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 |
|
A23 F74 I1 R1
|
13 |
20.1 |
450294 |
97.3% |
438136 |
141.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
USA300TCH1516_ALE |
2,857,170 |
G→A |
G195R (GGA→AGA) |
nixA → |
High‑affinity nickel‑transport protein NixA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | USA300TCH1516_ALE | 2,857,170 | 0 | G | A | 95.8%
| 66.1
/ ‑3.3
| 25 | G195R (GGA→AGA) | nixA | High‑affinity nickel‑transport protein NixA |
| Reads supporting (aligned to +/- strand): ref base G (0/1); new base A (8/15); total (8/17) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.46e-01 |
CGTCGTGAACACATTGAAGAAGCTGAAGTCGATGCATTACTTGAATCTAGAGGATTGGTTTCTCGATTTGTAGGACCTTATTTCAAATTAATCACGCGTAGTTGGCACGTATTGCCACTTGGCTTTTTATTTGGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCACAACAAGCCATTTCATTTATCGGAATCTTATCTTTACCAATTTTATTCGCATCAGGTATGAGTTTA > USA300TCH1516_ALE/2857038‑2857295
|
cgtcgtGAACACATTGAAGAAGCTGAAGTCGATGCATTACTTGAATCTAGAGGATTGGTTTCTCGATTTGTAGGACCTTATTTCAAATTAATCACGCGTAGTTGGCACGTATTGCCACTTGGCTTTTTATTTAGACTTGGt > 1:130337/1‑141 (MQ=255)
acacATTGAAGAAGCTGAAGTCGATGCATTACTTGAATCTAGAGGATTGGTTTCTCGATTTGTAGGACCTTATTTCAAATTAATCACGCGTAGTTGGCACGTATTGCCACTTGGCTTTTTATTTAGACTTGGTTTTGATAc < 1:65452/141‑1 (MQ=255)
gTCGATGCATTACTTGAATCTAGAGGATTGGTTTCTCGATTTGTAGGACCTTATTTCAAATTAATCACGCGTAGTTGGCACGTATTGCCACTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTa > 1:760/1‑141 (MQ=255)
tGCATTACTTGAATCTAGAGGATTGGTTTCTCGATTTGTAGGACCTTATTTCAAATTAATCACGCGTAGTTGGCACGTATTGCCACTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGc > 2:87354/1‑141 (MQ=255)
aTTGGTTTCTCGATTTGTAGGACCTTATTTCAAATTAATCACGCGTAGTTGGCACGTATTGCCACTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATcaca < 1:202876/141‑1 (MQ=255)
aTTGGTTTCTCGATTTGTAGGACCTTATTTCAAATTAATCACGCGTAGTTGGCACGTATTGCCACTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATcaca < 1:35931/141‑1 (MQ=255)
tGGTTTCTGGATGTGTAGGACTTTATTGCAAATTAATCTCGCGTAGTTGGCACGTATTGCAACTTGGCTTTTTATTTTGACTTGGTTTTGGTACAGCTAGTGAAATTGCGTTATTCGCTTTTTCTTCAGGTGCATCacaac < 2:82910/141‑1 (MQ=255)
tGGTTTCTCGATTTGTAGGACCTTATTTCAAATTAATCACGCGTAGTTGGCACGTATTGCCACTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCacaac < 2:60949/141‑1 (MQ=255)
tttCTCGATTTGTAGGACCTTATTTCAAATTAATCACGCGTAGTTGGCACGTATTGCCACTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCACAACAAg > 1:156921/1‑141 (MQ=255)
cGATTTGTAGGACCTTATTTCAAATTAATCACGCGTAGTTGGCACGTATTGTCACTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCGGGCGCATCACAACAAGCcatt > 2:221093/1‑141 (MQ=255)
gATTTGTAGGACCTTATTTCAAGTTAATCACGCGTAGTTGGCACGTATTGCCACTTGGCTTTTTATTTGGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCACAACAAGCcattt < 1:117722/141‑1 (MQ=255)
ttGTAGGACCTTATTTCAAATTAATCACGCGTAGTTGGCACGTATTGCCACTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCACAACAAGCcatttcat > 2:97602/1‑141 (MQ=255)
tGTAGGACCTTATTTCAAATTAATCACGCGTAGTTGGCACGTATTGCCACTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCACAACAAGCcatttcatt < 1:125943/141‑1 (MQ=255)
gTAGGACCGTATTTCAAATTAATCACGCGTAGTTGGCACGTATTGCCACTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCACAACAAGCcatttcattt > 2:43375/1‑141 (MQ=255)
gcgTAGTTGGCACTTATTGCCACTTGGGTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCTCAACAAGCCATTTCATTTATCGGAATCTTATCTTTACCAAtgtt < 2:147401/141‑1 (MQ=255)
gcgTAGTTGGCACGTATTGCCACTTGGCTTTTTATTTAGCCTTGGTTTTGATCCAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCACAACAAGCCATTTCATTTATCGGAATCTTATCTTTACCAAtttt < 2:122036/141‑1 (MQ=255)
gTAGTTGGCACGTATTGCCACTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCACAACAAGCCATTTCATTTATCGGAATCTTATCTTTACCAATTTTAt < 1:2373/141‑1 (MQ=255)
gTTGGCACGTATTGCCACTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCACAACAAGCCATTTCATTTATCGGAATCTTATCTTTACCAATTTTATTCg > 2:11017/1‑141 (MQ=255)
aTTGCCACTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCAGCACAACAAGCCATTTCATTTATCGGAATCTTATCTTTACCAATTTTATTCGCATCAGGTAt < 2:148848/141‑1 (MQ=255)
ttGCCACTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCACAACAAGCCATTTCATTTATCGGAATCTTATCTTTACCAATTTTATTCGCATCAGGTATg < 2:760/141‑1 (MQ=255)
ttGCCACTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCACAACAAGCCATTTCATTTATCGGAATCTTATCTTTACCAATTTTATTCGCATCAGGTATg < 1:19186/141‑1 (MQ=255)
tGCCACTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCACAACAAGCCATTTCATTTATCGGAATCTTATCTTTACCAATTTTATTCGCATCAGGTATGa < 1:69688/141‑1 (MQ=255)
aCTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCACAACAAGCCATTTCATTTATCGGAATCTTATCTTTACCAATTTTATTCGCATCAGGTATGAGttt < 1:11017/141‑1 (MQ=255)
cTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCACAACAAGCCATTTCATTTATCGGAATCTTATCTTTACCAATTTTATTCGCATCAGGTATGAGTTTa < 2:173164/141‑1 (MQ=255)
cTTGGCTTTTTATTTAGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCACAACAAGCCATTTCATTTATCGGAATCTTATCTTTACCAATTTTATTCGCATCAGGTATGAGTTTa < 2:93541/141‑1 (MQ=255)
|
CGTCGTGAACACATTGAAGAAGCTGAAGTCGATGCATTACTTGAATCTAGAGGATTGGTTTCTCGATTTGTAGGACCTTATTTCAAATTAATCACGCGTAGTTGGCACGTATTGCCACTTGGCTTTTTATTTGGACTTGGTTTTGATACAGCTAGTGAAATTGCGTTACTCGCTCTTTCTTCAGGCGCATCACAACAAGCCATTTCATTTATCGGAATCTTATCTTTACCAATTTTATTCGCATCAGGTATGAGTTTA > USA300TCH1516_ALE/2857038‑2857295
|
| 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
