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 F212 I1 R1
|
174 |
80.0 |
3892211 |
96.7% |
3763768 |
99.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,564,501 |
T→C |
intergenic (+129/‑22) |
yffR → / → yffS |
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 | 2,564,501 | 0 | T | C | 84.3%
| 204.5
/ 24.6
| 83 | intergenic (+129/‑22) | yffR/yffS | CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein |
| Reads supporting (aligned to +/- strand): ref base T (6/7); new base C (38/32); total (44/39) |
| Fisher's exact test for biased strand distribution p-value = 7.64e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.48e-01 |
CCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGACAATATAAGGGCGCTCAACG > NC_000913/2564405‑2564596
|
cccGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATg < 1:679033/100‑1 (MQ=255)
ccGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATga < 2:460023/100‑1 (MQ=255)
cTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGga < 1:856981/100‑1 (MQ=255)
cTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGga < 1:897886/100‑1 (MQ=255)
tCGCCGGGTTTTGTGTGATCTGCGTCAATATTCCCGTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGgat < 1:882291/100‑2 (MQ=255)
ccGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATa < 1:747589/100‑1 (MQ=255)
gTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATaaaaa < 2:874023/100‑1 (MQ=255)
gTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATaaaaa > 2:1425928/1‑100 (MQ=255)
gTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATaaaaa > 2:476727/1‑100 (MQ=255)
ttttttGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAAt < 1:712059/100‑1 (MQ=255)
ttttttGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAAt < 1:314439/100‑1 (MQ=255)
tttttGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATc > 2:853224/1‑100 (MQ=255)
tttttGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATc < 2:237583/100‑1 (MQ=255)
tttttGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATc > 1:473243/1‑100 (MQ=255)
tttttGTGATCTGCGTCAATACTCCCTTCCGTGCCGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGTATTCTATGAGATTGGAGATaaaaa < 1:1453050/98‑1 (MQ=255)
ttttGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCa < 1:1112145/100‑1 (MQ=255)
tttGTGATCTGCGTCATTATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCAt < 1:1138908/100‑1 (MQ=255)
tttGTGATCTGCGTCATTATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCAt < 1:1137632/100‑1 (MQ=255)
ttGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCAta < 1:187722/100‑2 (MQ=255)
gtgATCTGCGTCAATATTCCCTCCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCTATGAGATGGTAGATAAAAATCATGAg < 2:455214/100‑1 (MQ=255)
gATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGtt > 2:1102017/1‑100 (MQ=255)
gATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGtt > 1:566660/1‑100 (MQ=255)
gATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGtt > 2:1395894/1‑100 (MQ=255)
tCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑Ac < 1:853223/100‑1 (MQ=255)
tGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGa > 2:547680/1‑100 (MQ=255)
gCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGaa < 1:1118174/100‑1 (MQ=255)
cGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGaaa > 2:1893266/1‑100 (MQ=255)
cGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCAGGAGATGGGAGATAAAAATCATAAGTT‑ACGaaa > 1:1618686/1‑100 (MQ=255)
tatTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCaaaa > 1:50769/1‑100 (MQ=255)
tatTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCaaaa < 2:37443/100‑1 (MQ=255)
atTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAAt > 2:12860/1‑100 (MQ=255)
ttCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAAtt < 1:161808/100‑1 (MQ=255)
ttCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAAtt > 1:1272431/1‑100 (MQ=255)
ttCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCAT‑AGTTGACGAAATCAAAAt > 1:159087/1‑99 (MQ=255)
cccTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTT‑ACGAAATCAAAATTTg > 1:1935901/1‑100 (MQ=255)
cccTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTg > 1:928686/1‑100 (MQ=255)
cTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTT‑ACGGAATCAAAATTTGCg > 1:1322688/1‑100 (MQ=255)
cTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCg < 2:1887521/100‑1 (MQ=255)
cTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCg < 2:1153686/100‑1 (MQ=255)
cTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCg < 1:1102016/100‑1 (MQ=255)
cTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCg > 1:1229707/1‑100 (MQ=255)
ttCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCGa < 1:1012669/100‑1 (MQ=255)
ccGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCGACa < 2:1673920/100‑1 (MQ=255)
gTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCGACATc > 1:336652/1‑100 (MQ=255)
tACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCGACATCCt < 2:706360/100‑1 (MQ=255)
cGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCGACATCCTCa < 1:903109/100‑1 (MQ=255)
cTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCGACATCCTCaaa > 1:1147042/1‑100 (MQ=255)
tACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGAAGGGAGATAAAAATCATAAGTT‑CCGAAATCAAAATTTGCGACATCATCAAAg > 1:873479/1‑99 (MQ=255)
cccTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGgcg > 2:371599/1‑100 (MQ=255)
cccTCCACCAATACGCGTGTTAACCTACCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGgcg > 2:1183355/1‑100 (MQ=255)
ccTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGgcgc < 1:765580/100‑1 (MQ=255)
ccTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGgcgc > 1:659909/1‑100 (MQ=255)
ccTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGgcgc > 2:1142124/1‑100 (MQ=255)
ccTCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGgcgc > 1:817284/1‑100 (MQ=255)
tCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTg < 2:50769/100‑1 (MQ=255)
tCCACCAATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTg > 2:1793078/1‑100 (MQ=255)
ccaccaATACGCGTGTTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGc > 1:775817/1‑100 (MQ=255)
ccaccaATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGc > 2:1273239/1‑100 (MQ=255)
ccaATACGCGTGTTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGAt > 2:1934099/1‑100 (MQ=255)
caATACGCGTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATg > 1:650028/1‑100 (MQ=255)
cgcgTGTTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAgg > 2:1837354/1‑100 (MQ=255)
cgcgTGTTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAg < 1:179626/99‑1 (MQ=255)
cgcgTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAgg > 1:73731/1‑100 (MQ=255)
cgTGTTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGAc < 1:979119/100‑1 (MQ=255)
cgTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGAc > 1:1149763/1‑100 (MQ=255)
cgTGTTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGAc < 2:1641434/100‑1 (MQ=255)
gtgtTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGACa > 2:627628/1‑100 (MQ=255)
gtgtTAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGACa < 1:346862/100‑1 (MQ=255)
tAACCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGAGATGGAAGGACAatat > 1:1901371/1‑100 (MQ=255)
aaCCTCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGACAAtata > 1:529475/1‑100 (MQ=255)
tCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGACAATATAAggg < 2:1748969/100‑1 (MQ=255)
tCCCAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGACAATATAAggg < 1:1395886/100‑1 (MQ=255)
cccAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGACAATGTAAGGgc > 1:753623/1‑100 (MQ=255)
ccAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGACAATATAAGGgcg > 1:1173339/1‑100 (MQ=255)
ccAATGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGACAATATAAGGgcg > 2:1279320/1‑100 (MQ=255)
cAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGACAATATAAGGgcgc < 2:1238591/100‑1 (MQ=255)
aaTGGATTCTATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGACAATATAAGGGCGCt < 2:1057826/100‑1 (MQ=255)
aaTGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGACAATATAAGGGCGCt > 2:1610756/1‑100 (MQ=255)
aaTGGATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGACAATATAAGGGCGCt > 2:659447/1‑100 (MQ=255)
ggATTCCATGAGATGGGAGATAAAAATCATAAGTG‑ACGAAATCAAAATTTGCGCAAACCTCAAAGGCACTGCGATGGAAGGAGAATATAAGGgcgaaca > 1:1925103/1‑95 (MQ=255)
gATTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGACAATATAAGGGCGCTCAAc < 2:936532/100‑1 (MQ=255)
aTTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGACAATATAAGGGCGCTCAACg < 2:1229711/100‑1 (MQ=255)
aTTCCATGAGATGGGAGATAAAAATCATAAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGACAATATAAGGGCGCTCAACg > 1:410806/1‑100 (MQ=255)
|
CCCGGCCCCTCGCCGGGTTTTTTGTGATCTGCGTCAATATTCCCTTCCGTTACGCTTACCCTCCACCAATACGCGTGTTAACCTCCCAATGGATTCTATGAGATGGGAGATAAAAATCATGAGTT‑ACGAAATCAAAATTTGCGACATCCTCAAAGGCGCTGCGATGGAAGGACAATATAAGGGCGCTCAACG > NC_000913/2564405‑2564596
|
| 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
