGGTACCGGCGCACTAGGGGCGAGCAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTGAA > minE/2816691‑2816828
|
gACGGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTa‑ga < 1:633351/71‑1 (MQ=255)
tGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGagaaga < 1:3084124/71‑1 (MQ=255)
aTTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTA‑GAGAAGAAgg > 1:1235420/1‑70 (MQ=255)
ttGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTa‑ga > 1:2469353/1‑61 (MQ=255)
ttGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAgaagaa > 1:3360926/1‑68 (MQ=255)
ttGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGt < 1:3301379/71‑1 (MQ=255)
ttGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGt < 1:330405/71‑1 (MQ=255)
ttGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGt < 1:114862/71‑1 (MQ=255)
ttGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGt < 1:4163965/71‑1 (MQ=255)
ttGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCg > 1:2987377/1‑71 (MQ=255)
gtgGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCgg > 1:3159841/1‑70 (MQ=255)
gtgGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGgc > 1:3133796/1‑71 (MQ=255)
ggCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTa < 1:1357467/51‑1 (MQ=255)
cTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCAc > 1:1460765/1‑71 (MQ=255)
cTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCAc > 1:2044613/1‑71 (MQ=255)
tCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTa‑gga > 1:2078559/1‑43 (MQ=255)
tCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTA‑GAGAAGAAGGTACCGGCGCACTAGGGGc > 1:5490880/1‑70 (MQ=255)
cgcgCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTa‑ga > 1:5518853/1‑43 (MQ=255)
cgcgCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTa‑ga > 1:1083296/1‑43 (MQ=255)
cgcgCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTA‑GAGAAGAAgg > 1:872420/1‑51 (MQ=255)
cgcgCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTA‑GAGAAGAAgg > 1:1182128/1‑51 (MQ=255)
cAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTAGGAGAAGAAGGTACCGGCGCAc < 1:399633/59‑1 (MQ=255)
aGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTA‑GAGAAGAAGGTACCGGCGCACTAGGGGCGAGCAAt > 1:1961746/1‑71 (MQ=255)
aTTGCCCGTTGCGTAACCCGGGCGACCGCTTA‑GAGAAGAAGGTACCGGCGCACTAGGGGCGAGCATTGt < 1:2844756/69‑1 (MQ=255)
tGCCCGTTGCGTAACCCGGGCGACCGCTTA‑GAGAAGAAGGTAcc > 1:3681458/1‑44 (MQ=255)
gCGTAACCCGGGCGACCGCTTA‑GAGAAGAAGGTACCGGCGCACTAGGGGCGAGCAATGTCATGACAgtg > 1:2026325/1‑69 (MQ=255)
cGTAACCCGGGCGACCGCTTA‑GAGAAGAAGGTACCGGCGCACTAGGGGCGAGCAATGTCATGACAGTGTa < 1:3984659/70‑1 (MQ=255)
gTAACCCGGGCGACCGCTTA‑GAGAAGAAGGTACCGGCGCACTAGGGGCGAGCAATGTCATGACAGTGTAgg < 1:4382118/71‑1 (MQ=255)
tAACCCGGGCGACCGCTTA‑GAGAAGAAGGTACCGGCGCACTAGGGGCGAGCAATGTCATGACAGTGTAGGt > 1:1017079/1‑71 (MQ=255)
aaCCCGGGCGACCGCTTAGGAGAAGAAGCTACCGgcgc > 1:3559808/1‑38 (MQ=25)
aaCCCGGGCGACCGCTTA‑GAGAAGAAGGTACCGGCGCACTAGGGGCGAGCAATGTCATGACAGTGTAGGt > 1:2020063/1‑70 (MQ=255)
ttA‑GAGAAGAAGGTACCGGCGCACTAGGGGCGAGCAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTg > 1:166431/1‑70 (MQ=255)
ttA‑GAGAAGAAGGTACCGGCGCACTAGGGGAGAGCAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTg > 1:1358416/1‑70 (MQ=255)
a‑gagAAGAAGGTACCGGCGCACTAGGGGCGAGCAATGTCATGa > 1:1012375/1‑43 (MQ=255)
a‑gagAAGAAGGTACCGGCGCACTAGGGGCGAGCAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTGaa < 1:146302/70‑1 (MQ=255)
a‑gagAAGAAGGTACCGGCGCACTAGGGGCGAGCAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTGa < 1:1139932/69‑1 (MQ=255)
|
GACGGATGTATTGGTTGTGGCTGCCTTTCGCGCAGTGATTGCCCGTTGCGTAACCCGGGCGACCGCTTA‑GAGAAGAAGGTACCGGCGCACTAGGGGCGAGCAATGTCATGACAGTGTAGGTGCGGTTACTGTCGTGAA > minE/2816691‑2816828
|
| 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
