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 F21 I0 R1
|
476 |
35.3 |
2812105 |
96.7% |
2719305 |
61.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,500,231 |
C→T |
85.3% |
A115T (GCG→ACG) |
yijE ← |
predicted permease |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,500,231 | 0 | C | T | 85.3%
| 78.4
/ 8.0
| 34 | A115T (GCG→ACG) | yijE | predicted permease |
| Reads supporting (aligned to +/- strand): ref base C (2/3); new base T (10/19); total (12/22) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.08e-01 |
GCCGAAAGCGGCAATCAGAATCGCGAAATATTGCCCACGTCGCAGGCGTTCACCGAGAAACAACGCGGCGAAAATCACCACCCAGAACGGCATGGTATAGCTCAGGATCGCCACCTTCCCCGCACCTCCGCTG > W3110S.gb/3500166‑3500298
|
gCCGAAAGCGGCAATCAGAATCGCGAAATATTGCCCACGTCGCAGGCGTTCACCGAGAAACAACGCGGCGa < 1:2102111/71‑1 (MQ=255)
cGAAAGCGGCAATCAGAATCGCGAAATATTGCCCACGTCGCAGGCGTTCACCGAGAAACAACGTGGCGaa > 1:1472159/1‑70 (MQ=255)
cGAAAGCGGCAATCAGAATCGCGAAATATTGCCCACGTCGCAGGCGTTCACCGAGAAACAACGTGGCGaa < 1:1716196/70‑1 (MQ=255)
aaGCGGCAATCAGAATCGCGAAATATTGCCCACGTCGCAGGCGTTCACCGAGAAACAACGTGGCGAAAAt < 1:2040382/70‑1 (MQ=255)
tCAGAATCGCGAAATATTGCCCACGTCGCAGGCGTTCACCGAGAAACAACGTGGCGAAAATCACCACCCAg < 1:585935/71‑1 (MQ=255)
tCAGAATCGCGAAATATTGCCCACGTCGCAGGCGTTCACCGAGAAACAACGTGGCGAAAATCACCACCCAg < 1:565879/71‑1 (MQ=255)
cAGAATCGCGAAATATTGCCCACGTCGCAGGCGTTCACCGAGAAACAACGTGGCGAAAATCACCACCCAg > 1:376567/1‑70 (MQ=255)
gAATCGCGAAATATTGCCCACGTCGCAGGCGTTCACCGAGAAACAACGTGGCGaa < 1:253572/55‑1 (MQ=255)
gAATCGCGAAATATTGCCCACGTCGCAGGCGTTCACCGAGAAACAACGTGGCGaa < 1:1980888/55‑1 (MQ=255)
gAATCGCGAAATATTGCCCACGTCGCAGGCGTTCACCGAGAAACAACGTGGCGAAAATCACAACCCAGAAc > 1:1141889/1‑71 (MQ=255)
aTCGCGAAATATTGCCCACGTCGCAGGCGTTCACCGAGAAACAACGTGGCGAAAATCACCACCCAGAACg > 1:1093627/1‑70 (MQ=255)
tCGCGAAATATTGCCCACGTCGCAGGCGTTCACCGAGAAACAACGTGGCGAAAATCACCACCCAGaa > 1:95988/1‑67 (MQ=255)
gcgAAATATTGCCCACGTCGCAGGCGTTCACCGAGAAACAACgtgg > 1:584151/1‑46 (MQ=255)
aaTATTGCCCACGTCGCAGGCGTTCACCGAGAAACAACGCGGCGAAAATCACCACCCAGAACGGCATGGta < 1:260937/71‑1 (MQ=255)
ttGCCCACGTCGCAGGCGTTCACCGAGAAACAACGTGGCGAAAATCACCACCCAGAACgg < 1:239098/60‑1 (MQ=255)
ttGCCCACGTCGCAGGCGTTCACCGAGAAACAACGTGGCGAAAATCACCACCCAGAACGGCATg < 1:138727/64‑1 (MQ=255)
ttGCCCACGTCGCAGGCGTTCACCGAGAAACAACGCGGCGAAAATcac > 1:2159916/1‑48 (MQ=255)
gCCCACGTCGCAGGCGTTCACCGAGAAACAACGTGGCGAAAATCACCACCCAGAACGGCATGGTATAGCt > 1:1154007/1‑70 (MQ=255)
gCCCACGTCGCAGGCGTTCACCGAGAAACAACGTGGCGAAAATCACCACCCAGAACGGCATGGTATAGCt > 1:2078735/1‑70 (MQ=255)
cACGTCGCAGGCGTTCACCGAGAAACAACGTGGCGAAAATCACCACCCAGAACGGCATGGTATAGCTCAgg < 1:2486968/71‑1 (MQ=255)
cACGTCGCAGGCGTTCACCGAGAAACAACGTGGCGAAAATCACCACCCAGAACGGCATGGTATAGCTCAg < 1:2671895/70‑1 (MQ=255)
gTCGCAGGCGTTCACCGAGAAACAACGCGGCGAAAATcacca > 1:2045433/1‑42 (MQ=255)
gCGTTCACCGAGAAACAACGTGGCGAAAATCACCACCCAGAACGGCATGGta > 1:2475888/1‑52 (MQ=255)
gCGTTCACCGAGAAACAACGTGGCGAAAATCACCACCCAGAACGGCATGGta > 1:1326422/1‑52 (MQ=255)
ttCACCGAGAAACAACGTGGCGAAAATCACCACCCAGAACGGCATGGTATAGCTc < 1:2266379/55‑1 (MQ=255)
tCACCGAGAAACAACGTGGCGAAAATCACCACCCAGAACGGCATGGTATAGCTc < 1:2145964/54‑1 (MQ=255)
tCACCGAGAAACAACGTGGCGAAAATCACCACCCAGAACGGCATGGTATAGCTCAGGATc < 1:1221275/60‑1 (MQ=255)
cACCGAGAAACAACGTGGCGAAAATCACCACCCAGAACGGCATGGTATAGCTCAGGATCGCCACCTTcccc > 1:771703/1‑71 (MQ=255)
ccGAGAAACAACGCGGCGAAAATCACCACCCAGAACGGCATGGTATAGCTCAGGATCGCCACCTTCCCCGc < 1:1992425/71‑1 (MQ=255)
acaacGTGGCGAAAATCACCACCCAGAACGGCATGGtat < 1:981251/39‑1 (MQ=255)
acaacGTGGCGAAAATCACCACCCAGAACGGCATGGtat < 1:1815386/39‑1 (MQ=255)
acaacGTGGCGAAAATCACCACCCAGAACGGCATGGtat < 1:2389046/39‑1 (MQ=255)
acaacGTGGCGAAAATCACCACCCAGAACGGCATGGTATAGCTCAGGATCGcc < 1:2342863/53‑1 (MQ=255)
aacGTGGCGAAAATCACCACCCAGAACGGCATGGTATAGCTCAGGATCGCCACCTTCCCCGCACCTCCGCt < 1:1991230/71‑1 (MQ=255)
acGTGGCGAAAATCACCACCCAGAACGGCATGGTATAGCTCAGGATCGCCACCTTCCCCGCACCTCCGCTg < 1:2200631/71‑1 (MQ=255)
|
GCCGAAAGCGGCAATCAGAATCGCGAAATATTGCCCACGTCGCAGGCGTTCACCGAGAAACAACGCGGCGAAAATCACCACCCAGAACGGCATGGTATAGCTCAGGATCGCCACCTTCCCCGCACCTCCGCTG > W3110S.gb/3500166‑3500298
|
| 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
