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 |
2,075,214 |
C→T |
49.1% |
N513N (AAC→AAT) |
flu → |
antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,075,214 | 0 | C | T | 49.1%
| ‑0.7
/ 80.4
| 55 | N513N (AAC→AAT) | flu | antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| Reads supporting (aligned to +/- strand): ref base C (18/10); new base T (15/12); total (33/22) |
| Fisher's exact test for biased strand distribution p-value = 5.87e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.77e-01 |
GCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTA > W3110S.gb/2075147‑2075281
|
gCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAATCtg < 1:427158/71‑1 (MQ=255)
aaaaTCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAATCTGAATGAAg > 1:1095331/1‑71 (MQ=255)
aaaTCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAATCTGAATGAAgg < 1:1369463/71‑1 (MQ=255)
aTCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAATCTTATTGAAGGCa < 1:1111441/71‑1 (MQ=255)
aGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAAc > 1:2070739/1‑55 (MQ=255)
aGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAAc > 1:1661176/1‑55 (MQ=255)
ggAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCacgct < 1:1639440/71‑1 (MQ=255)
aaGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGATAGCCGTCAATCtg < 1:1307236/55‑1 (MQ=255)
cacaCTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAATCTGAATGAAGGCAcgctgacgctga < 1:1370797/71‑1 (MQ=255)
ctcactGTCAGCAACACCACACTCACCCAGAAAGCCGTCAATCTGAATGAAGGCac > 1:2795258/1‑56 (MQ=255)
ctcactGTCAGCAACACCACACTCACCCAGAAAGCCGTCAATCTGAATGAAGGCACGCTGACGCTGAACGa > 1:1532590/1‑71 (MQ=255)
ctcactGTCAGCAACACCACACTCACCCAGAAAGCCGTCAATCTGAATGAAGGCACGCTGACGCTGAACGa < 1:1698548/71‑1 (MQ=255)
actGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGAc < 1:1542461/69‑1 (MQ=255)
actGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGAc < 1:399807/69‑1 (MQ=255)
ctGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGt < 1:2526082/71‑1 (MQ=255)
gTCAGCAACACCACACTCACCCAGAAAGCCGTCAATCTGAATGAAGGCACGCTGACGCTGAACGACAGTAc > 1:1326684/1‑71 (MQ=255)
gTCAGCAACACCACACTCACCCAGAAAGCCGTCAATCTGAATGAAGGCACGCTGACGCTGAACGACAGTAc > 1:2164387/1‑71 (MQ=255)
gTCAGCAACACCACACTCACCCAGAAAGCCGTCAATCTGAATGAAGGCACGCTGACGCTGAACGACAGTAc > 1:1173332/1‑71 (MQ=255)
gTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGaa > 1:265525/1‑62 (MQ=255)
tCAGCAACACCACACTCACCCAGAAAGCCGTCAATCtgaatga < 1:438311/43‑1 (MQ=255)
tCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTAcc > 1:232388/1‑71 (MQ=255)
tCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTAcc > 1:641544/1‑71 (MQ=255)
tCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTAcc > 1:93359/1‑71 (MQ=255)
tCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTAcc > 1:571291/1‑71 (MQ=255)
aaCACCACACTCACCCAGAAAGCCGTCAATCtgaa > 1:2796137/1‑35 (MQ=255)
caccacACTCACCCAGAAAGCCGTCAATCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTcacca < 1:488993/71‑1 (MQ=255)
caccacACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGAc < 1:1159278/58‑1 (MQ=255)
caccacACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGAc < 1:2132204/58‑1 (MQ=255)
accacACTCACCCAGAAAGCCGTCAATCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTcaccac > 1:635010/1‑71 (MQ=255)
accacACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCacgc > 1:2121396/1‑43 (MQ=255)
ccacACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCacgct < 1:822144/43‑1 (MQ=255)
acacTCACCCAGAAAGCCGTCTACCTGAATGAAGGCACGCTGACGCTGAACGACAg > 1:329705/1‑56 (MQ=255)
acacTCACCCAGAAAGCCGTCAATCTGAATGAAGGCacgctga > 1:1644735/1‑43 (MQ=255)
acacTCACCCAGAAAGCCGTCAATCTGAATGAAGGCacgctga > 1:507857/1‑43 (MQ=255)
acTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGt < 1:986349/55‑1 (MQ=255)
cTCACCCAGAAAGCCGTCAATCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGt < 1:318193/71‑1 (MQ=255)
cTCACCCAGAAAGCCGTCAATCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGt < 1:1454559/71‑1 (MQ=255)
cTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGt < 1:2203093/71‑1 (MQ=255)
tCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGt > 1:2134503/1‑70 (MQ=255)
cACCCAGAAAGCCGTCAACCTGAATGAAGGCacgctga > 1:2319800/1‑38 (MQ=255)
cccAGAAAGCCGTCAATCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGt < 1:1237/67‑1 (MQ=255)
cAGAAAGCCGTCAATCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCa > 1:2513252/1‑67 (MQ=255)
cAGAAAGCCGTCAATCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCa > 1:2123894/1‑67 (MQ=255)
aaGCCGTCAATCTGAATGAAGGCACGCTGACGCTGAAc > 1:1798517/1‑38 (MQ=255)
gCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCa < 1:2490960/61‑1 (MQ=255)
cGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCAtt > 1:968488/1‑61 (MQ=255)
cGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCAtt > 1:2225004/1‑61 (MQ=255)
cGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCAtt > 1:1966344/1‑61 (MQ=255)
gTCAATCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCgg < 1:1026636/71‑1 (MQ=255)
tCAATCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCgg > 1:1889122/1‑70 (MQ=255)
cAATCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTa > 1:1952054/1‑71 (MQ=255)
aaCCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTcacca > 1:1589011/1‑46 (MQ=255)
aaCCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTcacca > 1:984545/1‑46 (MQ=255)
aaCCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGa > 1:1558340/1‑50 (MQ=255)
aaCCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGa > 1:124614/1‑50 (MQ=255)
aaCCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGa > 1:2291663/1‑50 (MQ=255)
aaCCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGa > 1:2499160/1‑50 (MQ=255)
ccTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGt < 1:1254972/51‑1 (MQ=255)
|
GCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACCGTCACCACGGATGTCATTGCTCAGCGCGGTA > W3110S.gb/2075147‑2075281
|
| 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
