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 |
1,632,688 |
A→G |
31.9% |
E230E (GAA→GAG) |
narQ → |
sensory histidine kinase in two‑component regulatory system with NarP (NarL) |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,632,688 | 0 | A | G | 31.9%
| 37.7
/ 23.5
| 50 | E230E (GAA→GAG) | narQ | sensory histidine kinase in two‑component regulatory system with NarP (NarL) |
| Reads supporting (aligned to +/- strand): ref base A (7/27); new base G (7/9); total (14/36) |
| Fisher's exact test for biased strand distribution p-value = 1.05e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.44e-01 |
GCAAAAACCTTTAACCAGATGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAAGCGTCAGTAGAAGAAAAGACCCGCGATCTCCACGAGGCCAAGCGTCGTCTGGAGGTGT > minE/1632632‑1632746
|
gCAAAAACCTTTAACCAGATGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGTAGGCGTCAGTaga > 1:2830716/1‑68 (MQ=255)
gCAAAAACCTTTAACCAGATGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAGGc > 1:1900644/1‑59 (MQ=255)
gCAAAAACCTTTAACCAGATGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAGGCGTCAGTaga > 1:117779/1‑68 (MQ=255)
gCAAAAACCTTTAACCAGATGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAGGCGTCAGTaga > 1:2429224/1‑68 (MQ=255)
gCAAAAACCTTTAACCAGATGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAGGCGTCAGTaga > 1:1502989/1‑68 (MQ=255)
gCAAAAACCTTTAACCAGATGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAGGCGTCAGTaga > 1:3286138/1‑68 (MQ=255)
gCAAAAACCTTTAACCAGATGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAGGCGTCAGTaga > 1:1805224/1‑68 (MQ=255)
cTTTACCCAGATGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAGGCGTCAGTAGAAGAAAAGAc < 1:911249/69‑1 (MQ=255)
cTTTAACCAGATGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAGGCGTCAGTAGAAGAAAAGAc < 1:3122076/69‑1 (MQ=255)
cTTTAACCAGATGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAGGCGTCAGTAGAAGAAAAGAc < 1:2874980/69‑1 (MQ=255)
cTTTAACCAGATGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAGGCGTCAGTAGAAGAAAAGAc < 1:1748056/69‑1 (MQ=255)
cTTTAACCAGATGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAGGCGTCAGTAGAAGAAAAGAc < 1:1709581/69‑1 (MQ=255)
cTTTAACCAGATGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAGGCGTCAGTAGAAGAAAAGAc < 1:523552/69‑1 (MQ=255)
cTTTAACCAGATGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAGGCGTCAGTAGAAGAAAAGAc < 1:634656/69‑1 (MQ=255)
cTTTAACCAGATGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAGGCGTCAGTAGAAGAAAAGAc < 1:1186629/69‑1 (MQ=255)
cTTTAACCAGATGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAGGCGTCAGTAGAAGAAAAGAc < 1:1098605/69‑1 (MQ=255)
cTTTAACCAGATGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAAGCGt > 1:1623926/1‑53 (MQ=255)
cTTTAACCAGATGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAAGCGTCAGTAGAAGAAAAGAc > 1:993811/1‑69 (MQ=255)
cTTTAACCAGATGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAAGCGTCAGTAGAAGAAAAGAc > 1:3066159/1‑69 (MQ=255)
cTTTAACCAGATGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAAGCGTCAGTAGAAGAAAAGAc > 1:22871/1‑69 (MQ=255)
cTTTAACCAGATGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAAGCGTCAGTAGAAGAAAAGAc > 1:1675530/1‑69 (MQ=255)
cTTTAACCAGATGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAAGCGTCAGTAGAAGAAAAGAc > 1:1896970/1‑69 (MQ=255)
cTTTAACCAGATGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAAGCGTCAGTAGAAGAAAAGAc > 1:1496608/1‑69 (MQ=255)
ccAGATGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAAGCGTCAGTAGAAGAAAAGACCcgcg < 1:2591717/68‑1 (MQ=255)
cAGATGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAAGCGTCAGTAGAAGAAAAGACCcgcg < 1:1960322/67‑1 (MQ=255)
cAGATGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAAGCGTCAGTAGAAGAAAAGACCcgcg < 1:2202776/67‑1 (MQ=255)
cAGATGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAAGCGTCAGTAGAAGAAAAGACCcgcg < 1:3114247/67‑1 (MQ=255)
aTGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAAGCGTCAGTAGAAGAAACGACCCGCGAtctc < 1:3142464/69‑1 (MQ=255)
aTGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAAGCGTCAGTAGAAGAAAAGACCCGCGAtctc < 1:3303094/69‑1 (MQ=255)
aTGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAAGCGTCAGTAGAAGAAAAGACCCGCGAtctc < 1:1597091/69‑1 (MQ=255)
aTGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAAGCGTCAGTAGAAGAAAAGACCCGCGAtctc < 1:3099964/69‑1 (MQ=255)
aTGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAAGCGTCAGTAGAAGAAAAGACCCGCGAtctc < 1:2925288/69‑1 (MQ=255)
aTGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAAGCGTCAGTAGAAGAAAAGACCCGCGAtctc < 1:1828871/69‑1 (MQ=255)
aTGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAAGCGTCAGTAGAAGAAAAGACCCGCGAtctc < 1:2856125/69‑1 (MQ=255)
aTGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAAGCGTCAGTAGAAGAAAAGACCCGCGAtctc < 1:1855381/69‑1 (MQ=255)
aTGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAAGCGTCAGTAGAAGAAAAGACCCGCGAtctc < 1:2768512/69‑1 (MQ=255)
aTGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAAGCGTCAGTAGAAGAAAAGACCCGCGAtctc < 1:929423/69‑1 (MQ=255)
aTGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAAGCGTCAGTAGAAGAAAAGACCCGCGAtctc < 1:1903246/69‑1 (MQ=255)
cTGCATAAATTGTACCGTTCGCTGGAAGCGTCAGTAgaagaa < 1:417075/42‑1 (MQ=255)
cTGCATAAATTGTACCGTTCGCTGGAAGCGTCAGTAgaagaa < 1:1202878/42‑1 (MQ=255)
cTGCATAAATTGTACCGTTCGCTGGAAGCGTCAGTAgaagaa < 1:937732/42‑1 (MQ=255)
cTGCATAAATTGTACCGTTCGCTGGAAGCGTCAGTAgaagaa < 1:1063834/42‑1 (MQ=255)
cTGCATAAATTGTACCGTTCGCTGGAAGCGTCAGTAgaagaa < 1:2329530/42‑1 (MQ=255)
cTGCATAAATTGTACCGTTCGCTGGAAGCGTCAGTAgaagaa < 1:2014777/42‑1 (MQ=255)
aaTTGTACCGTTCGCTGGAAGCGTCAGTAgaagaa < 1:1376290/35‑1 (MQ=255)
aaTTGTACCGTTCGCTGGAAGCGTCAGTAgaagaa < 1:2351028/35‑1 (MQ=255)
aaTTGTACCGTTCGCTGGAAGCGTCAGTAgaagaa < 1:1900138/35‑1 (MQ=255)
ttGTACCGTTCGCTGGAAGCGTCAGTAGAAGAAAAGACCCGCGATCTCCACGAGGCCAAGCGTCGTCTg < 1:1782688/69‑1 (MQ=255)
ttGTACCGTTCGCTGGAAGCGTCAGTAGAAGAAAAGACCCGCGATCTCCACGAGGCCAAGCGTCGTCTg < 1:2808970/69‑1 (MQ=255)
gTTCGCTGGAAGCGTCAGTAGAAGAAAAGACCCGCGATCTCCACGAGGCCAAGCGTCGTCTGGAGgtgt < 1:343741/69‑1 (MQ=255)
|
GCAAAAACCTTTAACCAGATGTCGAGCGAGCTGCATAAATTGTACCGTTCGCTGGAAGCGTCAGTAGAAGAAAAGACCCGCGATCTCCACGAGGCCAAGCGTCGTCTGGAGGTGT > minE/1632632‑1632746
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
