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 |
|
A1 F17 I0 R2
|
276 |
45.3 |
3729697 |
93.0% |
3468618 |
60.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,867,123 |
G→A |
69.2% |
P96L (CCG→CTG) |
nlpD ← |
predicted outer membrane lipoprotein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,867,123 | 0 | G | A | 69.2%
| 65.8
/ 43.7
| 52 | P96L (CCG→CTG) | nlpD | predicted outer membrane lipoprotein |
| Reads supporting (aligned to +/- strand): ref base G (9/7); new base A (16/20); total (25/27) |
| Fisher's exact test for biased strand distribution p-value = 5.51e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.34e-01 |
TAACTGCCTTTCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCGGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGGTTGTTGAGTAGCCTGAATT > W3110S.gb/2867057‑2867179
|
taACTGCCTTTCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAgc > 1:173228/1‑69 (MQ=255)
taACTGCCTTTCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAgc > 1:1996091/1‑69 (MQ=255)
aCTGCCTTTCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCGgct < 1:1322393/68‑1 (MQ=255)
aCTGCCTTTCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCGgct < 1:812811/68‑1 (MQ=255)
aCTGCCTTTCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAgctg > 1:1357402/1‑69 (MQ=255)
aCTGCCTTTCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAgctg > 1:2453408/1‑69 (MQ=255)
aCTGCCTTTCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAgctg > 1:390206/1‑69 (MQ=255)
gCCTTTCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCGGctgctg < 1:262226/69‑1 (MQ=255)
tttCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGc < 1:2424959/69‑1 (MQ=255)
tttCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGc < 1:3681974/69‑1 (MQ=255)
ttCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGc < 1:1983710/68‑1 (MQ=255)
gAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACt < 1:2870784/68‑1 (MQ=255)
aTGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCGGCTGCTGAGCTACTGGc > 1:1832583/1‑69 (MQ=255)
gTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTg < 1:475356/69‑1 (MQ=255)
aCTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCGGCTGCTGAGCTACTGGCTGc > 1:3411024/1‑62 (MQ=255)
aCTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCGGCTGCTGAGCTACTGGCTGc > 1:95057/1‑62 (MQ=255)
aCTGACCGTTATAGACGATGCGTCCGTTTTCCATCTGTACCGGCTGCTGAGCTACTGGCTGc > 1:906767/1‑62 (MQ=255)
cTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCGGCTGCTGAGCTACTGGCTGCActggctg > 1:113742/1‑69 (MQ=255)
cTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCATCTGCTGAGCTACTGGCTGCActggctg < 1:3320427/69‑1 (MQ=255)
cTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGCActggctg < 1:3145309/69‑1 (MQ=255)
cTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGCActggctg > 1:423360/1‑69 (MQ=255)
gACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCGGCTGCTGAGCTACTGGCTGCActgtctgg < 1:3499825/68‑1 (MQ=255)
gACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGa > 1:2931028/1‑69 (MQ=255)
gACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGa > 1:1308961/1‑69 (MQ=255)
gACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGa > 1:761646/1‑69 (MQ=255)
gACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGa > 1:716628/1‑69 (MQ=255)
gACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGa > 1:1984287/1‑69 (MQ=255)
gACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGa > 1:2394188/1‑69 (MQ=255)
ttATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGc < 1:325734/44‑1 (MQ=255)
ttATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGc < 1:2606671/44‑1 (MQ=255)
ttATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGc < 1:1637458/44‑1 (MQ=255)
ttATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGc < 1:3132804/44‑1 (MQ=255)
ttATAGACGATGCGTACGTTTTCCATCTGTACCAGCTGCTGAGc < 1:3022644/44‑1 (MQ=38)
tataGACGATGCGTCCGTTTTCCATCTGTACCGGCTGCTGAGCTACtc > 1:137116/1‑47 (MQ=255)
tataGACGATGCGTCCGTTTTCCATCTGTACCGGCTGCTGAGCTACTg > 1:328155/1‑48 (MQ=255)
cGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGc > 1:1510964/1‑47 (MQ=255)
cGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGc > 1:812225/1‑47 (MQ=255)
cGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGgttgtt < 1:3504596/69‑1 (MQ=255)
cGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGgttgtt < 1:395322/69‑1 (MQ=255)
cGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGgttgtt < 1:1632471/69‑1 (MQ=255)
cGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGgttgtt < 1:3203107/69‑1 (MQ=255)
cGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGgttgtt < 1:793932/69‑1 (MQ=255)
aTGCGTCCGTTTTCCATCTGTACCGGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGGttgttg > 1:935899/1‑68 (MQ=255)
aTGCGTCCGTTTTCCATCTGTACCGGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGGttgttg > 1:841433/1‑68 (MQ=255)
cGTTTTCCATCTGTACCGGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGGTTGTTGAg < 1:2504333/63‑1 (MQ=255)
cGTTTTCCATCTGTACCGGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGGTTGTTGAg < 1:349595/63‑1 (MQ=255)
cGTTTTCCATCTGTACCGGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGGTTGTTGAg < 1:665956/63‑1 (MQ=255)
ttttCCATCTGTACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGGTTGTTGAGTAGCCTGa < 1:665770/69‑1 (MQ=255)
ttCCATCTGTACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGGTTGTTGAGTAGCCTGaa > 1:1351878/1‑68 (MQ=255)
ttCCATCTGTACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGGTTGTTGAGTAGCCTGAAt > 1:2238559/1‑69 (MQ=255)
tACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGGTTGTTGAGTAGCCTGAAtt < 1:2946196/61‑1 (MQ=255)
aCCAGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGGTTGTTGAGTAGCCTGAAtt < 1:775429/60‑1 (MQ=255)
|
TAACTGCCTTTCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCGGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGGTTGTTGAGTAGCCTGAATT > W3110S.gb/2867057‑2867179
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
