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 |
|
A6 F21 I0 R2
|
370 |
72.1 |
3738297 |
91.5% |
3420541 |
62.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
980,278 |
C→T |
5.9% |
V9V (GTG→GTA) |
cspI ← |
cold shock protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 980,278 | 0 | C | T | 5.9%
| 221.0
/ 3.4
| 68 | V9V (GTG→GTA) | cspI | cold shock protein |
| Reads supporting (aligned to +/- strand): ref base C (26/38); new base T (2/2); total (28/40) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01 |
GACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAGAATGGTCC > minE/980209‑980348
|
gACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCa > 1:479987/1‑71 (MQ=255)
aaaCACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTa < 1:2727818/71‑1 (MQ=255)
aaaCACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTa < 1:2277477/71‑1 (MQ=255)
acacATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTaaa < 1:2227212/71‑1 (MQ=255)
cacaTCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAAc < 1:3266168/71‑1 (MQ=255)
cacaTCTTTACTACCATCAACAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAAACCATTTTACTAAAc > 1:1670177/1‑71 (MQ=255)
cacaTCTTTACTACCATCAACAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAAACCATTTTACTAAAc > 1:2214762/1‑71 (MQ=255)
acaTCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAAc > 1:68072/1‑70 (MQ=255)
acaTCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAAc > 1:1952714/1‑70 (MQ=255)
acaTCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAAc > 1:801449/1‑70 (MQ=255)
cTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTa < 1:3571749/63‑1 (MQ=255)
tttGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAAc > 1:1066563/1‑65 (MQ=255)
ttGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCa > 1:1605349/1‑58 (MQ=255)
tgctgcCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGt < 1:2879782/67‑1 (MQ=255)
ctgcCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCAtttt < 1:841682/71‑1 (MQ=255)
ccATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGt > 1:1378120/1‑70 (MQ=255)
ccATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGt < 1:3508796/70‑1 (MQ=255)
ccATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGt < 1:1004229/70‑1 (MQ=255)
aTCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAg < 1:2090371/71‑1 (MQ=255)
tCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGa > 1:1199119/1‑71 (MQ=255)
cTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGa > 1:1120168/1‑70 (MQ=255)
cGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCAc > 1:22512/1‑45 (MQ=255)
ggCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTc < 1:1717763/42‑1 (MQ=255)
ggCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTc < 1:2020739/42‑1 (MQ=255)
ggCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTc < 1:1159330/42‑1 (MQ=255)
gagTGATAAAGCCAAAACCTTTATCTGCGTTAAACCATTTTACTAAACCAGTCATTTTATTAGACATAttt < 1:3226215/69‑1 (MQ=255)
gagTGATAAAGCCAAAACCTTTATCTGCGTTAAACCATTTTACTAAACCAGTCATTTTATTAGACATAttt < 1:1639919/69‑1 (MQ=255)
gCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAatt < 1:2358719/71‑1 (MQ=255)
cGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCAc > 1:628724/1‑42 (MQ=255)
cGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAatta < 1:1436152/71‑1 (MQ=255)
gTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAattat < 1:2450815/71‑1 (MQ=255)
gaAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCAtttt < 1:3716857/51‑1 (MQ=255)
gaAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCAtttt < 1:759609/51‑1 (MQ=255)
gaAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCAtttt < 1:1065795/51‑1 (MQ=255)
aaaCCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAatta < 1:2523530/64‑1 (MQ=255)
aaaCCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCtt > 1:1085912/1‑71 (MQ=255)
aaCCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCtt > 1:1945841/1‑70 (MQ=255)
aaaCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTg > 1:932530/1‑68 (MQ=255)
aaCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTgaag > 1:3236980/1‑70 (MQ=255)
aCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTgaagaa < 1:1315181/71‑1 (MQ=255)
ccTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTg < 1:2692405/65‑1 (MQ=255)
cTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGt < 1:514736/42‑1 (MQ=255)
tttttCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCtttt < 1:763565/62‑1 (MQ=255)
ttttCAGGGTTAAACCATTTCACTAAACCAGTCAtttt < 1:3455549/38‑1 (MQ=255)
ttttCAGGGTTAAACCATTTCACTAAACCAGTCAtttt < 1:3532901/38‑1 (MQ=255)
ttttCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTa > 1:2921583/1‑42 (MQ=255)
ttttCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTa > 1:1723033/1‑42 (MQ=255)
ttttCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCtttt < 1:2428180/61‑1 (MQ=255)
tttCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTa < 1:2002147/70‑1 (MQ=255)
tttCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAACAAATTa < 1:6368/70‑1 (MQ=255)
aGGGTTAAACCATTTCACTAAACCAGTCATTTTGt > 1:1208505/1‑35 (MQ=255)
ttAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGaaa < 1:2767683/59‑1 (MQ=255)
aaaGCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTgg > 1:2135431/1‑68 (MQ=255)
aaaCCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTggg > 1:1933826/1‑69 (MQ=255)
aaCCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAg < 1:3432025/71‑1 (MQ=255)
aCCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAAt < 1:9595/56‑1 (MQ=255)
aCCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAAt < 1:414305/56‑1 (MQ=255)
aCCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAAt < 1:3235119/56‑1 (MQ=255)
aCCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTgg < 1:306052/66‑1 (MQ=255)
aCCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAg > 1:1755339/1‑70 (MQ=255)
aCCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAGa < 1:1001381/71‑1 (MQ=255)
aCCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAGa < 1:2459803/71‑1 (MQ=255)
ccATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAg > 1:2551409/1‑58 (MQ=255)
ccATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAGa > 1:288853/1‑70 (MQ=255)
cATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCt < 1:2944285/43‑1 (MQ=255)
cATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAg > 1:503320/1‑68 (MQ=255)
aTTTCACTAAACCAGTCATTTTGTTAGACATAatt < 1:1512045/35‑1 (MQ=255)
aTTTCACTAAACCAGTCATTTTGTTAGACATAatt < 1:1471160/35‑1 (MQ=255)
tttCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGcc > 1:523269/1‑57 (MQ=255)
tttCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAGAATgg > 1:426641/1‑71 (MQ=255)
tttCACTAAACCAATCATTTTGTTAGACATAattatt < 1:802611/37‑1 (MQ=255)
cACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAGAATGGTcc > 1:2085563/1‑71 (MQ=255)
|
GACAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAGAATGGTCC > minE/980209‑980348
|
| 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
