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 F8 I0 R1
|
311 |
50.1 |
4085234 |
95.9% |
3917739 |
60.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
4,549,754 |
G→A |
46.5% |
intergenic (+43/‑24) |
fimC → / → fimD |
chaperone, periplasmic/outer membrane usher protein, type 1 fimbrial synthesis |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 4,549,754 | 0 | G | A | 46.5%
| 7.8
/ 57.3
| 43 | intergenic (+43/‑24) | fimC/fimD | chaperone, periplasmic/outer membrane usher protein, type 1 fimbrial synthesis |
| Reads supporting (aligned to +/- strand): ref base G (7/16); new base A (11/9); total (18/25) |
| Fisher's exact test for biased strand distribution p-value = 1.30e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.24e-01 |
CAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAACACACAATGCT > W3110S.gb/4549687‑4549823
|
cAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCCAGGt > 1:3168458/1‑71 (MQ=255)
cAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCCAGGt > 1:164500/1‑71 (MQ=255)
aaaaTGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGTCGGGTg < 1:2621393/71‑1 (MQ=255)
aTGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCggagg < 1:2427834/71‑1 (MQ=255)
gAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGaa > 1:2858956/1‑70 (MQ=255)
gAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCCAGGTGATTTTAAGCCGGAGGaat < 1:938272/71‑1 (MQ=255)
gAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCCAGGTGATTTTAAGCCGGAGGaat < 1:3197661/71‑1 (MQ=255)
aCGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGTCGGGTGATTTTAAGc > 1:3444801/1‑57 (MQ=255)
aCGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGTCGGGTGATTTTAAGc > 1:2692213/1‑57 (MQ=255)
aCGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCCAGGTGATTTTAAGCCGGAGGAATAATGt < 1:1677941/71‑1 (MQ=255)
cAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCCGGGTGATTTTAAGc > 1:947169/1‑54 (MQ=255)
cAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCCGGGTGATTTTAAGc > 1:2344935/1‑54 (MQ=255)
cAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCat < 1:345578/71‑1 (MQ=255)
cAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCCAGGTGATTTTAAGCCGGAGGAATAATGTCat < 1:2183052/71‑1 (MQ=255)
ggggAATTTTTCGCCTGAATAAAAAGAATTGACTGTCGGGTGATTTTAAGCCGGAGGAATAATGTCATATc < 1:1411765/71‑1 (MQ=255)
ggggAATTTTTCCCCTGAATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGaat < 1:3395254/60‑1 (MQ=255)
gggAATTTTTCGCCTGAATAAAAAGAATTGACTGCCAGGTGATTTTAAGCCGGAGGAATAATGTCATATCt > 1:33858/1‑71 (MQ=255)
gggAATTTTTCGCCTGAATAAAAAGAATTGACTGCCAGGTGATTTAAAGCCGGAGGAATAATGTCATATCt > 1:312495/1‑71 (MQ=255)
ggAATTTTTCGCCTGAATAAAAAGAATTGACTGTCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTg < 1:3269839/71‑1 (MQ=255)
gAATTTTTCGCCTGAATAAAAAGAATTGACTGCCAGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGa < 1:2482821/71‑1 (MQ=255)
gAATTTTTCGCCTGAATAAAAAGAATTGACTGCCAGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGa < 1:1477343/71‑1 (MQ=255)
aaTTTTTCGCCTGAATAAAAAGAATTGACTGTCGGGTGAttt < 1:3426901/42‑1 (MQ=255)
aaTTTTTCGCCTGAATAAAAAGAATTGACTGTCGGGTGATTTTAAGCCGGAGGaata < 1:3243236/57‑1 (MQ=255)
aaTTTTTCGCCTGAATAAAAAGAATTGACTGCCAGGTGATTTTAAGCCGGAGGAATAATGTCata > 1:3195902/1‑65 (MQ=255)
aaTTTTTCGCCTGAATAAAAAGAATTGACTGCCAGGTGATTTTAAGCCGGAGGAATAATGTCata > 1:3924618/1‑65 (MQ=255)
aTTTTTCGCCTGAATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGt < 1:3556455/60‑1 (MQ=255)
ttttCGCCTGAATAAAAAGAATTGACTGCCGGGTGATTTTAAGCTGGAGGAATAATGTCATATCTGAAt > 1:855033/1‑69 (MQ=255)
tttCGCCTGAATAAAAAGAATTGACTGCCGGGTGATTTTAAGCTGGAGGaataa > 1:2938381/1‑54 (MQ=255)
tttCGCCTGAATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAAttt < 1:1448135/70‑1 (MQ=255)
tttCGCCTGAATAAAAAGAATTGACTGCCAGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAAttt > 1:3437946/1‑70 (MQ=255)
tttCGCCTGAATAAAAAGAATTGACTGCCAGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAAttt > 1:1639499/1‑70 (MQ=255)
cTGAATAAAAAGAATTGACTGCCAGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGa < 1:1863206/60‑1 (MQ=255)
tGAATAAAAAGAATTGACTGCCAGGTGATTTTAAGCCggagg > 1:1161664/1‑42 (MQ=255)
aaTAAAAAGAATTGACTGCCGGGTGATTTTAAGCTGGAGGAATAATGTCATATCTGAATTTAAGACttt < 1:3463185/69‑1 (MQ=255)
aaTAAAAAGAATTGACTGCCGGGTGATTTTAAGCTGGAGGAATAATGTCATATCTGAATTTAAGACttt < 1:3763624/69‑1 (MQ=255)
aaTAAAAAGAATTGACTGCCGGGTGATTTTAAGCTGGAGGAATAATGTCATATCTGAATTTAAGACttt < 1:1021252/69‑1 (MQ=255)
aaTAAAAAGAATTGACTGCCAGGTGATTTTAAGCCGGAGGAATAATGt < 1:374880/48‑1 (MQ=255)
tAAAAAGAATTGACTGCCAGGTGATTTTAAGCCgg < 1:816948/35‑1 (MQ=255)
aaGAATTGACTGTCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGa < 1:2944041/71‑1 (MQ=255)
aaGAATTGACTGCCAGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTaa > 1:1285920/1‑57 (MQ=255)
aaGAATTGACTGCCAGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTaa > 1:2799701/1‑57 (MQ=255)
cTGCCGGGTGATTTTAAGCTGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAACACACaa < 1:3974341/71‑1 (MQ=255)
cGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAACACACAATGCt < 1:3301734/71‑1 (MQ=255)
|
CAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAACACACAATGCT > W3110S.gb/4549687‑4549823
|
| 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
