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 F56 I1 R1
|
155 |
65.2 |
3164312 |
95.9% |
3034575 |
99.8 |
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 | 90.6%
| 165.1
/ 12.1
| 53 | intergenic (+396/‑79) | yffP/yffQ | CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein |
| Reads supporting (aligned to +/- strand): ref base . (3/2); new base A (22/26); total (25/28) |
| Fisher's exact test for biased strand distribution p-value = 6.58e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.39e-01 |
GGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGT‑AAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTT > NC_000913/2563415‑2563602
|
ggTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGT‑a > 1:203544/1‑100 (MQ=255)
gAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGT‑aaaa > 2:965627/1‑100 (MQ=255)
tttGTGATGCAGATCGGTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGAAAAGT‑aaaaaatg < 2:923976/100‑4 (MQ=255)
tttGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGT‑aaaaaatg < 1:418198/100‑4 (MQ=255)
ttGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGT‑aaaaaatga > 1:1329691/1‑96 (MQ=255)
ctgATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAAATGaaa < 1:339575/99‑1 (MQ=255)
gATGCATATCGCTTTTTCCCTGCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAAATGAAAc < 1:290708/99‑1 (MQ=255)
gATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAAATGaaaag > 2:339575/1‑98 (MQ=255)
tGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAAATGAAACGGt < 1:224400/100‑1 (MQ=255)
gCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAAATGAAACGGTg > 2:1347367/1‑100 (MQ=255)
gCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTAAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAAAAAAGATGGGAGGTAAAAAATGAAACGGTg > 2:950673/1‑100 (MQ=255)
cAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGT‑AAAAATGAAACGGTg > 2:1053348/1‑98 (MQ=255)
gATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAAATGAAACGGTggg < 2:1429471/99‑1 (MQ=255)
gCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAAATGAAACGGTGGGAAGTg < 2:1005517/100‑1 (MQ=255)
gCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGT‑AAAAATGAAACGGTGGGAAGTgg > 1:428012/1‑100 (MQ=255)
tttttCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGCTGGGAGGTAAAAAATGAAACGGTGGGAAGTGGc > 1:344058/1‑100 (MQ=255)
tttCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAAATGAAACGGTGGGAAGTGGCtt > 1:1266514/1‑100 (MQ=255)
ttCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAAATGAAACGGTGGGAAGTGGCttt < 2:142176/100‑1 (MQ=255)
ttCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAAATGAAACGGTGGGAAGTGGCttt < 2:203544/100‑1 (MQ=255)
cccTTCAGGCATCTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAAATGAAACGGTGGGAAGTGGCTTTAc > 2:1148557/1‑100 (MQ=255)
ccTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAAATGAAACGGTGGGAAGTGGCTTTAc > 1:797162/1‑99 (MQ=255)
ccTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAAATGAAACGGTGGGAAGTGGCTTTACt > 1:796657/1‑100 (MQ=255)
ccTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAAAAAAGATGGGAGGTAAAAAATGAAACGGTGGGAAGTGGCTTTACt > 1:546621/1‑100 (MQ=255)
ggCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAACGATGGGAGGTAAAAAATGAAACGGAGGGAAGTAGCTTTACTGGTGAt > 2:442332/1‑100 (MQ=255)
ggCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGAt < 2:661496/100‑1 (MQ=255)
ggCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGAt > 2:92502/1‑100 (MQ=255)
ggCATTCTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAAATGAAACGGTGGGAAGTGGCTTTAATGGTGa > 1:932750/1‑99 (MQ=255)
aTTTTTGTTTAATACAAACAACGAAAGGCAGATCCCAACAACAAAATAAAGATGGCAGGTAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATgg < 2:942127/99‑1 (MQ=255)
tttttGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTa < 2:1356622/100‑1 (MQ=255)
gTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGtt > 2:178179/1‑100 (MQ=255)
ttAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTg < 2:1268479/99‑1 (MQ=255)
tAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTgg < 2:1230593/99‑1 (MQ=255)
tAATTCAATCAACGAAAGGCAGTTATCAACAATAAAAAAAAGATGGGAGGTAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGt < 2:853645/100‑1 (MQ=255)
aTTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGttt > 2:207984/1‑100 (MQ=255)
caatcaaCGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGc < 1:111096/99‑1 (MQ=255)
aatcaaCGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTg < 2:1329684/100‑1 (MQ=255)
aatcaaCGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTg < 2:434384/100‑1 (MQ=255)
aCGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTg < 1:1417468/100‑1 (MQ=255)
aCGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTg < 1:451102/100‑1 (MQ=255)
aaGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACt > 2:1286721/1‑100 (MQ=255)
ggCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACtgt > 1:114325/1‑100 (MQ=255)
ttCCCAACAACAAAATAAAGATGGGAGGTAAAAAATGACACGGTGGGAAGTGGCTTTATTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAagg < 2:860864/100‑1 (MQ=255)
ttCCCAACAACAAAATAAAGATGGGAGGTAAAAAATGACACGGTGGGAAGTGGCTTTATTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAagg < 2:860850/100‑1 (MQ=255)
ttCCCAACAACAAAATAAAGATGGGAGGTAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAagg < 1:1105348/100‑1 (MQ=255)
tCCCAACAACAAATTAAAGATGGGAGGT‑AAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAaggag > 1:1069191/1‑100 (MQ=255)
cccAACAACAAAATAAAGATGGGAGGTAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAaggag > 2:1352810/1‑100 (MQ=255)
cccAACAACAAAATAAAGATGGGAGGTAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAaggag > 1:534701/1‑100 (MQ=255)
cccAACAACAAAATAAAGATGGGAGGT‑AAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAaggagg < 2:428011/100‑1 (MQ=255)
ccAACAACAAAATAAAGATGGGAGGTAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAaggagg > 2:572352/1‑100 (MQ=255)
acaacaaAATAAAGATGGGAGGTAAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACg < 2:143154/100‑1 (MQ=255)
aacaaAATAAAGATGGGAGGTAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGcc < 2:191055/100‑1 (MQ=255)
aacaaAATAAAGATGGGAGGTAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGcc < 2:708744/100‑1 (MQ=255)
acaaAATAAAGATGGGAGGTAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTAAAGGTAATGGTGGTTTGCTGTATTGAACTGTGAAGGAGGACg > 2:694020/1‑97 (MQ=255)
aaaaTAAAGATGGGAGGT‑AAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGa < 2:1504285/100‑1 (MQ=255)
aaTAAAGATGGGAGGTAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGaa > 2:103087/1‑100 (MQ=255)
aaaGATGGGAGGTAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACt > 2:94887/1‑100 (MQ=255)
aGATGGGAGGTAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACttt < 1:1024124/100‑1 (MQ=255)
gATGGGAGGTAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACtttt < 1:92502/100‑1 (MQ=255)
|
GGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGT‑AAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTT > NC_000913/2563415‑2563602
|
| 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
