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 |
2,074,177 |
G→A |
29.8% |
V168I (GTC→ATC) |
flu → |
antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,074,177 | 0 | G | A | 29.8%
| 69.3
/ 34.1
| 47 | V168I (GTC→ATC) | flu | antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| Reads supporting (aligned to +/- strand): ref base G (17/16); new base A (2/12); total (19/28) |
| Fisher's exact test for biased strand distribution p-value = 2.37e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TGAACACCACGCTGAATGGTGGCGAACAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCGTCATTAATGATAAGGGCTGGCAGGTCGTCAAGCCCGGTACAGTGGCAACGGATACCGTTGTTAAT > W3110S.gb/2074115‑2074242
|
tgAACACCACGCTGAATGGTGGCGAACAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCGTCAtt > 1:673779/1‑68 (MQ=255)
tgAACACCACGCTGAATGGTGGCGAACAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCGTCATTa > 1:2634748/1‑69 (MQ=255)
aaCACCACGCTGAATGGTGGCGAACAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCGTCATTa < 1:865329/67‑1 (MQ=255)
aaCACCACGCTGAATGGTGGCGAACAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCGTCATTa < 1:305365/67‑1 (MQ=255)
caccacGCTGAATGGTGGCGAATAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCATCATTAATGa < 1:1181116/69‑1 (MQ=255)
caccacGCTGAATGGTGGCGAATAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCATCATTAATGa < 1:2743842/69‑1 (MQ=255)
cTGAATGGTGGCGAATAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCATCATTAATGAt < 1:1034058/63‑1 (MQ=255)
cTGAATGGTGGCGAATAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCATCATTAATGAt < 1:30815/63‑1 (MQ=255)
tGAATGGTGGCGAATAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCATCATTAATGAt < 1:2445838/62‑1 (MQ=255)
tGAATGGTGGCGAACAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCGTCATTAATGATAAGGGCt < 1:893886/69‑1 (MQ=255)
tGAATGGTGGCGAACAGTGGATGCATGAGGCGGCGATAGCCACAGGAACCGTCATTAATGATAAGGGCt < 1:2853933/69‑1 (MQ=255)
tggtggCGAATAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCATCATTAATGATAAGGGCTGGc < 1:1342576/68‑1 (MQ=255)
tggtggCGAATAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCATCATTAATGATAAGGGCTGGc < 1:1511137/68‑1 (MQ=255)
tggtggCGAATAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCATCATTAATGATAAGGGCTGGc < 1:1767146/68‑1 (MQ=255)
gTGGATGCATGAGGGGGCGATAGCCACAGGAACCATCATTAAt < 1:930430/43‑1 (MQ=255)
gTGGATGCATGAGGGGGCGATAGCCACAGGAACCATCATTAATGATAAGGGCTGGCAGGTCGTCAAGcc > 1:869765/1‑69 (MQ=255)
gTGGATGCATGAGGGGGCGATAGCCACAGGAACCAACATTAATGATAAGGGCTGGAAGGTCGTCAAGcc > 1:2396549/1‑69 (MQ=255)
tGGATGCATGAGGGGGCGATAGCCACAGGAACCGTCATTAATGAt < 1:3217395/45‑1 (MQ=255)
tGGATGCATGAGGGGGCGATAGCCACAGGAACCGTCATTAATGAt < 1:3137086/45‑1 (MQ=255)
tGGATGCATGAGGGGGCGATAGCCACAGGAACCATCATTAAt < 1:1951734/42‑1 (MQ=255)
gATGCATGAGGGGGCGATAGCCACAGGAACCGTCATTAATGAt > 1:525441/1‑43 (MQ=255)
gATGCATGAGGGGGCGATAGCCACAGGAACCGTCATTAATGAt > 1:2564770/1‑43 (MQ=255)
gATGCATGAGGGGGCGATAGCCACAGGAACCGTCATTAATGAt > 1:330102/1‑43 (MQ=255)
gATGCATGAGGGGGCGATAGCCACAGGAACCGTCATTAATGAt > 1:3072372/1‑43 (MQ=255)
gATGCATGAGGGGGCGATAGCCACAGGAACCGTCATTAATGAt > 1:2826059/1‑43 (MQ=255)
gATGCATGAGGGGGCGATAGCCACAGGAACCGTCATTAATGAt > 1:2657681/1‑43 (MQ=255)
gATGCATGAGGGGGCGATAGCCACAGGAACCGTCATTAATGATAAGGGCTGGCAGGTCGTCAAGCCCgg > 1:3045492/1‑69 (MQ=255)
aGGGGGCGATAGCCACAGGAACCGTCATTAATGAt > 1:2952784/1‑35 (MQ=255)
aGGGGGCGATAGCCACAGGAACCGTCATTAATGAt < 1:1865999/35‑1 (MQ=255)
aGGGGGCGATAGCCACAGGAACCGTCATTAATGAt > 1:2898928/1‑35 (MQ=255)
aGGGGGCGATAGCCACAGGAACCGTCATTAATGAt < 1:1893282/35‑1 (MQ=255)
aGGGGGCGATAGCCACAGGAACCGTCATTAATGAt > 1:1850234/1‑35 (MQ=255)
aGGGGGCGATAGCCACAGGAACCGTCATTAATGATAAGGGCTGGCAg < 1:2649341/47‑1 (MQ=255)
aGGGGGCGATAGCCACAGGAACCGTCATTAATGATAAGGGCTGGCAg < 1:797890/47‑1 (MQ=255)
aGGGGGCGATAGCCACAGGAACCGTCATTAATGATAAGGGCTGGCAg < 1:3499587/47‑1 (MQ=255)
aGGGGGCGATAGCCACAGGAACCGTCATTAATGATAAGGGCTGGCAg < 1:1276669/47‑1 (MQ=255)
aGGGGGCGATAGCCACAGGAACCGTCATTAAAGAt > 1:368468/1‑35 (MQ=255)
gggggCGATAGCCACAGGAACCGTCATTAATGATAAGGGCTGGCAg > 1:3300866/1‑46 (MQ=255)
gggggCGATAGCCACAGGAACCGTCATTAATGATAAGGGCTGGCAg > 1:3166181/1‑46 (MQ=255)
aGCCACAGGAACCATCATTAATGATAAGGGCTGGc < 1:1350666/35‑1 (MQ=255)
acaGGAACCGTCATTAATGATAAGGGCTGGCAGGTCGTCAAGcc > 1:249966/1‑44 (MQ=255)
aGGAACCATCATTAATGATAAGGGCTGGCAGGTCGTCAAGCCCGGTACAGTGGCAACGGATACCgttg < 1:1901737/68‑1 (MQ=255)
ggAACCGTCATTAATGATAAGGGCTGGCAGGTCGTCAAGCCCGGTACAGTGGCAACGGATACCgttgtt < 1:1429215/69‑1 (MQ=255)
ggAACCGTCATTAATGATAAGGGCTGGCAGGTCGTCAAGCCCGGTACAGTGGCAACGGATACCgttgtt < 1:385023/69‑1 (MQ=255)
ggAACCGTCATTAATGATAAGGGCTGGCAGGTCGTCAAGCCCGGTACAGTGGCAACGGATACCgttgtt < 1:1121049/69‑1 (MQ=255)
aaCCGTCATTAATGATAAGGGCTGGCAGGTCGTCAAGCCCGGTAc < 1:3189011/45‑1 (MQ=255)
aCCGTCATTAATGATAAGGGCTGGCAGGTCGTCAAGCCCGGTACAGTGGCAACGGATACCGTTGTTAAt > 1:3067409/1‑69 (MQ=255)
|
TGAACACCACGCTGAATGGTGGCGAACAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCGTCATTAATGATAAGGGCTGGCAGGTCGTCAAGCCCGGTACAGTGGCAACGGATACCGTTGTTAAT > W3110S.gb/2074115‑2074242
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
