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 |
|
A9 F1 I2 R1
|
78 |
48.0 |
2243616 |
94.8% |
2126947 |
114.4 |
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 | 95.7%
| 151.3
/ ‑1.0
| 46 | coding (1292/1617 nt) | yfjL | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein |
| Reads supporting (aligned to +/- strand): ref base . (1/1); new base T (21/23); total (22/24) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01 |
TAGAGTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGA‑‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGCTGATCAC > NC_000913/2763737‑2763988
|
tAGAGTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGA‑‑ttttttttacgcg > 1:346097/1‑133 (MQ=255)
agTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCgg > 1:885051/1‑139 (MQ=255)
cGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTAt < 1:285172/139‑1 (MQ=255)
tAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGA‑‑TTTTTTT‑‑‑GCGCGCGGTATCGa > 2:373665/1‑139 (MQ=255)
cGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAAt > 2:1085346/1‑139 (MQ=255)
cGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAAt > 2:642231/1‑139 (MQ=255)
gaacaAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGaaa > 2:725491/1‑139 (MQ=255)
gaacaAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGaaa < 1:658106/139‑1 (MQ=255)
gaacaAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGaaa > 2:503215/1‑139 (MQ=255)
aacaAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGAAAt > 2:808836/1‑139 (MQ=255)
caAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGAAATGt < 1:538522/139‑1 (MQ=255)
aaCGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGaaa < 1:543781/134‑1 (MQ=255)
aaCGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGaaa > 2:543781/1‑134 (MQ=255)
aCGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACaa < 1:540069/139‑1 (MQ=255)
aTCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTg > 1:298059/1‑139 (MQ=255)
cGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGAt > 2:155354/1‑139 (MQ=255)
aGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTAt < 2:1029875/139‑1 (MQ=255)
cATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTAtc > 2:609154/1‑139 (MQ=255)
cATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTAtct > 1:98984/1‑139 (MQ=255)
ggCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGA‑‑TTTTTTTTGCGCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCt < 1:828113/139‑1 (MQ=255)
tGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACgg < 2:298059/139‑1 (MQ=255)
gCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGc < 1:503215/139‑1 (MQ=255)
gCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGc < 1:642231/139‑1 (MQ=255)
ccATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCa < 1:1107626/139‑1 (MQ=255)
aTGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCAcc > 2:445242/1‑139 (MQ=255)
gTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCa < 1:450959/116‑1 (MQ=255)
gTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCa > 2:450959/1‑116 (MQ=255)
aaGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGAAATGTCCTCGt < 2:978388/75‑1 (MQ=255)
aaGCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGAAATGTCCTCGt > 1:978388/1‑75 (MQ=255)
gCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGc < 2:885051/139‑1 (MQ=255)
gCAGGTAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATATTAATATCAGTCACCAACTCGCTGAAGc < 2:693435/139‑1 (MQ=255)
cAGGTAGTTATCGTCTTTAATGTCGAGGATTTTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGc < 1:609154/139‑1 (MQ=255)
tAGTTATCGTCTTTAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATc > 1:1042271/1‑139 (MQ=255)
ttATCGTCTTTAATGTCGAGGAT‑TTTTTTT‑‑‑GCGAGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACt < 1:323995/71‑1 (MQ=255)
ttATCGTCTTTAATGTCGAGGAT‑TTTTTTT‑‑‑GCGAGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACt > 2:323995/1‑71 (MQ=255)
tCGTCTTTAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGc > 1:183035/1‑139 (MQ=255)
tttAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGCTGATc < 2:346097/139‑1 (MQ=255)
tttAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGCTGATc < 1:725491/139‑1 (MQ=255)
tttAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGCTGATc < 1:155354/139‑1 (MQ=255)
tttAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGCTGATc < 2:1042271/139‑1 (MQ=255)
tAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGc > 1:181930/1‑89 (MQ=255)
tAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGc < 2:181930/89‑1 (MQ=255)
tAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCa < 1:1070915/90‑1 (MQ=255)
tAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCa > 2:1070915/1‑90 (MQ=255)
tAATGTCGAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGCTGATCAc > 2:755156/1‑139 (MQ=255)
gAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGa < 2:146189/78‑1 (MQ=255)
gAGGAT‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGa > 1:146189/1‑78 (MQ=255)
|
TAGAGTCGTAGCCCACGAACAGAACAAACGTGAAACGATCGAGGTGAGCATCGAAAGGTTGGCTGCCATCAAGAATTTCGTCAATGTCGTGGCGAAGCAGGTAGTTATCGTCTTTAATGTCGAGGA‑‑TTTTTTT‑‑‑GCGCGCGGTATCGATGCAATCCGAAATGTCCTCGTACAACTGATCCCGTATCTCCGGCAATCTGACGGCAATGTTAATATCAGTCACCAACTCGCTGAAGCCAATCCAAAGCTGATCAC > NC_000913/2763737‑2763988
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
