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 |
768,228 |
G→A |
34.4% |
Y268Y (TAC→TAT) |
phoQ ← |
sensory histidine kinase in two‑compoent regulatory system with PhoP |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 768,228 | 0 | G | A | 34.4%
| 40.9
/ 31.0
| 58 | Y268Y (TAC→TAT) | phoQ | sensory histidine kinase in two‑compoent regulatory system with PhoP |
| Reads supporting (aligned to +/- strand): ref base G (15/23); new base A (3/17); total (18/40) |
| Fisher's exact test for biased strand distribution p-value = 7.56e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.01e-01 |
CGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGTACCAGACTGGTC > minE/768160‑768291
|
cGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACgg < 1:202851/69‑1 (MQ=255)
gCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGATCGTCGTACGGt < 1:627239/69‑1 (MQ=255)
gCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACgg < 1:2419284/68‑1 (MQ=255)
gCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGt < 1:2158291/69‑1 (MQ=255)
gCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGt < 1:2064040/69‑1 (MQ=255)
gCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGt < 1:1302999/69‑1 (MQ=255)
gCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGt < 1:3187764/69‑1 (MQ=255)
cAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACTGTa < 1:1437706/69‑1 (MQ=255)
cAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTa < 1:1058165/69‑1 (MQ=255)
cAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTa < 1:2402106/69‑1 (MQ=255)
cAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTa < 1:180877/69‑1 (MQ=255)
cAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTa < 1:16408/69‑1 (MQ=255)
cAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTa < 1:3049396/69‑1 (MQ=255)
cAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTa < 1:1340447/69‑1 (MQ=255)
cAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTa < 1:535544/69‑1 (MQ=255)
cAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTa < 1:662577/69‑1 (MQ=255)
cAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTa < 1:812323/69‑1 (MQ=255)
aGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTa < 1:3431611/68‑1 (MQ=255)
agcaCCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGATATTTGTCGTAACGt > 1:1626321/1‑69 (MQ=255)
agcaCCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGATATTTGTCGTAACGt > 1:2514984/1‑69 (MQ=255)
agcaCCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGATATTTGTCGTAACGt > 1:216123/1‑69 (MQ=255)
gcaCCGCGAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTa < 1:2314222/55‑1 (MQ=255)
ccAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTa < 1:3397626/49‑1 (MQ=255)
gTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCAc < 1:283298/69‑1 (MQ=255)
ttgCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTa < 1:662517/43‑1 (MQ=255)
gCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTa < 1:2318006/43‑1 (MQ=255)
gCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACtt > 1:933268/1‑68 (MQ=255)
ttCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAAc < 1:189727/69‑1 (MQ=255)
cTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCgg < 1:580871/69‑1 (MQ=255)
tGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTc > 1:1113015/1‑69 (MQ=255)
tGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTc > 1:1907952/1‑69 (MQ=255)
tGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTc > 1:1728029/1‑69 (MQ=255)
tGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTc > 1:2791090/1‑69 (MQ=255)
tGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTc > 1:1154012/1‑69 (MQ=255)
cGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGt > 1:1280788/1‑68 (MQ=255)
cGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGt > 1:418225/1‑68 (MQ=255)
cGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGt > 1:388377/1‑68 (MQ=255)
cGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGt > 1:1529335/1‑68 (MQ=255)
cGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGt > 1:2335636/1‑68 (MQ=255)
gtcgtACGATATTTGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg < 1:290117/69‑1 (MQ=255)
gtcgtACGATATTTGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg < 1:1324565/69‑1 (MQ=255)
gtcgtACGATATTTGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg < 1:440871/69‑1 (MQ=255)
gtcgtACGATATTTGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg < 1:1741757/69‑1 (MQ=255)
gtcgtACGATATTTGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg < 1:2780576/69‑1 (MQ=255)
gtcgtACGATATTTGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg < 1:1377229/69‑1 (MQ=255)
gtcgtACGATATTTGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg < 1:3400868/69‑1 (MQ=255)
gtcgtACGATATTTGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg < 1:1398755/69‑1 (MQ=255)
gtcgtACGATATTTGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg < 1:32631/69‑1 (MQ=255)
gtcgtACGATATTTGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg < 1:1399689/69‑1 (MQ=255)
gtcgtACGATATTTGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg < 1:1501092/69‑1 (MQ=255)
gtcgtACGATATTTGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg < 1:3025811/69‑1 (MQ=255)
gtcgtACGATATTTGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg < 1:3021683/69‑1 (MQ=255)
gtcgtACGATATTTGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg < 1:2967579/69‑1 (MQ=255)
atcgtACGATATTTGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg < 1:3274733/68‑1 (MQ=255)
tcgtACGATATTTGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg < 1:1015313/68‑1 (MQ=255)
gtACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGTACCAGACTGGTc > 1:2840487/1‑69 (MQ=255)
gtACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGTACCAGACTGGTc > 1:1931800/1‑69 (MQ=255)
gtACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGTACCAGACTGGTc > 1:852748/1‑69 (MQ=255)
gtACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGTACCAGACTGGTc > 1:2236270/1‑69 (MQ=255)
gtACGATATTTGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg < 1:1324081/66‑1 (MQ=255)
|
CGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGTACCAGACTGGTC > minE/768160‑768291
|
| 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
