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 F142 I1 R1
|
99 |
64.8 |
3148104 |
96.3% |
3031624 |
99.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,563,518 |
(A)5→6 |
intergenic (+401/‑74) |
yffP → / → yffQ |
CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,563,513 | 1 | . | A | 94.4%
| 182.6
/ 4.2
| 54 | intergenic (+396/‑79) | yffP/yffQ | CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein |
| Reads supporting (aligned to +/- strand): ref base . (3/0); new base A (24/27); total (27/27) |
| Fisher's exact test for biased strand distribution p-value = 2.36e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.81e-01 |
GGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGT‑AAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATC > NC_000913/2563415‑2563606
|
ggTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGT‑a > 1:1037279/1‑100 (MQ=255)
ggTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGT‑a > 2:94325/1‑100 (MQ=255)
ggTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGT‑a > 1:696553/1‑100 (MQ=255)
gTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGT‑aa > 2:906641/1‑100 (MQ=255)
gAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTACCAACAACAAAATAAAGATGGGAGGT‑aa > 2:974294/1‑98 (MQ=255)
aTTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGT‑aaa‑aaa > 1:1329330/1‑99 (MQ=255)
tttGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGT‑aaa‑aaatg > 2:29696/1‑97 (MQ=255)
tCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAg < 2:1422584/100‑1 (MQ=255)
ncTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTg > 2:407630/2‑100 (MQ=255)
gCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTg > 1:6838/1‑100 (MQ=255)
gCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGCGGGAAGt > 1:224434/1‑99 (MQ=255)
tttttCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGc < 2:386394/100‑1 (MQ=255)
ttttCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGcn < 1:85941/100‑2 (MQ=255)
ttCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCttt < 1:1189206/100‑1 (MQ=255)
tCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGt > 1:206914/1‑100 (MQ=255)
cAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTg < 1:860617/100‑1 (MQ=255)
aGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAAGAACAAAATAAAGATGGGAGGTAAAA‑AATGAAGCGGTGGGAAGTGGCTTTACTGGTGa > 2:729304/1‑100 (MQ=255)
aGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTg > 1:606701/1‑99 (MQ=255)
aGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGa > 2:1271101/1‑100 (MQ=255)
gCATTTTTGTTTTTTTTTATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGT‑AAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGAt > 2:1438442/1‑98 (MQ=255)
gCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTTGTGATg < 1:906649/100‑1 (MQ=255)
cATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATgg < 2:1037272/100‑1 (MQ=255)
cATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATgg < 1:176454/100‑1 (MQ=255)
ttttGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTaa < 2:1024146/100‑1 (MQ=255)
ttGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAACATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATg < 1:529145/100‑1 (MQ=255)
gTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGtt > 1:254001/1‑100 (MQ=255)
tttAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTg < 1:205972/100‑1 (MQ=255)
aTTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGttt > 1:518713/1‑100 (MQ=255)
tcaatcaaCGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGc < 2:1447646/100‑1 (MQ=255)
aatcaaCGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTg < 2:948562/100‑1 (MQ=255)
caaCGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTa < 1:250610/99‑1 (MQ=255)
caaCGAAAGGCAGTTCCCAACAACAAAATAAAGAAGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTAt > 2:1085705/1‑100 (MQ=255)
aaCGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTAtt > 2:788114/1‑100 (MQ=255)
aaCGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTAtt > 2:506845/1‑100 (MQ=255)
aaCGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTAtt < 1:605283/100‑1 (MQ=255)
aCGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTg > 2:743359/1‑100 (MQ=255)
aCGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTg < 2:1363575/100‑1 (MQ=255)
aCGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTg > 1:421850/1‑100 (MQ=255)
aCGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTg < 2:405855/100‑1 (MQ=255)
aCGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGT‑AAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGa > 1:821865/1‑100 (MQ=255)
aaaGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAAc < 2:48932/100‑1 (MQ=255)
ggCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACtgt < 1:133956/100‑1 (MQ=255)
gCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACtgtg < 2:606698/100‑1 (MQ=255)
gCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACtgtg < 1:94325/100‑1 (MQ=255)
cAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGa < 2:720959/100‑1 (MQ=255)
gTTCCCAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAACCAGTGGGAAGTGGCTTTACTGGTGAAGGTAATGGTGGTTTGCTGTATTGAACTGTGAag > 2:344086/1‑100 (MQ=255)
tCCCAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAagga < 1:1568201/100‑1 (MQ=255)
cccAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGCAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAagg > 1:406004/1‑98 (MQ=255)
cccAACAACAAAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAaggag < 1:1265120/100‑1 (MQ=255)
caacaacaaAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAggagga > 2:466341/1‑100 (MQ=255)
caacaaAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGc > 2:1535904/1‑100 (MQ=255)
acaaAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCa > 2:643970/1‑100 (MQ=255)
caaAATAAAGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCAt > 1:1268961/1‑100 (MQ=255)
caaAATAAAGATGGGAGGT‑AAACAATGAAACGGTGGGAAGTGGCTCTACTGGTGATGGTAATGTTGGTTTGCTGCATTGAACGGTGAAGGAGGACGCCAt > 2:1089772/1‑100 (MQ=255)
aaaTAAAGATGGGAGGTAAAA‑AATGAAACGGAGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGa > 2:569888/1‑100 (MQ=255)
aaaGATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACt > 1:1240663/1‑100 (MQ=255)
gATGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACtttt < 1:870058/100‑1 (MQ=255)
aTGGGAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACttt < 2:1326750/98‑1 (MQ=255)
gggAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAAt > 1:819963/1‑100 (MQ=255)
gggAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAAt < 1:1002350/100‑1 (MQ=255)
ggAGGTAAAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATc > 2:1200608/1‑100 (MQ=255)
|
GGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGT‑AAA‑AATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATC > NC_000913/2563415‑2563606
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
