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 |
|
A5 F21 I0 R2
|
316 |
65.6 |
5147759 |
97.4% |
5013917 |
60.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,745,181 |
A→G |
40.7% |
Y4C (TAT→TGT) |
mdtK → |
multidrug efflux system transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,745,181 | 0 | A | G | 40.7%
| 25.8
/ 64.9
| 54 | Y4C (TAT→TGT) | mdtK | multidrug efflux system transporter |
| Reads supporting (aligned to +/- strand): ref base A (15/17); new base G (10/12); total (25/29) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.95e-01 |
CCATTCAGGCGGCTTTTTAGTCTCTCATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATCCCGGTGATTCTCGCGCAAATCGCCCA > W3110S.gb/1745118‑1745244
|
ccATTCAGGCGGCTTTTTAGTCTCTCATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGt > 1:2994761/1‑71 (MQ=255)
aTTCAGGCGGCTTTTTAGTCTCTCATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTGTATCAGTGa < 1:1666031/71‑1 (MQ=255)
ttCAGGCGGCTTTTTAGTCTCTCATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTGTATCAGt > 1:2367250/1‑68 (MQ=255)
ttCAGGCGGCTTTTTAGTCTCTCATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTg > 1:3947059/1‑69 (MQ=255)
ttCAGGCGGCTTTTTAGTCTCTCATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTg > 1:2875435/1‑69 (MQ=255)
cAGGCGGCTTTTTAGTCTCTCATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTGTATCAGTGAAgc > 1:4837396/1‑71 (MQ=255)
cAGGAGGCTTTTTAGTCTCTCATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAgc > 1:1543471/1‑71 (MQ=255)
cTTTTTAGTCTCTCATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTg < 1:3551557/71‑1 (MQ=255)
ttttAGTCTCTCATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTGTATCAGTGAAGCGCGTCTGt > 1:2088693/1‑70 (MQ=255)
ttttACTCTCTCATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTGTATCAGTGAAGCGCGt > 1:3434825/1‑66 (MQ=255)
tttAGTCTCTCATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTGTATCAGTGAAGCGCGTCTGtta > 1:757531/1‑71 (MQ=255)
tttAGTCTCTCATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGtta > 1:546276/1‑71 (MQ=255)
ttAGTCTCTCATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAg > 1:1552380/1‑59 (MQ=255)
gTCTCTCATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGTTattag < 1:4462132/71‑1 (MQ=255)
gTCTCTCATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGAGTCTGTTattag < 1:170823/71‑1 (MQ=255)
atatAACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGTTattagcattag > 1:2153560/1‑70 (MQ=255)
atatAACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGTTattagcat < 1:1037769/67‑1 (MQ=255)
atatAACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGTTattagcat < 1:4129527/67‑1 (MQ=255)
atatAACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGTTattagcat < 1:4123804/67‑1 (MQ=255)
tataACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAg > 1:1048326/1‑43 (MQ=255)
tataACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAg > 1:2795895/1‑43 (MQ=255)
taACTACAAATAAAAGGTGTTCACGTGCAGAAGTatat < 1:681470/38‑1 (MQ=255)
taACTACAAATAAAAGGTGTTCACGTGCAGAAGTGTATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAAt < 1:5129429/71‑1 (MQ=255)
taACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAgcgc > 1:3296431/1‑49 (MQ=255)
aCTACAAATAAAAGGTGTTCACGTGCAGAAGTGTATCAGTGAAGCGCGTCTGTTATTAGCATTAGCACTcc > 1:3923238/1‑71 (MQ=255)
aCTACAAATAAAAGGTGTTCACGTGCAGAAGTGTATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATcc > 1:3011314/1‑71 (MQ=255)
aCTACAAATAAAAGGTGTTCACGTGCAGAAGTGTATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATcc > 1:1340976/1‑71 (MQ=255)
cTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGa < 1:583702/41‑1 (MQ=255)
cAAATAAAAGGTGTTCACGTGCAGAAGTGTATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATCCCGGt < 1:4423548/71‑1 (MQ=255)
cAAATAAAAGGTGTTCACGTGCAGAAGTGTATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATCCCGGt < 1:2813982/71‑1 (MQ=255)
cAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATCCCGGt > 1:4687768/1‑71 (MQ=255)
aaaTAAAAGGTGTTCACGTGCAGAAGTGTATCAGTGa < 1:4323958/37‑1 (MQ=255)
aaTAAAAGGTGTTCACGTGCAGAAGTATATCATTGAAGCGCGTc < 1:4524450/44‑1 (MQ=255)
aaTAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTc < 1:609971/44‑1 (MQ=255)
aaTAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTc < 1:4276704/44‑1 (MQ=255)
tAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATCCCGGTGAtt > 1:511397/1‑71 (MQ=255)
tAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATCAAGGTGAt > 1:3298682/1‑70 (MQ=255)
aaaGGTGTTCACGTGCAGAAGTGTATCAGTGAAGCGCGTCTGttatta < 1:3109729/48‑1 (MQ=255)
aaaGGTGTTCACGTGCAGAAGTGTATCAGTGAAGCGCGTCTGttatta < 1:5019640/48‑1 (MQ=255)
aaGGTGTTCACGTGCAGAAGTGTATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATCCCGGTGATtctc < 1:2642492/71‑1 (MQ=255)
aaGGTGTTCACGTGCAGAAGTGTATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATCCCGGTGATtct < 1:608713/70‑1 (MQ=255)
aGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTg < 1:1883726/40‑1 (MQ=255)
ggTGTTCACGTGCAGAAGTGTATCAGTGAAGCGCGTCTGTTattagcattagc < 1:320276/53‑1 (MQ=255)
tgtTCACGTGCAGAAGTGTATCAGTGAAGCGCGTCTGt < 1:3714168/38‑1 (MQ=255)
gtTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATCCCGGTGATTCTCgcgc > 1:4780401/1‑70 (MQ=255)
ttCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGTTattagcattag < 1:220133/48‑1 (MQ=255)
ttCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGTTattagcattag < 1:4691270/48‑1 (MQ=255)
ttCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGTTattagcattag < 1:346421/48‑1 (MQ=255)
ttCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATCCCGGTGATTCTCGCGCaa < 1:2789091/71‑1 (MQ=255)
cACGTGCAGAAGTGTATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATCCCGGTGATTCTCGCGCaaa > 1:380220/1‑70 (MQ=255)
cACGTGCAGAAGTGTATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATCCCGGTGATTCTCGCGCAAAt > 1:2117486/1‑71 (MQ=255)
cACGTGCAGAAGTATATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATCCCGGTGATTCTCGCGCAAAt > 1:674630/1‑71 (MQ=255)
cAGAAGTGTATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATCCCGGTGATTCTCGCGCAAATCGCCCa < 1:3644146/71‑1 (MQ=255)
gTATATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATCCCGGTGATTCTCGCGCa < 1:2528918/57‑1 (MQ=255)
gTATATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATCCCGGTGATTCTCGCGCa < 1:648488/57‑1 (MQ=255)
|
CCATTCAGGCGGCTTTTTAGTCTCTCATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATCCCGGTGATTCTCGCGCAAATCGCCCA > W3110S.gb/1745118‑1745244
|
| 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
