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 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
980,278 |
C→T |
14.8% |
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 | 14.8%
| 192.7
/ 20.3
| 74 | V9V (GTG→GTA) | cspI | cold shock protein |
| Reads supporting (aligned to +/- strand): ref base C (32/31); new base T (2/9); total (34/40) |
| Fisher's exact test for biased strand distribution p-value = 5.53e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAGAATGGTC > minE/980211‑980347
|
cAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCAc > 1:1534400/1‑70 (MQ=255)
cAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACt < 1:2728011/71‑1 (MQ=255)
cAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACt < 1:1450160/71‑1 (MQ=255)
aaaCACATCTTTACTACCATCAACAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAAACCATTTTACTa < 1:3525091/71‑1 (MQ=255)
aaCACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTaa < 1:3226106/71‑1 (MQ=255)
aaCACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTaa < 1:1430417/71‑1 (MQ=255)
acacATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTaaa > 1:3760251/1‑71 (MQ=255)
acgtCTTTGCTGCCATCATCAGGAGTGATAAAGCCAAAACCTTTATCTGCGTTAAACCATTTTACTAAAcc < 1:2092435/68‑1 (MQ=9)
acgtCTTTGCTGCCATCATCAGGAGTGATAAAGCCAAAACCTTTATCTGCGTTAAACCATTTTACTAAAc > 1:3505348/4‑70 (MQ=9)
acaTCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAAcc < 1:3379269/71‑1 (MQ=255)
gctgcCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCAttt > 1:1066236/1‑71 (MQ=255)
gctgcCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCAtt < 1:2909648/70‑1 (MQ=255)
gagcCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTACGATACCAGTCAtttt < 1:2536224/69‑1 (MQ=255)
gagcCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTACGATACCAGTCAtttt < 1:3804793/69‑1 (MQ=255)
agcCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTACGATACCAGTCAtttt < 1:2864534/69‑1 (MQ=255)
ccATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCAc < 1:833754/53‑1 (MQ=255)
ccATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGt < 1:2761567/70‑1 (MQ=255)
cATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCa > 1:400185/1‑51 (MQ=255)
cATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTa < 1:1984849/71‑1 (MQ=255)
aTCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAAc < 1:2536476/56‑1 (MQ=255)
cTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTg > 1:1881533/1‑65 (MQ=255)
tttCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCAtt > 1:3310296/1‑61 (MQ=255)
tttCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACa > 1:1521667/1‑71 (MQ=255)
ctgCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATa < 1:2200645/68‑1 (MQ=255)
cGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATaa > 1:3118615/1‑71 (MQ=255)
cGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATaa > 1:1203435/1‑71 (MQ=255)
gCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCAtt < 1:3418694/56‑1 (MQ=255)
gCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAatt < 1:3671569/71‑1 (MQ=255)
cGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAat < 1:3395416/69‑1 (MQ=255)
agTGATAAAGCCAAAACCTTTATCTGCGTTAAACCATTTTACTAAAc > 1:825724/2‑47 (MQ=16)
gaAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGt > 1:3460537/1‑53 (MQ=255)
gaAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCt > 1:2399905/1‑71 (MQ=255)
gaAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCt > 1:3817724/1‑71 (MQ=255)
aaCCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCttt > 1:3280759/1‑71 (MQ=255)
ccAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTg < 1:800234/71‑1 (MQ=255)
ccAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTg < 1:2936467/71‑1 (MQ=255)
ccAAAACCTTTATCTGCGTTAAACCATTTTACTAAACCAGTCAtttt < 1:1918042/47‑1 (MQ=255)
aaaaCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATGATTACCTTTTg > 1:1369223/1‑69 (MQ=255)
aaaCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCAttt > 1:590728/1‑43 (MQ=255)
aCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTgaaga > 1:769702/1‑70 (MQ=255)
aCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTgaaga > 1:3047348/1‑70 (MQ=255)
aCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTgaag > 1:2201983/1‑69 (MQ=255)
cTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAAt < 1:2112271/71‑1 (MQ=255)
cTTTGTCAGCGTTGAACCATTTTACGATACCAGTCAtttt < 1:2318751/40‑1 (MQ=16)
ttttCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTg > 1:3350166/1‑62 (MQ=255)
ttttCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAAt > 1:3311983/1‑69 (MQ=255)
tttCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGt > 1:3499314/1‑39 (MQ=255)
tttCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAattat > 1:2159221/1‑52 (MQ=255)
tCAGCGTTAAACCATTTTACTAAACCAGTCATTTTATTTGACAtt < 1:3601552/45‑2 (MQ=255)
cAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGccc > 1:1412852/1‑71 (MQ=255)
cAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGccc > 1:1707663/1‑71 (MQ=255)
cAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGcc < 1:349227/70‑1 (MQ=255)
aGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTa > 1:554007/1‑37 (MQ=255)
aGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAAtt > 1:3329426/1‑65 (MQ=255)
aGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGccc < 1:222247/70‑1 (MQ=255)
gggTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCtt < 1:726070/71‑1 (MQ=255)
gggTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCtt < 1:3305656/71‑1 (MQ=255)
gggTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCtt < 1:541404/71‑1 (MQ=255)
ttAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAatt < 1:3056771/42‑1 (MQ=255)
ttAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTggg > 1:2737401/1‑71 (MQ=255)
ttAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTggg > 1:480068/1‑71 (MQ=255)
tAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAatt < 1:2716530/41‑1 (MQ=255)
tAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGc > 1:599499/1‑63 (MQ=255)
aaCCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAg < 1:2058300/71‑1 (MQ=255)
aCCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTggg > 1:130865/1‑67 (MQ=255)
ccATTTTACTAAACCAGTCATTTTATTAGACATAtttt < 1:641789/38‑2 (MQ=25)
ccATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAGaa < 1:1168142/71‑1 (MQ=255)
ccATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAGaa < 1:1934247/71‑1 (MQ=255)
ccATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAGaa < 1:2647146/71‑1 (MQ=255)
aTTTCACTAAACCAGTCATTTTGTTATACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAGAATg < 1:3279613/71‑1 (MQ=255)
tttCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAGAATgg < 1:522104/71‑1 (MQ=255)
tttCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAGAATgg < 1:2416290/71‑1 (MQ=255)
tCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAGa > 1:2227239/1‑65 (MQ=255)
tCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAGAATGGTc > 1:2714531/1‑71 (MQ=255)
cACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTgaa > 1:634468/1‑44 (MQ=255)
cACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTa > 1:2233963/1‑51 (MQ=255)
|
CAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAGAATGGTC > minE/980211‑980347
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
