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 |
|
A73 F1 I1 R1
|
21 |
62.0 |
3993596 |
96.1% |
3837845 |
76.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
4,520,058 |
T→C |
intergenic (‑419/‑1037) |
yjhA ← / → fimB |
N‑acetylnuraminic acid outer membrane channel protein/recombinase involved in phase variation; regulator for fimA; b4312_1 |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 4,520,058 | 0 | T | C | 82.3%
| 190.5
/ 28.7
| 68 | intergenic (‑419/‑1037) | yjhA/fimB | N‑acetylnuraminic acid outer membrane channel protein/recombinase involved in phase variation; regulator for fimA; b4312_1 |
| Reads supporting (aligned to +/- strand): ref base T (5/7); new base C (28/28); total (33/35) |
| Fisher's exact test for biased strand distribution p-value = 7.53e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01 |
CACCCGATGAGAAAGAACTGAAGTGATGTTTGCCATAGATTGCGAGATGCCCTGTCTCATTGACTATCTTGGTGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATCCATACAACAAAACCAGATTTGCAATTCGTGTCA > REL606/4519986‑4520133
|
caCCCGATGAGAAAGAACTGAAGTGATGTTTGCCATAGATTGCGAGATACCCTGTCTCATTGACTATCTTGGCGCa > 2:305038/1‑76 (MQ=255)
caCCCGATGAGAAAGAACTGAAGTGATGTTTGCCATAGATTGCGAGATACCCTGTCTCATTGACTATCTTGGCGCa > 2:305065/1‑76 (MQ=255)
caaTGAGAAAGAACTGAAGTGATGTTTGCCATAGATTGCGAGATGCCCTGTCTCATTTACTATCTTGGCGCACAtt < 2:744395/74‑1 (MQ=255)
cGATGAGAAAGAACTGAAGTGATGTTTGCCATAGATTGCGAGATGCCCTGTCTCATTGACTATCTTGGCGCACCtt < 2:744359/76‑1 (MQ=255)
gATGAGAAAGAACTGAAGTGATGTTTGCCATAGATTGCGAGATGCCCTGTCTCATTGACTATCTTGGTGCACCttt < 1:312491/76‑1 (MQ=255)
gATGAGAAAGAACTGAAGTGATGTTTGCCATAGATTGCGAGATGCCCTGTCTCATTGACTATCTTGGCGCACCttt > 2:165746/1‑76 (MQ=255)
tGAGAAAGAACTGAAGTGATGTTTGCCATAGATTGCGAGATGCCCTGTCTCATTGACTATCTTGGCGCACCTTtat < 1:792321/76‑1 (MQ=255)
tGAGAAAGAACTGAAGTGATGTTTGCCATAGATTGCGAGATGCCCTGTCTCATTGACTATCTTGGCGCACCTTtat < 1:1492231/76‑1 (MQ=255)
tGAGAAAGAACTGAAGTGATGTTTGCCATAGATTGCGAGATGCCCTGTCTCATTGACTATCTTGGCGCACCTTtat < 2:1724055/76‑1 (MQ=255)
gagaAAGAACTGAAGTGATGTTTGCCATAGATTGCGAGATGCCCTGTCTCATTGACTATCTTGGCGCACCTTtata > 2:176111/1‑76 (MQ=255)
agaaagaaCTGAAGTGATGTTTGCCATAGATTGCGAGATGCCCTGTCTCATTGACTATCTTGGCGCACCTTTATAc > 1:1285716/1‑76 (MQ=255)
gaaagaaCTGAAGTGATGTTTGCCATAGATTGCGAGATGCCCTGTCTCATTGACTATCTTGGCGCACCTTTATAcc < 2:1448734/76‑1 (MQ=255)
aaagaaCTGAAGTGATGTTTGCCATAGATTGCGAGATGCCCTGTCTCATTGACTATCTTGGCGCACCTTTATACCt < 1:1115889/76‑1 (MQ=255)
aaagaaCTGAAGTGATGTTTGCCATAGATTGCGAGATGCCCTGTCTCATTGACTATCTTGGCGCACCTTTATACCt < 2:209578/76‑1 (MQ=255)
aagaaCTGAAGTGATGTTTGCCATAGATTGCGAGATGCCCTGTCTCATTGACTATCTTGGCGCACCTTTATACCTg < 2:1611352/76‑1 (MQ=255)
agaaCTGAAGTGATGTTTGCCATAGATTGCGAGATGCCCTGTCTCATTGACTATCTTGGTGCACCTTTATACCTGt < 1:161369/76‑1 (MQ=255)
cTGAAGTGATGTTTGCCATAGATTGCGAGATGCCCTGTCTCATTGACTATCTTGGCGCACCTTTATACCTGTtata > 1:1747737/1‑76 (MQ=255)
gAAGTGATGTTTGCCATAGATTGCGAGATGCCCTGTCTCATTGACTATCTTGGCGCACCTTTATACCTGTTATAcc > 2:41324/1‑76 (MQ=255)
gAAGTGATGTTTGCCATAGATTGCGAGATGCCCTGTCTCATTGACTATCTTGGCGCACCTTTATACCTGTTATAcc > 1:293939/1‑76 (MQ=255)
gAAGTGATGTTTGCCATAGATTGCGAGATGCCCTGTCTCATTGACTATCTTGGCGCACCTTTATACCTGTTATAcc > 2:1971866/1‑76 (MQ=255)
gAAGTGATGTTTGCCATAGATTGCGAGATGCCCTGTCTCATTGACTATCTTGGCGCACCTTTATACCTGTTATAcc > 2:1452870/1‑76 (MQ=255)
caaGTGATGTTTGCCATAGATTGCGAGATGCCCTGTCTCATTGACTATCTTGGTGCACCTTTATACCTGTTATccc < 2:326355/75‑1 (MQ=255)
aaGTGATGTTTGCCATAGATTGCGAGATGCCCTGTCTCATTGACTATCTTGGCGCACCTTTATACCTGTTATACCa > 2:1675458/1‑76 (MQ=255)
gATGTTTGCCATAGATTGCGAGATGCCCTGTCTCATTGACTATCTTGGCGCACCTTTATACCTGTTATACCAGATc < 1:235175/76‑1 (MQ=255)
gTTTGCCATAGATTGCGAGATGCCCTGTCTCATTGACTATCTTGGCGCACCTTTATACCTGTTATACCAGATCaaa > 1:1484673/1‑76 (MQ=255)
gTTTGCCATAGATTGCGAGATGCACTGTCTCATTGACTATCTTGGTGCACCTTTATACCTGTTATACCAGATCaaa > 2:885227/1‑76 (MQ=255)
tttGCCATAGATTGCGAGATGCCCTGTCTCATTGACTATCTTGGCGCACCTTTATACCTGTTATACCAGATCaaaa < 1:939930/76‑1 (MQ=255)
tGCCATAGATTGCGAGATGCCCTGTCTCATTGACTATCTTGGTGCACCTTTATACCTGTTATACCAGATCAAAAAt > 2:891800/1‑76 (MQ=255)
gCCATAGATTGCGAGATGCCCTGTCTCATTGACTATCTTGGCGCACCTTTATACCTGTTATACCAGATCAAAAATc < 2:697271/76‑1 (MQ=255)
cATAGATTGCGAGATGCCCTGTCTCATTGACTATCTTGGCGCACCTTTATACCTGTTATACCAGATCAAAAATCAc < 1:150265/76‑1 (MQ=255)
tAGATTGCGAGATGCCCTGTCTCATTGACTATCTTGGCGCACCTTTATACCTGTTATACCAGATCAAAAATCACGc > 2:832183/1‑76 (MQ=255)
aGATTGCGAGATGCCCTGTCTCATTGACTATCTTGGCGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCa > 2:837098/1‑76 (MQ=255)
gATTGCGAGATGCCCTGTCTCATTGACTATCTTGGCGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCaa > 1:1658597/1‑76 (MQ=255)
ttGCGAGATGCCCCGTCTCATTGACTATCTTGGTGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATc < 2:1483549/76‑1 (MQ=255)
tGCGAGATGCCCTGTCTCATTGACTATCTTGGCGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATcc < 2:1190757/76‑1 (MQ=255)
tGCGAGATGCCCTGTCTCATTGACTATCTTGGCGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATcc > 1:287403/1‑76 (MQ=255)
tGCGAGATGCCCTGTCTCATTGACTATCTTGGCGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATcc > 2:1054124/1‑76 (MQ=255)
cGAGATGCCCTGTCTCATTGACTATCTTGGCGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATCCAt < 2:544567/76‑1 (MQ=255)
cGAGATGCCCTGTCTCATTGACTATCTTGGCGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATCCAt < 1:567479/76‑1 (MQ=255)
gaTGCCCTGTCTCATTGACTATCTTGGCGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATCCATaca < 1:495357/76‑1 (MQ=255)
aTGCCCTGTCTCATTGACTATCTTGGTGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATCCATacaa < 1:1821330/76‑1 (MQ=255)
aTGCCCTGTCTCATTGACTATCTTGGCGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATCCATacaa < 2:806734/76‑1 (MQ=255)
tGCCCTGTCTCATTGACTATCTTGGCGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATCCATacaac > 1:406434/1‑76 (MQ=255)
tGCCCTGTCTCATTGACTATCTTGGCGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATCCATacaac > 1:1307148/1‑76 (MQ=255)
gCCCTGTCTCATTGACTATCTTGGCGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATCCATacaaca < 1:584159/76‑1 (MQ=255)
cccTGTCTCATTGACTATCTTGGCGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATCCATAcaacaa > 1:643839/1‑76 (MQ=255)
tctcATTGACTATCTTGGCGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATCCATACAACAAAACCa > 1:320214/1‑76 (MQ=255)
ctcATTGACTATCTTGGCGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATCTATACAACAAAACCAg > 1:1842328/1‑76 (MQ=255)
ctcATTGACTATCTTGGCGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATCCATACAACAAAACCAg > 2:882154/1‑76 (MQ=255)
ctcATTGACTATCTTGGCGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATCCATACAACAAAACCAg > 2:882169/1‑76 (MQ=255)
ctcATTGACTATCTTGGCGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATCCATACAACAAAACCAg < 1:719428/76‑1 (MQ=255)
ctcATTGACTATCTTGGCGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATCCATACAACAAAACCAg > 1:894835/1‑76 (MQ=255)
tcATTGACTATCTTGGCGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATCCATACAACAAAACCAGa < 1:176111/76‑1 (MQ=255)
tcATTGACTATCTTGGCGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATCCATACAACAAAACCAGa > 2:478213/1‑76 (MQ=255)
cATTGACTATCTTGGCGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATCCATACAACAAAACCAGAt < 2:1651933/76‑1 (MQ=255)
cATTGACTATCTTGGCGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATCCATACAACAAAACCAGAt > 1:1795465/1‑76 (MQ=255)
aTTGACTATCTTGGTGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATCCATACAACAAAACCAGAtt < 2:1106330/76‑1 (MQ=255)
aTTGACTATCTTGGTGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATCCATACAACAAAACCAGAtt < 2:1106327/76‑1 (MQ=255)
ttGACTATCTTGGCGCACCTTTATACCTGTTATTCCAGATCAAAAATCACGCAATCCATACAACAAAACCAGAttt < 2:1923520/76‑1 (MQ=255)
tGACTATCTTGGCGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATCCATACAACAAAACCAGATTTg < 1:1867506/76‑1 (MQ=255)
gACTATCTTGGCGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATCCATACAACAAAACCAGATTTGc < 2:656047/76‑1 (MQ=255)
aCTATCTTGGCGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATCCATACAACAAAACCAGATTTGCa < 1:1932934/76‑1 (MQ=255)
cTATCTTGGCGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATCCATACAACAAAACCAGATTTGCaa < 1:409667/76‑1 (MQ=255)
tATCTTGGCGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATCCATACAACAAAACCAGATTTGCAAt < 2:1336353/76‑1 (MQ=255)
tCTTGGTGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATCCATACAACAAAACCAGATTTGCAATTc < 1:27083/76‑1 (MQ=255)
cTTGGTGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATCCATACAACAAAACCAGATTTGCAATTCg > 2:1123518/1‑76 (MQ=255)
cTTGGCGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATCCATACAACAAAACCAGATTTGCAATTCg < 2:128162/76‑1 (MQ=255)
tGGTGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATCCATACAACAAAACCAGATTTGCAATTCgtg > 2:585664/1‑76 (MQ=255)
tGGTGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATCCATACAACAAAACCAGATTTGCAATTCgtg > 1:1760033/1‑76 (MQ=255)
tGGCGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATCCATACAACAAAACCAGATTTGCAATTCgtg > 2:165397/1‑76 (MQ=255)
tGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATCCATACAACAAAACCAGATTTGCAATTCGTGTca < 2:996979/76‑1 (MQ=255)
|
CACCCGATGAGAAAGAACTGAAGTGATGTTTGCCATAGATTGCGAGATGCCCTGTCTCATTGACTATCTTGGTGCACCTTTATACCTGTTATACCAGATCAAAAATCACGCAATCCATACAACAAAACCAGATTTGCAATTCGTGTCA > REL606/4519986‑4520133
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
