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 F999 I1 R1
|
225 |
156.4 |
11709729 |
83.8% |
9812752 |
75.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
3,389,812 |
Δ1 bp |
intergenic (‑149/+4151) |
tldD ← / ← cafA |
TldD/CafA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 3,389,811 | 0 | C | . | 97.1%
| 99.1
/ ‑3.1
| 34 | intergenic (‑148/+4152) | tldD/cafA | TldD/CafA |
| Reads supporting (aligned to +/- strand): ref base C (1/0); new base . (2/31); total (3/31) |
| Fisher's exact test for biased strand distribution p-value = 8.82e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCCGGCGTAAACGCCTTATCCG > NC_000913/3389736‑3389831
|
ccAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGc < 1:130241/76‑1 (MQ=255)
ccAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGc < 1:2731204/76‑1 (MQ=255)
ccAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGc < 1:4643862/76‑1 (MQ=255)
ccAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGGCTGATGc > 2:1650181/1‑76 (MQ=255)
cAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGGCGGGTGcg > 1:346526/1‑75 (MQ=255)
aGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGcgg < 1:5211521/76‑3 (MQ=255)
gCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCGCAGCGTCGCATCAGGCAACGGCTGTCGGATGcggc < 1:709349/76‑4 (MQ=255)
gCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGcggc < 1:3082397/76‑4 (MQ=255)
gCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGGCGGATGCggg > 1:3891249/1‑76 (MQ=255)
cTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGt < 2:1860482/76‑1 (MQ=255)
tACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTa < 2:839671/76‑1 (MQ=255)
tACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTa < 1:3160731/76‑1 (MQ=255)
cGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTaaa < 2:32652/76‑1 (MQ=255)
ggTTATGTTCCGGTTTGTAGGCCTGATCAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAAc < 2:3910360/76‑1 (MQ=11)
ggTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAAc < 1:5801250/76‑1 (MQ=255)
gTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACg < 1:4869095/76‑1 (MQ=255)
gTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACg < 1:2483518/76‑1 (MQ=255)
gTTATGTTCCGGTGTGTAGTCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGACGTAAACg < 1:2493329/76‑1 (MQ=11)
gTTATGTTCCGGTGTGTAGGCGTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACg < 2:5416041/76‑1 (MQ=11)
ttATGTTCCGGTTTGTAGCCCTGATAATACGCACAGCGTCGCATCCGGCACCGGCTGTCGGATG‑CGGCGTAAACGc < 1:5743007/76‑1 (MQ=11)
gtATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGc < 2:3069796/75‑1 (MQ=255)
tATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGcc < 2:4877413/76‑1 (MQ=255)
tATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGcc < 1:2110610/76‑1 (MQ=255)
gtGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCt < 2:5791986/75‑1 (MQ=255)
tGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCtt < 1:4141297/76‑1 (MQ=255)
tGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCtt < 1:4485042/76‑1 (MQ=255)
tGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGGCGGATG‑CGGGGTAAACGccct > 1:5146473/1‑74 (MQ=11)
gtgccGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCTTa < 1:399174/73‑1 (MQ=11)
gTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCTTa < 1:3526576/76‑1 (MQ=255)
gTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCTTa < 2:3733069/76‑1 (MQ=255)
gTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCTTa < 1:4852129/76‑1 (MQ=255)
gTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGGCGGATG‑CGGCGGAAAAGCCCTa > 1:3376912/1‑76 (MQ=11)
gTTCCGGTTGGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCTTa < 1:5663715/76‑1 (MQ=11)
ttCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCTTAt < 1:3330614/76‑1 (MQ=255)
ttCCGGTTTGCAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCTTAt < 1:3090152/76‑1 (MQ=11)
tCCGTTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCTTATc < 1:2150614/76‑1 (MQ=11)
tCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCTTATc < 2:3240369/76‑1 (MQ=255)
ccGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCTTATcc < 2:3677818/76‑1 (MQ=12)
ccGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCTTATcc < 1:5450969/76‑1 (MQ=12)
ccGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCTTATcc < 1:3783178/76‑1 (MQ=12)
ccGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCTTATcc < 1:1248525/76‑1 (MQ=12)
cGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATG‑CGGCGTAAACGCCTTATCCg < 1:4059183/76‑1 (MQ=9)
|
CCAGCCTACGGTTATGTTCCGGTTTGTAGGCCTGATAAGACGCACAGCGTCGCATCAGGCAACGGCTGTCGGATGCCGGCGTAAACGCCTTATCCG > NC_000913/3389736‑3389831
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
