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 |
|
A11 F1 I1 R1
|
63 |
64.8 |
2934156 |
93.7% |
2749304 |
111.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,763,869 |
(T)7→8 |
coding (1285/1617 nt) |
yfjL ← |
CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,763,862 | 1 | . | T | 98.3%
| 207.1
/ ‑4.3
| 60 | coding (1292/1617 nt) | yfjL | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base T (30/29); total (31/29) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TCGGTTAGTAGATTAGAGTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGA‑TT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGCTGATCACCTTCTGG > NC_000913/2763724‑2763995
|
tCGGTTAGTAGATTAGAGTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGa > 2:172721/1‑139 (MQ=255)
aTTAGAGTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGA‑tt‑ttttttgcg < 1:172721/139‑5 (MQ=255)
ttAGAGTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGA‑tt‑ttttttgcgc > 2:1329587/1‑134 (MQ=255)
tAGAGTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTgcgcg < 1:721264/139‑1 (MQ=255)
agagTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTgcgcgc < 2:423073/139‑1 (MQ=255)
agTTGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTGCGCGCgg > 1:996676/1‑139 (MQ=255)
agTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTGCGCGCgg > 2:744881/1‑139 (MQ=255)
tCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTa > 1:1437591/1‑139 (MQ=255)
tCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTa > 2:81093/1‑139 (MQ=255)
tCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGGTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTTGAGGA‑TTATTTTTGCGCGCGGTa > 2:84342/1‑139 (MQ=255)
tAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTgcgcg > 1:770170/1‑131 (MQ=255)
tAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTgcgcg < 2:770170/131‑1 (MQ=255)
gCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGAt < 2:718653/139‑1 (MQ=255)
acagaacaAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCg < 1:744881/139‑1 (MQ=255)
gaacaAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGA‑tt‑ttttttgcg < 1:385966/116‑5 (MQ=255)
gaacaAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGA‑tt‑ttttttgcg > 2:385966/1‑112 (MQ=255)
aaCGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTcc < 2:1389355/139‑1 (MQ=255)
aCGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCt > 2:1099297/1‑139 (MQ=255)
tGAAACGATCGAGGTGATCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGt > 1:917630/1‑139 (MQ=255)
aaaCGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTcc < 2:57168/133‑1 (MQ=255)
aaaCGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTcc > 1:57168/1‑133 (MQ=255)
aTCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATg > 2:283639/1‑113 (MQ=255)
aTCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATg < 1:283639/113‑1 (MQ=255)
ggTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATccc < 1:1099297/139‑1 (MQ=255)
aGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCGTCGTACAACTGATCCCGTAt > 2:100951/1‑139 (MQ=255)
cATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTAtct > 2:891401/1‑139 (MQ=255)
cGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCg > 1:590838/1‑139 (MQ=255)
aaaGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGc < 2:1437591/139‑1 (MQ=255)
ggTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGCAGCAGGTAGTTATCGTCTTTACTGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAAt > 2:695608/1‑139 (MQ=255)
ttGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTgcgcg > 1:1273912/1‑81 (MQ=255)
ttGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTgcgcg < 2:1273912/81‑1 (MQ=255)
ttGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCt < 1:1329587/139‑1 (MQ=255)
tGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTg > 2:943587/1‑139 (MQ=255)
tGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACgg < 1:255521/139‑1 (MQ=255)
tGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACgg < 2:590838/139‑1 (MQ=255)
gCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGc < 1:943587/139‑1 (MQ=255)
ccATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCa < 1:891401/139‑1 (MQ=255)
aTCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTgcgcg < 1:822351/72‑1 (MQ=255)
aTCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTgcgcg > 2:822351/1‑72 (MQ=255)
aTCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAAt < 1:549033/139‑1 (MQ=255)
tttCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTgcgcg > 2:197270/1‑64 (MQ=255)
tttCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTgcgcg < 1:197270/64‑1 (MQ=255)
tttCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTcc > 1:1252874/1‑90 (MQ=255)
tttCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTcc < 2:1252874/90‑1 (MQ=255)
tCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTc > 1:1090436/1‑139 (MQ=255)
cGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTTCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACt > 2:1047382/1‑139 (MQ=255)
gCAGGTAGTTATCGTCTTTAATGTCTAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAgg < 2:917630/139‑2 (MQ=255)
gCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCt < 2:643116/134‑1 (MQ=255)
gCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCt > 1:643116/1‑134 (MQ=255)
gCAGGTAGTTATCGTCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGc > 2:895538/1‑139 (MQ=255)
tCGTCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGc > 2:127242/1‑139 (MQ=255)
gTCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGCTg < 1:81093/139‑1 (MQ=255)
tCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGt < 2:190622/53‑1 (MQ=39)
tCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGt > 1:190622/1‑53 (MQ=255)
tCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGc < 2:583728/93‑1 (MQ=255)
tCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGc > 1:583728/1‑93 (MQ=255)
tCTTTAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGCTGa > 1:1154714/1‑139 (MQ=255)
tttAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGt < 2:553600/51‑1 (MQ=39)
tttAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGt > 1:553600/1‑51 (MQ=255)
tttAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGCTGATc < 1:84342/139‑1 (MQ=255)
tAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATg > 1:956866/1‑48 (MQ=255)
tAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATg < 2:956866/48‑1 (MQ=255)
tAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACaa < 1:461404/59‑1 (MQ=255)
tAATGTCGAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACaa > 2:461404/1‑59 (MQ=255)
gAGGATTT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGCTGATCACCTTCTgg > 2:618925/1‑139 (MQ=255)
|
TCGGTTAGTAGATTAGAGTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGA‑TT‑TTTTTGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGCTGATCACCTTCTGG > NC_000913/2763724‑2763995
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
