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 F1 I0 R1
|
2892 |
75.3 |
5698161 |
66.1% |
3766484 |
59.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,591,621 |
G→A |
48.9% |
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 | 48.9%
| 6.5
/ 177.0
| 133 | intergenic (+80/+109) | yfeS/cysM | conserved hypothetical protein/cysteine synthase B |
| Reads supporting (aligned to +/- strand): ref base G (36/32); new base A (35/30); total (71/62) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
Only 100 of 133 total aligned reads displayed.
TGTCGGCAGCAACAACTGTTAAAAAAGTGCGCTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCTTGTAGGCCTGATAAGCGTAGCGCATCA > minE/1591552‑1591687
|
ggCAGCAACAACTGTTAAAAAAGTGCGCTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATCCGGCCTAc < 1:4785641/71‑1 (MQ=255)
ctgataagacgcgttaagcgtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTa < 1:41480‑M1/31‑1 (MQ=255)
ctgataagacgcggcaagcgtcgcatcaggcgttgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTa < 1:2746008‑M1/31‑1 (MQ=255)
ctgataagacgcggcaagcgtcgcatcaggcattgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTAc > 1:2185675‑M1/40‑71 (MQ=255)
tgataagacgcggcaagcgtcgcatcaggcgttgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTAc < 1:2792159‑M1/32‑1 (MQ=255)
tgataagacgcggcaagcgtcgcatcaggcattgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTAc > 1:4427802‑M1/39‑70 (MQ=255)
gataagacgcgttaagcgtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACa < 1:1148611‑M1/33‑1 (MQ=255)
gataagacgcgttaagcgtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACa < 1:2192035‑M1/33‑1 (MQ=255)
gataagacgcggcaagcgtcgcatcaggcattgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTACa < 1:653082‑M1/33‑1 (MQ=255)
ctgataagacggcaagcgtcgcatcaggcgttgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTACa < 1:1112508‑M1/33‑1 (MQ=255)
ataagacgcgttaagcgtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACaaa > 1:224601‑M1/37‑71 (MQ=255)
ataagacgcgttaagcgtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACaa < 1:1293882‑M1/34‑1 (MQ=255)
ataagacgcggcaagcgtcgcatcaggcattgatgtCGGATGCGGCGTAAACGCCTTGTCCGACCTACa > 1:1598038‑M1/37‑69 (MQ=255)
ataagacgcggcaagcgtcgcatcaggcattgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTACaa < 1:4663289‑M1/34‑1 (MQ=255)
ataagacgcggcaagcgtcgcatcaggcattgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTACa > 1:3133308‑M1/37‑69 (MQ=255)
ataagacgcggcaagcgtcgcatcaggcattgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTACa > 1:3968541‑M1/37‑69 (MQ=255)
taagacgcgttaagcgtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACaaaa > 1:2930468‑M1/36‑71 (MQ=255)
aagacgcgttaagcgtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACaaaa < 1:3316933‑M1/36‑1 (MQ=255)
aagacgcgttaagcgtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACAAAAt < 1:3698561‑M1/37‑1 (MQ=255)
aagacgcgttaagcgtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACAAAAt < 1:1652032‑M1/37‑1 (MQ=255)
aagacgcggcaagcgtcgcatcaggcgttgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTACAAAAt < 1:5355782‑M1/37‑1 (MQ=255)
aagacgcggcaagcgtcgcatcaggcattgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTACAAAAt < 1:4347264‑M1/37‑1 (MQ=255)
aagacgcggcaagcgtcgcatcaggcattgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTACAAAAt < 1:701828‑M1/37‑1 (MQ=255)
aacaacTGTTAAAAAAGTGCGCTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAATc > 1:4471248/1‑71 (MQ=255)
aacaacTGTTAAAAAAGTGCGCTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAATc > 1:1993540/1‑71 (MQ=255)
gacgcgttaagcgtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACAAAAtca < 1:2919820‑M1/39‑2 (MQ=255)
gacgcgttaagcgtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACAAAAtca > 1:1472609‑M1/33‑70 (MQ=255)
gacgcggcaagcgtcgcatcaggcattgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTACAAAAtca < 1:2232205‑M1/39‑2 (MQ=255)
ttaagcgtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACaaaa > 1:670278‑M1/27‑62 (MQ=255)
ttaagcgtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACAAAATCACGCTaa > 1:4081563‑M1/27‑71 (MQ=255)
gTTAAAAAAGTGCGCTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGCTaa > 1:3292707/1‑71 (MQ=255)
ttAAAAAAGTGCGCTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAt < 1:2143460/62‑1 (MQ=39)
ttAAAAAAGTGCGCTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGCTaa < 1:2770226/70‑1 (MQ=255)
ttAAAAAAGTGCGCTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGCTAAt > 1:4599416/1‑71 (MQ=255)
caagcgtcgcatcaggcgttgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTACAAAATCACGCtaaa > 1:209120‑M1/26‑70 (MQ=255)
caagcgtcgcatcaggcattgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTACAAAATCACGCtaaa < 1:4873076‑M1/46‑2 (MQ=255)
tAAAAAAGTGCGCTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGCTAAtt > 1:2474244/1‑71 (MQ=40)
tAAAAAAGTGCGCTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGCTAAtt > 1:2591310/1‑71 (MQ=40)
aagcgtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACAAAATCACGCtaaa > 1:2920001‑M1/25‑69 (MQ=255)
aagcgtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACAAAATCACGCtaaa > 1:3968611‑M1/25‑69 (MQ=255)
aagcgtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACAAAATCACGCtaaa > 1:2446982‑M1/25‑69 (MQ=255)
agcgtcgcatcaggcgttgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTACAAAATCACGCtaaa < 1:2228188‑M1/46‑2 (MQ=255)
agcgtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACAAAATCACgctaaatc > 1:4238166‑M1/24‑68 (MQ=255)
agcgtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACAAAATCACGctaaat < 1:2089850‑M1/47‑3 (MQ=255)
agcgtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACAAAATCACGctaaat < 1:2082957‑M1/47‑3 (MQ=255)
gcgtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACAAAATCACGCTAAATCa > 1:655331‑M1/23‑71 (MQ=255)
gcgtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACAAAATCACGCTAAATCa > 1:4811518‑M1/23‑71 (MQ=255)
aaaaaGTGCGCTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCa < 1:2427778/71‑1 (MQ=38)
aaaaaGTGCGCTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCa < 1:3609408/71‑1 (MQ=38)
cgtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACAAAATCACGCTAAATcag > 1:5546817‑M1/22‑70 (MQ=255)
cgtcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACAAAATCACGCTAAATcag > 1:187267‑M1/22‑70 (MQ=255)
cgtcgcatcaggcattgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTACAAAATCACGCTAAATcag < 1:519117‑M1/50‑2 (MQ=255)
gtcgcatcaggcattgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTACAAAATCACGCTAAAtcagg < 1:1299606‑M1/51‑3 (MQ=255)
tcgcatcaggcgttgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTACAAAATCACGctaaat > 1:3384337‑M1/20‑64 (MQ=255)
tcgcatcaggcgttgatgtCGGATGCGGCGTAAACGCCTTATCCGACCTACAAAATCACGCTAAatcaggc > 1:3504489‑M1/20‑68 (MQ=255)
tcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACGTACAAAATCACGCTAAatcaggc < 1:3454996‑M1/52‑4 (MQ=255)
tcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACAAAATCACGCtaaa > 1:462860‑M1/20‑64 (MQ=255)
tcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACAAAATCACGCTAAatcaggc > 1:4696563‑M1/20‑68 (MQ=255)
tcgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACAAAATCACGCTAAatcagga > 1:1080715‑M1/20‑68 (MQ=255)
cgcatcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACAAAATCACGctaaat > 1:754138‑M1/19‑63 (MQ=255)
gTGCGCTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCAatata < 1:3988206/71‑1 (MQ=39)
tGCGCTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCAatatat < 1:2293409/71‑1 (MQ=39)
catcaggcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACAAAATCACGCTAAATCa < 1:3876066‑M1/49‑1 (MQ=255)
gcgcTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCAATATAtt > 1:1995596/1‑71 (MQ=39)
gcgttgatgtCGGATGCGGCATAAACGCCTTATCCGACCTACAAAATCACGCTAAATcag > 1:3826488‑M1/11‑59 (MQ=255)
gTTTATGCCGGATTCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTc < 1:3353321/56‑1 (MQ=255)
gTTTATGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTc < 1:2608126/56‑1 (MQ=35)
tATGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCt > 1:2820729/1‑71 (MQ=255)
tATGCCAGATGCGGCGTAAACGCCTTATCCGGCCTACAAATTCTTCCAAATTCAATATATTGCAGaaatca > 1:305977/1‑68 (MQ=11)
tATGCCAGATGCGGCGTAAACGCCTTATCCGGCCTACAAATTCTTCCAAATTCAATATATTGCAGaaatc < 1:4377490/70‑3 (MQ=11)
gatgtCGGATGCGGCGTAAACGCCTTATCCGACCTACAAAATCACGCTAAATcag < 1:228643‑M1/50‑2 (MQ=255)
gatgtCGGATGCGGCGTAAACGCCTTATCCGACCTACAAAATCACGCTAAATcag < 1:4317859‑M1/50‑2 (MQ=255)
gATGCGGCGTAAACGCCTTATCCGGCCTACAAATTCTTCCAAATTCAATATATTGCAGAAATCATGTAGGc > 1:2859712/1‑71 (MQ=11)
gATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGCt < 1:321210/41‑1 (MQ=32)
gATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCTTGTAgg > 1:161687/1‑70 (MQ=255)
gATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCTTGTAGGc > 1:3033291/1‑71 (MQ=255)
gATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCTTGTAGGc < 1:487477/71‑1 (MQ=255)
aTGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCAATATATTGc > 1:1538705/1‑55 (MQ=255)
tGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCTTGTAGGCCt < 1:4258487/71‑1 (MQ=255)
gcggcgTAAACGCCTTATCCGGCCTACAAATTCTTCCAAATTCAATATATTGCAGAAATCATGTa > 1:4840718/1‑65 (MQ=11)
cggcgTAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAAc > 1:5689638/1‑58 (MQ=255)
gTAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCTTGTAGGCCTGATAAg > 1:1172367/1‑71 (MQ=255)
tAAACGCCTTATCCGGCCTACAAATTCTTCCAAATTCAATATATTGCAGaaat < 1:5390949/53‑2 (MQ=11)
tAAACGCCTTATCCGGCCTACAAATTCTTCCAAATTCAATATATTGCAGaaat < 1:3676233/53‑2 (MQ=11)
tAAACGCCTTATCCGGCCTACAAATTCTTCCAAATTCAATATATTGCAGAAATCATGTAGGCCt < 1:3975788/64‑1 (MQ=11)
tAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCa < 1:750435/38‑1 (MQ=40)
tAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCTTGTAGGCCTGATAAg < 1:579092/70‑1 (MQ=255)
aaCGCCTTATCCGGCCTACAAAATCGTGCTAATTCaa > 1:2654557/1‑37 (MQ=40)
aaCGCCTTATCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCTTGTAGGCCTGATAAGCg > 1:3221703/1‑70 (MQ=255)
aaCGCCTTATCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCTTGTAGGCCTGATAAGCg > 1:3680747/1‑70 (MQ=255)
aaCGCCTTATCCGGCCTACAAAATCGTGCAAATTCAATACATTGCAg > 1:2013041/1‑47 (MQ=11)
aaCGCCTTATCCGGCCTACAAAATCGTGCAAATTCAATACATTGCAg > 1:2702139/1‑47 (MQ=11)
gCCTTATCCGGCCTACAAAATCGTGCAAATTCAATACATTGCAGaatt < 1:4338094/48‑3 (MQ=11)
cTTATCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCTTGTAGGCCTGATAAGCGTAgcg > 1:234498/1‑70 (MQ=255)
attATCCGGCCTACAAAATCGTGCTAATTCAATATATTGGAGAAACCTTg < 1:4279856/49‑1 (MQ=255)
tATCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCTTGTa > 1:3572312/1‑50 (MQ=255)
tATCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCTTGTAGGCCTGATAAGCGTAGCGCAt > 1:1725128/1‑71 (MQ=255)
tATCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCTTGTAGGCCTGATAAGCGTAGCGCAt > 1:1676644/1‑71 (MQ=255)
aTCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCtt < 1:136632/46‑1 (MQ=255)
aTCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCTTGTAGGCCTGATAAGCGTAGCGCAt > 1:1384668/1‑70 (MQ=255)
|
TGTCGGCAGCAACAACTGTTAAAAAAGTGCGCTTTGTTTATGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAATCGTGCTAATTCAATATATTGCAGAAACCTTGTAGGCCTGATAAGCGTAGCGCATCA > minE/1591552‑1591687
|
| 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
