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 |
1,591,621 |
G→A |
37.1% |
intergenic (+80/+109) |
yfeS → / ← cysM |
conserved hypothetical protein/cysteine synthase B |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,591,621 | 0 | G | A | 37.1%
| 53.9
/ 86.7
| 89 | intergenic (+80/+109) | yfeS/cysM | conserved hypothetical protein/cysteine synthase B |
| Reads supporting (aligned to +/- strand): ref base G (24/32); new base A (19/14); total (43/46) |
| Fisher's exact test for biased strand distribution p-value = 1.96e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TTGTCGGCAGCAACAACTGTTAAAAAAGTGCGCTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCTTGTAGGCCTGATAAGCGTAGCGCATCA > minE/1591551‑1591687
|
ttGTCGGCAGCAACAACTGTTAAAAAAGTGCGCTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATCCgg > 1:3899039/1‑71 (MQ=255)
tCGGCAGCAACAACTGTTAAAAAAGTGCGCTTTTTTTATGCCGGATGCGGCGTAAACGCCTTATCCGGCCt < 1:1372906/71‑1 (MQ=255)
gcctgataagacgcgttaagcgtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCt > 1:1841386‑M1/42‑71 (MQ=255)
cctgataagacgcgttaagcgtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTa < 1:2784971‑M1/31‑1 (MQ=255)
ctgataagacgcggcaagcgtcgcatcaggcgttgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTa < 1:2708781‑M1/31‑1 (MQ=255)
tgataagacgcgttaagcgtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTAc < 1:1576870‑M1/32‑1 (MQ=255)
tgataagacgcgttaagcgtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTAc < 1:1235923‑M1/32‑1 (MQ=255)
tgataagacgcggcaagcgtcgcatcaggcgttgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTAc < 1:2287383‑M1/32‑1 (MQ=255)
gcagcaACAACTGTTAAAAAAGTGCGCTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATCCGGc > 1:2064764/1‑66 (MQ=255)
gataagacgcgttaagcgtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACa < 1:3765823‑M1/33‑1 (MQ=255)
ataagacgcggcaagcgtcgcatcaggcattgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTACaa < 1:2019613‑M1/34‑1 (MQ=255)
gcaACAACTGTTAAAAAAGTGCGCTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACaaaa < 1:3877167/71‑1 (MQ=255)
agacgcggcaagcgtcgcatcaggcgttgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTACAAAAt > 1:1342290‑M1/34‑70 (MQ=255)
gacgcgttaagcgtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACAAAATc > 1:1099010‑M1/33‑70 (MQ=255)
gacgcgttaagcgtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACAAAATc > 1:2433217‑M1/33‑70 (MQ=255)
caacTGTTAAAAAAGTGCGCTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGt < 1:3351350/71‑1 (MQ=255)
acgcgttaagcgtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACAAAatcac > 1:1139882‑M1/32‑69 (MQ=255)
aacTGTTAAAAAAGTGCGCTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTg > 1:3868984/1‑71 (MQ=255)
aacTGTTAAAAAAGTGCGCTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTg < 1:3597778/71‑1 (MQ=255)
aacTGTTAAAAAAGTGCGCTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTg > 1:2877013/1‑71 (MQ=255)
gcgttaagcgtcgcatccggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACAAaatcacg < 1:3529163‑M1/41‑4 (MQ=255)
cTGTTAAAAAAGTGCGCTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGc > 1:1170133/1‑70 (MQ=255)
ttAAAAAAGTGCGCTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGCTaa < 1:2719/70‑1 (MQ=255)
taagcgtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACAAAATCACGCtaaa < 1:873801‑M1/46‑2 (MQ=255)
aagcgtcgcatcaggcgttgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTACAAAATCACGctaaat > 1:2856372‑M1/25‑69 (MQ=255)
aagcgtcgcatcaggcgttgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTACAAAATCACGctaaat < 1:3521988‑M1/47‑3 (MQ=255)
aagcgtcgcatcaggcgttgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTACAAAATCACGctaaat > 1:1298180‑M1/25‑69 (MQ=255)
aagcgtcgcatcaggcgttgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTACAAAATCACGctaaat > 1:2248164‑M1/25‑69 (MQ=255)
aagcgtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACAAAATCACGctaaat < 1:3225617‑M1/47‑3 (MQ=255)
agcgtcgcatcaggcgttgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTACAAAATCACgctaaatc > 1:351329‑M1/24‑68 (MQ=255)
agcgtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACAAAATCACGctaaat > 1:541617‑M1/24‑68 (MQ=255)
agcgtcgcatcaggcattgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTACAAAATCACgctaaatc > 1:800747‑M1/24‑68 (MQ=255)
cgtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACaa > 1:969151‑M1/22‑55 (MQ=255)
aaaaGTGCGCTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCaa > 1:312931/1‑71 (MQ=35)
gtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACAAAATCACGCTAAAtcagg > 1:279019‑M1/21‑69 (MQ=255)
tcgcatcaggcgttgatgtCGGATGCGGCATTAACGCCTTATCCGACCTACAAAATCACGCTAAatcaggc > 1:1712698‑M1/20‑68 (MQ=255)
tGCGCTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTc < 1:120748/64‑1 (MQ=35)
catcaggcattgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTACAAAATCACGCTAAATCa > 1:2714985‑M1/17‑65 (MQ=255)
atcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACAAAATCACGCtaaa > 1:189275‑M1/16‑60 (MQ=255)
gcTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCAATATATTGc < 1:2956338/71‑1 (MQ=39)
caggcattgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTACAAAATCACGCTAAATcag < 1:573430‑M1/50‑2 (MQ=255)
caggcattgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTACAAAATCACGCTAAATcag < 1:1515700‑M1/50‑2 (MQ=255)
caggcattgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTACAAAATCACGCTAAATcag < 1:3023827‑M1/50‑2 (MQ=255)
ttGTTTATGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCaa < 1:1793520/60‑1 (MQ=35)
tGTTTATGCCGGATGCGGCGTTAACGCCTTATCCGGCCTACAAAATCGTGCAAATTCAATACATTGCAGaa > 1:178762/1‑71 (MQ=11)
gttgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTACa > 1:2163208‑M1/9‑41 (MQ=255)
gTTTATGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGaaa > 1:3629449/1‑71 (MQ=255)
ttgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTACAAAATCACGctaaat > 1:421014‑M1/8‑52 (MQ=255)
ttATGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAAcc > 1:2415884/1‑71 (MQ=255)
tATGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAAcc < 1:2674011/70‑1 (MQ=255)
atgtCGGATGCGGCGTAAACGCCTTATCCGACCTACAAAATCACGCTAAATCa > 1:2038921‑M1/5‑53 (MQ=255)
tGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCTTg < 1:3094598/71‑1 (MQ=255)
gCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCTTg > 1:368045/1‑70 (MQ=255)
gATGCGGCGTTAACGCCTTATCCGGCCTACAAAATCGTGCAAATTCAATACATTGCAGaatt > 1:7191/1‑60 (MQ=11)
gATGCGGCGTTAACGCCTTATCCGGCCTACAAAATAGTGCAAATTCAATACATTGCAGaatt > 1:521196/1‑60 (MQ=11)
gATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCTTGTAgg > 1:914177/1‑70 (MQ=255)
tGCGGCGTTAACGCCTTATCCGGCCTACAAAATCGTGCAAATTCAATACATTGCAGaa > 1:2794054/1‑58 (MQ=11)
tGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCTTGTa > 1:3191892/1‑66 (MQ=255)
cggcgTAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCTTGTAGGCCTGa > 1:1079344/1‑71 (MQ=255)
ggcgTAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCTTGTAGGCCTGAt < 1:1043999/71‑1 (MQ=255)
ggcgTAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCTTGTAGGCCTGAt < 1:3787615/71‑1 (MQ=255)
ggcgTAAACGCCTTATCCGGCCTACAAAATCGTGATAATTCAATATATTGCAGAAACCTTGTAGGCCTGa > 1:1335392/1‑70 (MQ=255)
cgTAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCtt < 1:902035/58‑1 (MQ=255)
tAAACGCCTTATCCGGGCTACAAAATCGTGCTAATTCAATATATTGCAGAAAcc < 1:194189/54‑1 (MQ=255)
tAAACGCCTTATCCGGCCTACAAATTCTTCCAAATTCAATATATTGCAGAAATCATGTAGGc < 1:3232102/62‑1 (MQ=11)
tAAACGCCTTATCCGGCCTACAAATTCTTCCAAATTCAATATATTGCAGAAATCATGTAGGCCTGATAAGc < 1:1552453/71‑1 (MQ=11)
tAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCAata < 1:1871677/41‑1 (MQ=255)
tAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCAATATATTg < 1:1078776/46‑1 (MQ=255)
tAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAAcc < 1:822651/54‑1 (MQ=255)
tAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCttc < 1:3376450/57‑2 (MQ=255)
aaCGCCTTATCCGGCCTACAAAATCGTGCTAATTc > 1:2590870/1‑35 (MQ=40)
aCGCCTTATCCGGCCTACAAAATCGTGCTAATTCAATATATTGc < 1:1044093/44‑1 (MQ=255)
aCGCCTTATCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCTTGTAGGCCTGATAAGCGTa < 1:767442/71‑1 (MQ=255)
cGCCTTATCCGGCCTACAAATTCTTCCAAATTCAATATATTGTAGAAATCATGTAGGCCTGATAAGCGTAg < 1:885947/71‑1 (MQ=11)
ttATCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGa < 1:3654295/42‑1 (MQ=255)
tATCCGGCCTACAAATTCTTCCAAATTCAATATATTGCAGAAATCATGTAGGCCTGATAAGCGTAGCGCAt > 1:1982966/1‑71 (MQ=11)
tATCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCTTGTa > 1:2455354/1‑50 (MQ=255)
tATCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCTTGTAGGCCTGATAAGCGTAGCGCAt > 1:3651780/1‑71 (MQ=255)
tATCCGGCCTACAAAATCGTGCTAATTCAATATATT‑CAGAAACCCTGt < 1:2019118/48‑1 (MQ=17)
aTCCGGCCTACAAATTCTTCCAAATTCAATATATTGCAGAAATCATGTAGGCCTGATAAGCGTAGCGCAt > 1:3311919/1‑70 (MQ=11)
aTCCGGCCTACAAATTCTTCCAAATTCAATATATTGCAGAAATCATGTAGGCCTGATAAGCGTAGCGCAt < 1:3337832/70‑1 (MQ=11)
aTCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCTTGTAGGCCTGATAAGCGt < 1:796068/63‑1 (MQ=255)
aTCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCTTGTAGGCCTGATAAGCGTAGCGCa < 1:902692/69‑1 (MQ=255)
aTCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCTTGTAGGCCTGATAAGCGTAGCGCAt < 1:1139618/70‑1 (MQ=255)
aTCCGGCCTACAAAATCGTGCAAATTCAATACATTGCAGa < 1:3096282/40‑1 (MQ=11)
tacGGCCTACAAAATCGTGCAAATTCAATACATTGCAGaa > 1:1756942/3‑40 (MQ=11)
tCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCTTGTAGGCCTGATAAGCGTAGCGCAt > 1:3479931/1‑69 (MQ=255)
tCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCTTGTAGGCCTGATAAGCGTAGCGCATCa < 1:2009982/71‑1 (MQ=255)
tCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCTTGTAGGCCTGATAAGCGTAGCGCATCa < 1:2904689/71‑1 (MQ=255)
tCCGGCCTACAAAATCGTGCAAATTCAATACATTGCAGaa > 1:3711414/1‑40 (MQ=11)
|
TTGTCGGCAGCAACAACTGTTAAAAAAGTGCGCTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCTTGTAGGCCTGATAAGCGTAGCGCATCA > minE/1591551‑1591687
|
| 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
