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 |
|
A12 F56 I1 R1
|
165 |
53.8 |
2611523 |
96.4% |
2517508 |
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 | 98.0%
| 171.1
/ ‑3.1
| 49 | intergenic (+396/‑79) | yffP/yffQ | CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base A (29/19); total (30/19) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.92e-01 |
ATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑T‑AAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCG > NC_000913/2563420‑2563607
|
aTTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑T‑aaaaaa < 1:758636/100‑2 (MQ=255)
aTTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑T‑aaaaaa > 2:1185745/1‑99 (MQ=255)
ttttGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑T‑aaaaaat < 2:1044231/100‑3 (MQ=255)
tttGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑T‑aaaaaatg < 2:1028815/100‑4 (MQ=255)
ttGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑T‑aaaaaatga < 2:395743/100‑5 (MQ=255)
ttGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑T‑aaaaaatga > 2:251562/1‑96 (MQ=255)
aGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑TAAAAAATGAAACGGTggn < 2:71364/100‑2 (MQ=255)
gATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGa > 1:311552/1‑100 (MQ=255)
gATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGa > 1:447757/1‑100 (MQ=255)
aTCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGaa > 1:975624/1‑100 (MQ=255)
aTCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGaa > 1:639081/1‑100 (MQ=255)
gCTTTTTCCCTTCAGGCATTTTTTTTTTTTTTTTTCAACGAAAGGCAGTTCCCAACAACAAAATAATGATGGGAGG‑TAAAAAATGAAACGGTGCGAAGTg > 2:1194378/1‑100 (MQ=255)
cTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTgg < 2:858759/100‑1 (MQ=255)
ttttCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCt < 1:232655/100‑1 (MQ=255)
tCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTa > 1:395152/1‑100 (MQ=255)
ccTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACt > 1:914712/1‑100 (MQ=255)
ccTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACt < 1:397750/100‑1 (MQ=255)
ccTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACt > 1:333062/1‑100 (MQ=255)
ccTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACt > 1:1002148/1‑100 (MQ=255)
ttCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACTgg < 2:321699/100‑1 (MQ=255)
tCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGt < 1:603067/100‑1 (MQ=255)
tCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGt < 2:527760/100‑1 (MQ=255)
cAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTg > 2:1002761/1‑100 (MQ=255)
ggCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTTCCAACAACAAAATAAAGAAGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACTgg < 2:1086952/96‑1 (MQ=255)
ggCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTg > 2:876043/1‑98 (MQ=255)
tttttGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTa > 1:209160/1‑100 (MQ=255)
ttGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGAAGGAA‑AAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATg > 2:525080/1‑100 (MQ=255)
gTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGtt > 1:1238957/1‑100 (MQ=255)
tAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGt > 2:68753/1‑100 (MQ=255)
aaTTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGt > 2:58998/1‑99 (MQ=255)
aTTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGttt > 1:476013/1‑100 (MQ=255)
tcaatcaaCGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGc < 1:273441/100‑1 (MQ=255)
aatcaaCGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTg < 1:104784/100‑1 (MQ=255)
atcaaCGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGt > 1:804773/1‑100 (MQ=255)
atcaaCGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGt > 2:393475/1‑100 (MQ=255)
caaCGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTAt < 1:1292853/100‑1 (MQ=255)
aaCGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTAtt > 1:1162070/1‑100 (MQ=255)
aaaGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAAc > 1:887479/1‑100 (MQ=255)
aaaGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAAc < 1:6223/100‑1 (MQ=255)
aaGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACt > 2:610236/1‑100 (MQ=255)
aGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACtg < 2:639077/100‑1 (MQ=255)
cAGTTCCCAACAACAAAATAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGa < 2:758723/100‑1 (MQ=255)
ttCCCAACAACAAAATAAAGATGAGAAA‑AAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAagg < 2:1162059/100‑1 (MQ=255)
ccAACAACAAAATAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAaggagg > 1:703860/1‑100 (MQ=255)
caacaaAATAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGc > 2:1115464/1‑100 (MQ=255)
aaaaTAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATg > 2:355016/1‑100 (MQ=255)
aaTAAAGATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGAGATGGTAATGTTGGATTGCTGTATTGAACTGTGAAGGAGGAAGCCATGa > 2:1293621/1‑99 (MQ=255)
aGATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACttt < 1:1002770/100‑1 (MQ=255)
aGATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACttt < 2:39678/100‑1 (MQ=255)
gATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACtttt < 1:68754/100‑1 (MQ=255)
gATGGGAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAAAGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACtttt > 2:123710/1‑100 (MQ=255)
gggAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAAt > 1:876106/1‑100 (MQ=255)
ggAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATc > 1:483757/1‑100 (MQ=255)
ggAGG‑TAAAAAACGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATc > 1:859000/1‑100 (MQ=255)
gAGG‑TAAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCg < 1:1185756/100‑1 (MQ=255)
|
ATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGG‑T‑AAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCG > NC_000913/2563420‑2563607
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
