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 |
1,071,158 |
A→G |
28.8% |
Y4C (TAT→TGT) |
mdtK → |
multidrug efflux system transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,071,158 | 0 | A | G | 28.8%
| 81.5
/ 41.8
| 59 | Y4C (TAT→TGT) | mdtK | multidrug efflux system transporter |
| Reads supporting (aligned to +/- strand): ref base A (27/15); new base G (11/6); total (38/21) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.11e-01 |
GCTGCCCATTCAGGCGGCTTTTTAGTCTCTCATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATCCCGGTGATTCTCGCGCAAATCGCCCAAACTGC > minE/1071090‑1071227
|
gctgcCCATTCAGGCGGCTTTTTAGTCTCTCATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGtat < 1:1546739/70‑1 (MQ=255)
cccATTCAGGAGGCTTTTTAGTCTCTCATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTGTATCAg > 1:3292398/1‑71 (MQ=255)
cATTCAGGCGGCTTTTTAGTCTCTCATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGt > 1:777755/1‑70 (MQ=255)
cAGGCGGCTTTTTAGTCTCTCATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAgc > 1:318381/1‑71 (MQ=255)
gcTTTTTAGTCTCTCATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGt < 1:3777969/69‑1 (MQ=255)
gcTTTTTAGTCTCTCATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGt < 1:3773546/69‑1 (MQ=255)
cTTTTTAGTCTCTCATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTg < 1:1044340/71‑1 (MQ=255)
cTTTTTAGTCTCTCATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTg < 1:1256265/71‑1 (MQ=255)
tttttAGTCTCTCATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTGTATCAGTGAAgc < 1:1685053/63‑1 (MQ=255)
tttttAGTCTCTCATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGcgcg < 1:1100386/66‑1 (MQ=255)
tttttAGTCTCTCATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTc < 1:2740223/68‑1 (MQ=255)
tttAGTCTCTCATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTGTATCAGTGAAGCGCGTCTGtta > 1:1686073/1‑71 (MQ=255)
tttAGTCTCTCATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGtta > 1:3907077/1‑71 (MQ=255)
tttAGTCTCTCATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGtta > 1:1011853/1‑71 (MQ=255)
tAGTCTCTCATGTAACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGttat < 1:3927690/70‑1 (MQ=255)
aGTCTCTCATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGttat > 1:1018456/1‑69 (MQ=255)
tctctcATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGtata < 1:558754/46‑1 (MQ=255)
tctctcATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGtata < 1:804849/46‑1 (MQ=255)
tctctcATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTGTATCAGTGAAGCGCGTCTGTTattagc < 1:121471/71‑1 (MQ=255)
ctctcATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTGTATCAGTGAAGCGCGTCTGTTattagca > 1:1152004/1‑71 (MQ=255)
tcATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTGTATCAg > 1:447629/1‑46 (MQ=255)
tcATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTGTATCAg > 1:3611626/1‑46 (MQ=255)
tcATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTGTATCAg > 1:2221259/1‑46 (MQ=255)
tcATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTGTATCAGTGAAGCGCGTCTGTTattagcat < 1:729630/69‑1 (MQ=255)
tcATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATc < 1:2138184/44‑1 (MQ=255)
tcATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATc < 1:1625403/44‑1 (MQ=255)
cATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGTTattagcattag > 1:748144/1‑71 (MQ=255)
cATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGTTattagca > 1:1604871/1‑67 (MQ=255)
atatAACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGTTattagcatta < 1:2902967/69‑1 (MQ=255)
tataACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGTTattagcattag > 1:2638146/1‑69 (MQ=255)
taACTACAAATAAAAGGTGTTCACGTGCAGAAGTGTATCAGTGAAGCGCGTCTGTTATTAGCATTAGCaa < 1:2953083/70‑1 (MQ=255)
aCTACAAATAAAAGGTGTTCACGTGCAGAAGTGTATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAAt > 1:3116788/1‑69 (MQ=255)
aCTACAAATAAAAGGTGTTCACGTGCAGAAGTGTATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAAt > 1:3321704/1‑69 (MQ=255)
aCTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATcc > 1:2869005/1‑71 (MQ=255)
aCTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATcc > 1:1572397/1‑71 (MQ=255)
aCTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATcc > 1:748747/1‑71 (MQ=255)
aCTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATc < 1:3142692/70‑1 (MQ=255)
cTACAAATAAAAGGTGTTCACGTGCAGAAGTGTATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATccc < 1:3756686/71‑1 (MQ=255)
cTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGa < 1:3120169/41‑1 (MQ=255)
cTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGa < 1:3743763/41‑1 (MQ=255)
cTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGa < 1:3361380/41‑1 (MQ=255)
aCAAATAAAAGGTGTTCACGTGCAGAAGTGTATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATCCCg > 1:2469902/1‑70 (MQ=255)
aaaTAAAAGGTGTTCACGTGCAGAAGTGTATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATCCCGGt > 1:2024576/1‑70 (MQ=255)
aaTAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATCCCGGTGa > 1:2911130/1‑71 (MQ=255)
aTAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGTTattagc < 1:958850/53‑1 (MQ=255)
aTAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATccc > 1:124702/1‑65 (MQ=255)
aTAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATcc > 1:16737/1‑64 (MQ=255)
aaaaGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCt > 1:770056/1‑42 (MQ=255)
aaaaGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCt > 1:3264177/1‑42 (MQ=255)
aaaaGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCt > 1:316732/1‑42 (MQ=255)
aaaGGTGTTCACGTGCAGAAGTGTATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATCCCGGTGATtct < 1:1133939/71‑1 (MQ=255)
aGGTGTTCACGTGCAGAAGTGTATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATCCCGGTGATtctc > 1:2553509/1‑70 (MQ=255)
aGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATccc > 1:1149524/1‑60 (MQ=255)
aGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATccc > 1:3846161/1‑60 (MQ=255)
tgtTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATCCCGGTGATTCTcgcg > 1:3492708/1‑70 (MQ=255)
tCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGttat > 1:1442973/1‑38 (MQ=255)
tCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATCCCGGTGATTCTCGCGCaa > 1:1624806/1‑70 (MQ=255)
gTGCAGAAGTATATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATCCCGGTGATTCTCGCGCAAATCGc > 1:884630/1‑71 (MQ=255)
gCAGAAGTATATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATCCCGGTGATTCTCGCGCAAATCGcc > 1:274410/1‑70 (MQ=255)
cAGAAGTATATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATCCCGGTGATTCTCGCGCAAATCGccc > 1:3490051/1‑70 (MQ=255)
aaGTATATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATCCCGGTGATTCTCGCGCAAATCGc > 1:270310/1‑65 (MQ=255)
aaGTATATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATCCCGGTGATTCTCGCGCAAATCGCCCaaa > 1:3139054/1‑70 (MQ=255)
tataTCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATCCCGGTGAtt < 1:2100105/48‑1 (MQ=255)
atatCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATCCCGGTGATTCTCGCGCAAATCGCCCAAACTGc > 1:1561611/1‑70 (MQ=255)
|
GCTGCCCATTCAGGCGGCTTTTTAGTCTCTCATATAACTACAAATAAAAGGTGTTCACGTGCAGAAGTATATCAGTGAAGCGCGTCTGTTATTAGCATTAGCAATCCCGGTGATTCTCGCGCAAATCGCCCAAACTGC > minE/1071090‑1071227
|
| 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
