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 F3 I0 R1
|
560 |
56.4 |
4650532 |
94.9% |
4413354 |
59.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
4,361,585 |
C→T |
35.8% |
P571P (CCG→CCA) |
cadA ← |
lysine decarboxylase 1 |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 4,361,585 | 0 | C | T | 35.8%
| 82.4
/ 80.7
| 81 | P571P (CCG→CCA) | cadA | lysine decarboxylase 1 |
| Reads supporting (aligned to +/- strand): ref base C (21/31); new base T (16/13); total (37/44) |
| Fisher's exact test for biased strand distribution p-value = 2.48e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.83e-01 |
GTGGATATTCTGAGCCAGTTCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAAGTCAGTCAGAGCACGCAGC > W3110S.gb/4361516‑4361651
|
gtgGATATTCTGAGCCAGTTCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGAc < 1:1298913/70‑1 (MQ=255)
atatTCTGAGCCAGTTCCTGAACACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGgcag < 1:1274892/71‑1 (MQ=255)
ttCTGAGCCAGTTCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGATGGCAGCAt < 1:1051181/71‑1 (MQ=255)
ttCTGAGCCAGTTCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGATGGCAGCAt < 1:2069289/71‑1 (MQ=255)
ttCTGAGCCAGTTCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGATGGCAGCAt > 1:880487/1‑71 (MQ=255)
cTGAGCCAGTTCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGt > 1:1557609/1‑71 (MQ=255)
aGCCAGTTCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGtttt > 1:3140495/1‑71 (MQ=255)
aGCCAGTTCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGttt < 1:1049280/70‑1 (MQ=255)
ccAGTTCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGATGGCAGCATGTTTTTc < 1:1843558/71‑1 (MQ=255)
ccAGTTCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGttttt < 1:362470/70‑1 (MQ=255)
cAGTTCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGATGGCAGCATGTTTTTca > 1:3100891/1‑71 (MQ=255)
gTTCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTca < 1:1594592/69‑1 (MQ=255)
tCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGATGGCAGCATGttttt > 1:2226242/1‑65 (MQ=255)
tCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTca > 1:1641579/1‑67 (MQ=255)
cTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGgcagca < 1:4432676/56‑1 (MQ=255)
cTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGgcagca < 1:630703/56‑1 (MQ=255)
cTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGc < 1:4267598/70‑1 (MQ=255)
gAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGATGGCAGCATGtt > 1:1378172/1‑58 (MQ=255)
gAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGgcagca < 1:60448/54‑1 (MQ=255)
aaTACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGt > 1:1980052/1‑71 (MQ=255)
aTACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGATGGCAGCATGTTTTTca > 1:2310410/1‑61 (MQ=255)
aTACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGtt < 1:1435167/71‑1 (MQ=255)
cATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGgcagca > 1:3827447/1‑47 (MQ=255)
cATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAg > 1:31195/1‑63 (MQ=255)
cATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGt > 1:1068270/1‑71 (MQ=255)
tGTTTTCATAGAATTCAGGATCTTCACGATACAGAGATGGCAGCATGttt < 1:1476549/50‑1 (MQ=255)
tGTTTTCATAGAATTCAGGATCTTCACGATACAGAGATGGCAGCATGttt < 1:2842401/50‑1 (MQ=255)
tGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAg < 1:3308826/67‑1 (MQ=255)
tGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCg < 1:273661/71‑1 (MQ=255)
tGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCg < 1:446700/71‑1 (MQ=255)
tGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCg < 1:4110158/71‑1 (MQ=255)
gTTTTCATAGAATTCAGGATCTTCACGATACAGAGATGGCAGCATGttt < 1:2847864/49‑1 (MQ=255)
gTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGttttt < 1:3045763/51‑1 (MQ=255)
gTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCg > 1:1151517/1‑70 (MQ=255)
ttttCATAGAATTCAGGATCTTCACGATACAGAGATGGCAGCATGTTTTTCACACGCAGGTTCAg < 1:4135637/65‑1 (MQ=255)
ttttCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGt > 1:3757809/1‑46 (MQ=255)
ttttCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTcac < 1:641888/53‑1 (MQ=255)
ttttCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGaa > 1:3363486/1‑71 (MQ=255)
ttttCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGaa > 1:3255720/1‑71 (MQ=255)
ttttCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGaa > 1:3181020/1‑71 (MQ=255)
ttttAATAGAATTCAGGATCTTCACGATACAGAGATGGCAGCATGTTTTTCACACGCa > 1:2634383/1‑58 (MQ=39)
ttCATAGAATTCAGGATCTTCACGATACAGAGATGGCAGCATGttt > 1:3529962/1‑46 (MQ=255)
tCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACg < 1:4291839/70‑1 (MQ=255)
cATAGAATTCAGGATCTTCACGATACAGAGATGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCa > 1:1660187/1‑71 (MQ=255)
tAGAATTCAGGATCTTCACGATACAGAGATGGCAGCATGtt < 1:3326784/41‑1 (MQ=255)
tAGAATTCAGGATCTTCACGATACAGAGATGGCAGCATGtt < 1:3865300/41‑1 (MQ=255)
aGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGt > 1:4210704/1‑71 (MQ=255)
aaTTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCa < 1:784360/49‑1 (MQ=255)
ttCAGGATCTTCACGATACAGAGATGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGa < 1:688595/59‑1 (MQ=255)
ttCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAg > 1:443783/1‑48 (MQ=255)
ttCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTaa < 1:3736698/71‑1 (MQ=255)
cAGGATCTTCACGATACAGAGATGGCAGCATGTTTTTCacac > 1:42730/1‑42 (MQ=255)
cAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAag > 1:2231150/1‑71 (MQ=255)
cAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAag > 1:4116003/1‑71 (MQ=255)
aGGATCTTCACGATACAGAGACGGCAGCATGttttt < 1:253420/36‑1 (MQ=255)
aTCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTa < 1:4382093/64‑1 (MQ=255)
tCTTCACGATACAGAGATGGCAGCATGTTTTTCacac > 1:1696099/1‑37 (MQ=255)
tCTTCACGATACAGAGATGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAagtcagt > 1:957887/1‑71 (MQ=255)
cTTCACGATACAGAGATGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGaa > 1:2845335/1‑52 (MQ=255)
cTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCa < 1:804359/56‑1 (MQ=255)
cTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTaaa > 1:3167975/1‑64 (MQ=255)
ttCACTATACAGAGACGGCAGCATGTTTTTCACACGCAGGt < 1:4632480/41‑1 (MQ=255)
ttCACGATACAGAGATGGCAGCATGTTTTTCACACGCAGGTTc > 1:2519472/1‑43 (MQ=255)
ttCACGATACAGAGATGGCAGCATGTTTTTCACACGCAGGTTc > 1:3850277/1‑43 (MQ=255)
ttCACGATACAGAGATGGCAACATGTTTTTCACACGCAGGTTc > 1:4442965/1‑43 (MQ=38)
tCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAagtcagt > 1:3537584/1‑68 (MQ=255)
cACGATACAGAGATGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAAgtcagtca > 1:3641168/1‑69 (MQ=255)
cACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACg > 1:4092250/1‑51 (MQ=255)
cACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACg > 1:4044436/1‑51 (MQ=255)
cACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAagtcagt < 1:3323914/67‑1 (MQ=255)
cACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAag > 1:41067/1‑62 (MQ=255)
cACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAAgtcagtca < 1:101141/69‑1 (MQ=255)
aCGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAAGTCAGTCagag < 1:2420750/71‑1 (MQ=255)
aCGATAAAGAGATGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAAGTCAGTCaga < 1:4300127/70‑1 (MQ=255)
cGATACAGAGACGGCAGCATGTTTTTCACACGCAGGtt < 1:1808541/38‑1 (MQ=255)
gATACAGAGACGGCAGCATGTTTTTCACACGCAGGtt < 1:1093980/37‑1 (MQ=255)
tACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTa < 1:3153361/54‑1 (MQ=255)
gagaTGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAAGTCAGTCAGAGCACgcagc < 1:2487682/71‑1 (MQ=255)
gagaCGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAAGTCAGTCAGAGCACgcagc < 1:516322/71‑1 (MQ=255)
gagaCGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAAGTCAGTCAGAGCACgcagc < 1:2941970/71‑1 (MQ=255)
agaTGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTa < 1:1116564/49‑1 (MQ=255)
gaCGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGa < 1:3632643/37‑1 (MQ=255)
|
GTGGATATTCTGAGCCAGTTCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAAGTCAGTCAGAGCACGCAGC > W3110S.gb/4361516‑4361651
|
| 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
