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 |
373,562 |
G→C |
26.2% |
E138Q (GAA→CAA) ‡ |
fepE → |
regulator of length of O‑antigen component of lipopolysaccharide chains |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 373,562 | 0 | G | C | 26.2%
| 153.3
/ 57.2
| 103 | E138Q (GAA→CAA) ‡ | fepE | regulator of length of O‑antigen component of lipopolysaccharide chains |
| Reads supporting (aligned to +/- strand): ref base G (37/39); new base C (8/19); total (45/58) |
| Fisher's exact test for biased strand distribution p-value = 1.15e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.68e-01 |
Only 100 of 129 total aligned reads displayed.
AGTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGTTGATGACAATGC > minE/373506‑373626
|
agTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGc < 1:1027761/69‑1 (MQ=255)
agTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGc < 1:1107463/69‑1 (MQ=255)
agTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGc < 1:79417/69‑1 (MQ=255)
agTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGc < 1:2723667/69‑1 (MQ=255)
gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa < 1:2803689/69‑1 (MQ=255)
gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa < 1:1592560/69‑1 (MQ=255)
gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa < 1:2769417/69‑1 (MQ=255)
gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa < 1:2757906/69‑1 (MQ=255)
gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa < 1:469183/69‑1 (MQ=255)
gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa < 1:479373/69‑1 (MQ=255)
gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa < 1:2644204/69‑1 (MQ=255)
gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa < 1:101392/69‑1 (MQ=255)
gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa < 1:831737/69‑1 (MQ=255)
gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa < 1:2412929/69‑1 (MQ=255)
gTACCTGCGTTCATCACCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCa < 1:2345649/69‑1 (MQ=255)
tACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCAt > 1:1843938/1‑69 (MQ=255)
ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga < 1:2705010/54‑1 (MQ=255)
ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga > 1:1618448/1‑54 (MQ=255)
ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga > 1:3074205/1‑54 (MQ=255)
ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga > 1:3072300/1‑54 (MQ=255)
ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga > 1:334122/1‑54 (MQ=255)
ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga > 1:1424753/1‑54 (MQ=255)
ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga > 1:875730/1‑54 (MQ=255)
ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga > 1:832966/1‑54 (MQ=255)
ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga > 1:373533/1‑54 (MQ=255)
ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga < 1:1245647/54‑1 (MQ=255)
ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga > 1:602756/1‑54 (MQ=255)
ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga > 1:1231593/1‑54 (MQ=255)
ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATcgacga > 1:546724/1‑54 (MQ=255)
ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCAt > 1:2049714/1‑67 (MQ=255)
ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATcg > 1:2662145/1‑69 (MQ=255)
ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATcg > 1:2426194/1‑69 (MQ=255)
ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATcg > 1:347173/1‑69 (MQ=255)
ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATcg > 1:3389758/1‑69 (MQ=255)
ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATcg > 1:2300291/1‑69 (MQ=255)
ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATcg > 1:2277955/1‑69 (MQ=255)
ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATcg > 1:2468898/1‑69 (MQ=255)
ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATcg > 1:1500968/1‑69 (MQ=255)
ccTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATc > 1:1779859/1‑68 (MQ=255)
tGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATcgc > 1:48746/1‑68 (MQ=255)
gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc > 1:1127555/1‑69 (MQ=255)
gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc > 1:1544905/1‑69 (MQ=255)
gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc < 1:1718465/69‑1 (MQ=255)
gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc > 1:2876191/1‑69 (MQ=255)
gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc > 1:288359/1‑69 (MQ=255)
gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc < 1:2648258/69‑1 (MQ=255)
gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc > 1:313586/1‑69 (MQ=255)
gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc < 1:3387097/69‑1 (MQ=255)
gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc < 1:1349102/69‑1 (MQ=255)
gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc < 1:44285/69‑1 (MQ=255)
gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc > 1:1317306/1‑69 (MQ=255)
gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc > 1:484610/1‑69 (MQ=255)
gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc < 1:222350/69‑1 (MQ=255)
gCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCgcgc > 1:2157912/1‑69 (MQ=255)
ttCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCa < 1:3123218/67‑1 (MQ=255)
ttCATCACCTTATGCGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAAt < 1:186153/69‑1 (MQ=255)
catcaCCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCATCGCGCCATTg > 1:653184/1‑69 (MQ=255)
catcaCCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCATCGCGCCATTg > 1:1127733/1‑69 (MQ=255)
catcaCCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCATCGCGCCATTg > 1:2840410/1‑69 (MQ=255)
catcaCCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCATCGCGCCATTg > 1:2097096/1‑69 (MQ=255)
catcaCCTTATGTGATGGATCAATTAAAAGAAGCGAAAATCGACCCACTGGATCTGCATCGCGCCATTg > 1:1923087/1‑69 (MQ=255)
caCCTTATGTGATGGATCAATTAAAAGAAGCGATAATCGACCCACTGGATCTGCa < 1:2664771/55‑1 (MQ=255)
caCCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCg < 1:1914623/69‑1 (MQ=255)
caCCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCg < 1:95979/69‑1 (MQ=255)
caCCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCg < 1:1744742/69‑1 (MQ=255)
tATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTg > 1:1053526/1‑69 (MQ=255)
tATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTg > 1:1508458/1‑69 (MQ=255)
tATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTg > 1:2145637/1‑69 (MQ=255)
tATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTg > 1:1198086/1‑69 (MQ=255)
tATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTg > 1:1416194/1‑69 (MQ=255)
aTGGATCAATTAAAAGACGCGAAAATCGACCCACTGGATCTGCa < 1:858057/44‑1 (MQ=21)
aaaaGAGGCGAAAATCGACGAACTGGATTTGCATCGCGTAATTGTCGCATTGAGCGAAAAAATGAAAGc > 1:1330454/1‑69 (MQ=255)
aaaaGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGc > 1:3161858/1‑69 (MQ=255)
aaaaGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGc > 1:3382077/1‑69 (MQ=255)
gagTCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGtt < 1:1230073/69‑1 (MQ=255)
gagGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCTAAAAAATGAAAGCGGtt < 1:3257639/69‑1 (MQ=255)
gagGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGtt < 1:280324/69‑1 (MQ=255)
gagGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGtt < 1:117502/69‑1 (MQ=255)
gagGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGtt < 1:659153/69‑1 (MQ=255)
gagGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGtt < 1:2161973/69‑1 (MQ=255)
gagGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGtt < 1:1978313/69‑1 (MQ=255)
gagGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGtt < 1:1673609/69‑1 (MQ=255)
gagGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGtt < 1:1704676/69‑1 (MQ=255)
gagGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGtt < 1:1414444/69‑1 (MQ=255)
gagGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGtt < 1:254274/69‑1 (MQ=255)
gagGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGtt < 1:2468131/69‑1 (MQ=255)
gagGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGtt < 1:1859922/69‑1 (MQ=255)
gagGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGtt < 1:3332300/69‑1 (MQ=255)
aaaaTCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGTTGATGAc < 1:2880706/69‑1 (MQ=255)
aaaaTCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGTTGATGAc < 1:20125/69‑1 (MQ=255)
aaaaTCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGTTGATGAc < 1:3300271/69‑1 (MQ=255)
cgacgaACTGGATTTTCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGTTGATGACAATGc < 1:773358/69‑1 (MQ=255)
cgacgaACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAg > 1:704717/1‑53 (MQ=255)
cgacgaACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGTTGATGACaa > 1:605401/1‑66 (MQ=255)
cgacgaACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGTTGATGACAAt > 1:1927034/1‑67 (MQ=255)
cgacgaACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGTTGATGACAATGc < 1:1448203/69‑1 (MQ=255)
cgacgaACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGTTGATGACAATGc < 1:507093/69‑1 (MQ=255)
cgacgaACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGTTGATGACAATGc < 1:2240456/69‑1 (MQ=255)
cgacgaACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGTTGATGACAATGc < 1:2699962/69‑1 (MQ=255)
cgacgaACTGGATTTGCATCGCGCAATTGTCCCATTGAGCGAAAAAATGAAAGCGGTTGATGACAATGc < 1:1622634/69‑1 (MQ=255)
|
AGTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGCGAAAATCGACGAACTGGATTTGCATCGCGCAATTGTCGCATTGAGCGAAAAAATGAAAGCGGTTGATGACAATGC > minE/373506‑373626
|
| 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
