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 |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
418,848 |
G→A |
59.2% |
E149E (GAG→GAA) |
ubiF → |
2‑octaprenyl‑3‑methyl‑6‑methoxy‑1,4‑benzoquinol oxygenase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 418,848 | 0 | G | A | 59.2%
| 24.3
/ 50.0
| 71 | E149E (GAG→GAA) | ubiF | 2‑octaprenyl‑3‑methyl‑6‑methoxy‑1,4‑benzoquinol oxygenase |
| Reads supporting (aligned to +/- strand): ref base G (22/7); new base A (8/34); total (30/41) |
| Fisher's exact test for biased strand distribution p-value = 2.29e-06 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.18e-01 |
GTGTGCCAGGCTCGCTGATTGCGCTGCATCGCCATGATGATCTTCAGGAGCTGGAGCTGAAAGGCGGTGAAGTGATTCGCGCGAAGCTGGTGATTGGTGCCGACGGCGCAAATTCGCA > minE/418793‑418910
|
gtgtGCCAGGCTCGCTGATTGCGCTGCATCGCCATGATGATCTTCAGGAGCTGGAGCTGAAAGGCGGt < 1:1545202/68‑1 (MQ=255)
gtgtGCCAGGCTCGCTGATTGCGCTGCATCGCCATGATGATCTTCAGGAGCTGGAGCTGAAAGGCGGt < 1:2398002/68‑1 (MQ=255)
ccAGGCTCGCTGATTGCGCTGCATCGCCATGATGATCTTCAGGAGCTGGAGCTGAAAGGCGGTGAAGTg > 1:1911494/1‑69 (MQ=255)
ccAGGCTCGCTGATTGCGCTGCATCGCCATGATGATCTTCAGGAGCTGGAGCTGAAAGGCGGTGAAGTg > 1:1811590/1‑69 (MQ=255)
ccAGGCTCGCTGATTGCGCTGCATCGCCATGATGATCTTCAGGAGCTGGAGCTGAAAGGCGGTGAAGTg > 1:2505494/1‑69 (MQ=255)
ccAGGCTCGCTGATTGCGCTGCATCGCCATGATGATCTTCAGGAGCTGGAGCTGAAAGGCGGTGAAGTg > 1:1512364/1‑69 (MQ=255)
ccAGGCTCGCTGATTGCGCTGCATCGCCATGATGATCTTCAGGAGCTGGAGCTGAAAGGCGGTGAAGTg > 1:980363/1‑69 (MQ=255)
cTCGCTGATTGCGCTGCATCGCCATGATGATCTTCAGGAGCTGGAGCTGAAAGGCGGTGAAGTGATTcg > 1:56166/1‑69 (MQ=255)
cTCGCTGATTGCGCTGCATCGCCATGATGATCTTCAGGAGCTGGAGCTGAAAGGCGGTGAAGTGATTcg > 1:2693694/1‑69 (MQ=255)
cTCGCTGATTGCGCTGCATCGCCATGATGATCTTCAGGAGCTGGAGCTGAAAGGCGGTGAAGTGATTcg > 1:1943667/1‑69 (MQ=255)
cTCGCTGATTGCGCTGCATCGCCATGATGATCTTCAGGAGCTGGAGCTGAAAGGCGGTGAAGTGATTcg > 1:2523600/1‑69 (MQ=255)
cTCGCTGATTGCGCTGCATCGCCATGATGATCTTCAGGAGCTGGAGCTGAAAGGCGGTGAAGTGATTc > 1:614945/1‑68 (MQ=255)
cTCGCTGATTGCGCTGCATCGCCATGATGATCTTCAGGAGCTGGAGCTGAAAGGCGGTGAAGTGATTc > 1:312049/1‑68 (MQ=255)
cTCGCTGATTGCGCTGCATCGCCATGATGATCTTCAGGAGCTGGAGCTGAAAGGCGGTGAAGTGATTc > 1:2922900/1‑68 (MQ=255)
gCTGATTGCGCTGCATCGCCATGATGATCTTCAGGAGCTGGAGCTGAAAGGCGGTGAAGTGATTcgcg > 1:335916/1‑68 (MQ=255)
ctcTGCATCGCCATAATGATCTTCAGGAGCTGGAACTGaa < 1:479292/38‑1 (MQ=37)
cacTGCATCGCCATAATGATCTTCATGAGCTGGAACTGaa < 1:2342064/38‑1 (MQ=25)
cacTGCATCGCCATAATGATCTTCAGGAGCTGGAACTGaa < 1:2188008/38‑1 (MQ=37)
cacTGCATCGCCATAATGATCTTCAGGAGCTGGAACTGaa < 1:2633191/38‑1 (MQ=37)
cacTGCATCGCCATAATGATCTTCAGGAGCTGGAACTGaa < 1:2450042/38‑1 (MQ=37)
cacTGCATCGCCATAATGATCTTCAGGAGCTGGAACTGaa < 1:248450/38‑1 (MQ=37)
cacTGCATCGCCATAATGATCTTCAGGAGCTGGAACTGaa < 1:2459705/38‑1 (MQ=37)
cacTGCATCGCCATAATGATCTTCAGGAGCTGGAACTGaa < 1:2322501/38‑1 (MQ=37)
cacTGCATCGCCATAATGATCTTCAGGAGCTGGAACTGaa < 1:2373467/38‑1 (MQ=37)
cacTGCATCGCCATAATGATCTTCAGGAGCTGGAACTGaa < 1:2675457/38‑1 (MQ=37)
cacTGCATCGCCATAATGATCTTCAGGAGCTGGAACTGaa < 1:2758391/38‑1 (MQ=37)
cacTGCATCGCCATAATGATCTTCAGGAGCTGGAACTGaa < 1:2938048/38‑1 (MQ=37)
cacTGCATCGCCATAATGATCTTCAGGAGCTGGAACTGaa < 1:3187700/38‑1 (MQ=37)
cacTGCATCGCCATAATGATCTTCAGGAGCTGGAACTGaa < 1:3262071/38‑1 (MQ=37)
cacTGCATCGCCATAATGATCTTCAGGAGCTGGAACTGaa < 1:3292803/38‑1 (MQ=37)
cacTGCATCGCCATAATGATCTTCAGGAGCTGGAACTGaa < 1:415377/38‑1 (MQ=37)
cacTGCATCGCCATAATGATCTTCAGGAGCTGGAACTGaa < 1:419343/38‑1 (MQ=37)
cacTGCATCGCCATAATGATCTTCAGGAGCTGGAACTGaa < 1:590279/38‑1 (MQ=37)
cacTGCATCGCCATAATGATCTTCAGGAGCTGGAACTGaa < 1:601412/38‑1 (MQ=37)
cacTGCATCGCCATAATGATCTTCAGGAGCTGGAACTGaa < 1:759506/38‑1 (MQ=37)
cacTGCATCGCCATAATGATCTTCAGGAGCTGGAACTGaa < 1:1229909/38‑1 (MQ=37)
cacTGCATCGCCATAATGATCTTCAGGAGCTGGAACTGaa < 1:1397566/38‑1 (MQ=37)
cacTGCATCGCCATAATGATCTTCAGGAGCTGGAACTGaa < 1:2144588/38‑1 (MQ=37)
cacTGCATCGCCATAATGATCTTCAGGAGCTGGAACTGaa < 1:2143545/38‑1 (MQ=37)
cacTGCATCGCCATAATGATCTTCAGGAGCTGGAACTGaa < 1:214197/38‑1 (MQ=37)
cacTGCATCGCCATAATGATCTTCAGGAGCTGGAACTGaa < 1:1506118/38‑1 (MQ=37)
cacTGCATCGCCATAATGATCTTCAGGAGCTGGAACTGaa < 1:1555435/38‑1 (MQ=37)
cacTGCATCGCCATAATGATCTTCAGGAGCTGGAACTGaa < 1:1718347/38‑1 (MQ=37)
cacTGCATCGCCATAATGATCTTCAGGAGCTGGAACTGaa < 1:2044598/38‑1 (MQ=37)
cacTGCATCGCCATAATGATCTTCAGGAGCTGGAACTGaa < 1:1772537/38‑1 (MQ=37)
cacTGCATCGCCATAATGATCTTCAGGAGCTGGAACTGaa < 1:1984055/38‑1 (MQ=37)
cacTGCATCGCAATAATGATCTTCAGGAGCTGGAACTGaa < 1:2176633/38‑1 (MQ=25)
cacTGCATCGACATAATGATCTTCAGGAGCTGGAACTGaa < 1:1550112/38‑1 (MQ=25)
acTGCATCGCCATAATGATCTTCAGGAGCTGGAACTGaa < 1:1682128/38‑1 (MQ=37)
cTGCATCGCCATGATGATCTTCAGGAGCTGGAGCTGAAAGGCGGTGAAGTGATTCGCGCGAAGCTGGt < 1:455346/68‑1 (MQ=255)
cTGCATCGCCATGATGATCTTCAGGAGCTGGAGCTGAAAGGCGGTGAAGTGATTCGCGCGAAGCTGGt < 1:454825/68‑1 (MQ=255)
cTGCATCGCCATGATGATCTTCAGGAGCTGGAGCTGAAAGGCGGTGAAGTGATTCGCGCGAAGCTGGt < 1:360170/68‑1 (MQ=255)
gCCATGATGATCTTCAGGAGCTGGAGCTGAAAGGCGGTGAAGTGATTCGCGCGAAGCTGGTGATTGGt > 1:473109/1‑68 (MQ=255)
gCCATGATGATCTTCAGGAGCTGGAGCTGAAAGGCGGTGAAGTGATTCGCGCGAAGCTGGTGATTGGTg > 1:2577747/1‑69 (MQ=255)
gCCATGATGATCTTCAGGAGCTGGAGCTGAAAGGCGGTGAAGTGATTCGCGCGAAGCTGGTGATTGGTg > 1:1212384/1‑69 (MQ=255)
gCCATGATGATCTTCAGGAGCTGGAGCTGAAAGGCGGTGAAGTGATTCGCGCGAAGCTGGTGATTGGTg > 1:957811/1‑69 (MQ=255)
gCCATGATGATCTTCAGGAGCTGGAGCTGAAAGGCGGTGAAGTGATTCGCGCGAAGCTGGTGATTGGTg > 1:1419572/1‑69 (MQ=255)
gCCATGATGATCTTCAGGAGCTGGAGCTGAAAGGCGGTGAAGTGATTCGCGCGAAGCTGGTGATTGGTg > 1:2065563/1‑69 (MQ=255)
gCCATGATGATCTTCAGGAGCTGGAGCTGAAAGGCGGTGAAGTGATTCGCGCGAAGCTGGTGATTGGTg > 1:192801/1‑69 (MQ=255)
gCCATGATGATCTTCAGGAGCTGGAGCTGAAAGGCGGTGAAGTGATTCGCGCGAAGCTGGTGATTGGTg > 1:1812324/1‑69 (MQ=255)
atggtCTTCAGGAGCTGGAACTGAAGGGCGGTGAAACGATCCTCGCGaa > 1:214702/1‑49 (MQ=16)
atgatCTTCAGGAGCTGGAACTGAAGGGCGGTGAAACGATCCTCGCGAAGCTGGTGATTGGTGCCGACg > 1:3262903/1‑69 (MQ=255)
atgatCTTCAGGAGCTGGAACTGAAGGGCGGTGAAACGATCCTCGCGAAGCTGGTGATTGGTGCCGACg > 1:795538/1‑69 (MQ=255)
atgatCTTCAGGAGCTGGAACTGAAGGGCGGTGAAACGATCCTCGCGAAGCTGGTGATTGGTGCCGACg > 1:2897647/1‑69 (MQ=255)
atgatCTTCAGGAGCTGGAACTGAAGGGCGGTGAAACGATCCTCGCGAAGCTGGTGATTGGTGCCGACg > 1:369775/1‑69 (MQ=255)
atgatCTTCAGGAGCTGGAACTGAAGGGCGGTGAAACGATCCTCGCGAAGCTGGTGATTGGTGCCGACg > 1:2149064/1‑69 (MQ=255)
atgatCTTCAGGAGCTGGAACTGAAGGGCGGTGAAACGATCCTCGCGAAGCTGGTGATTGGTGCCGACg > 1:663447/1‑69 (MQ=255)
atgatCTTCAGGAGCTGGAACTGAAGGGCGGTGAAACGATACTCGCGAAGCTGGTGATTGGTGCCGAc > 1:3242918/1‑68 (MQ=255)
atCTTCAGGAGCTGGAGCTGAAAGGCGGTGAAGTGATTCGCGCGAAGCTGGTGATTGGTGCCGACGgc > 1:2771690/1‑68 (MQ=255)
cTTCAGGAGCTGGAGCTGAAAGGCGGTGAAGTGATTCGCGCGAAGCTGGt < 1:796284/50‑1 (MQ=255)
ttCAGGAGCTGGAGCTGAAAGGCGGTGAAGTGATTCGCGCGAAGCTGGt < 1:19978/49‑1 (MQ=255)
ggagctggagctGAAAGGCGGTGAAGTGATTCGCGCGAAGCTGGTGATTGGTGCCGACGGCGCa < 1:2032465/64‑1 (MQ=255)
ggagctggagctGAAAGGCGGTGAAGTGATTCGCGCGAAGCTGGTGATTGGTGCCGACGGCGCa < 1:2594330/64‑1 (MQ=255)
ggagctggagctGAAAGGCGGTGAAGTGATTCGCGCGAAGCTGGTGATTGGTGCCGACGGCGCa < 1:1279733/64‑1 (MQ=255)
ggagctggagctGAAAGGCGGTGAAGTGATTCGCGCGAAGCTGGTGATTGGTGCCGACGGCGCa < 1:1758647/64‑1 (MQ=255)
ggagctggagctGAAAGGCGGTGAAGTGATTCGCGCGAAGCTGGTGATTGGTGCCGACGGCGCa < 1:1189371/64‑1 (MQ=255)
ggagctggagctGAAAGGCGGTGAAGTGATTCGCGCGAAGCTGGTGATTGGTGCCGACGGCGCa < 1:2442349/64‑1 (MQ=255)
ggagctggagctGAAAGGCGGTGAAGTGATTCGCGCGAAGCTGGTGATTGGTGCCGACGGCGCAAAtt < 1:1688532/68‑1 (MQ=255)
gctggagctgAAAGGCGGTGAAGTGATTCGCGCGAAGCTGGTGATTGGTGCCGACGGCGCAAATTCGc > 1:1487622/1‑68 (MQ=255)
gctggagctgAAAGGCGGTGAAGTGATTCGCGCGAAGCTGGTGATTGGTGCCGACGGCGCAAATTCGCa > 1:419949/1‑69 (MQ=255)
gctggagctgAAAGGCGGTGAAGTGATTCGCGCGAAGCTGGTGATTGGTGCCGACGGCGCAAATTCGCa > 1:1247551/1‑69 (MQ=255)
gctggagctgAAAGGCGGTGAAGTGATTCGCGCGAAGCTGGTGATTGGTGCCGACGGCGCAAATTCGCa > 1:631879/1‑69 (MQ=255)
gctggagctgAAAGGCGGTGAAGTGATTCGCGCGAAGCTGGTGATTGGTGCCGACGGCGCAAATTCGCa > 1:1450999/1‑69 (MQ=255)
gctggagctgAAAGGCGGTGAAGTGATTCGCGCGAAGCTGGTGATTGGTGCCGACGGCGCAAATTCGCa > 1:784420/1‑69 (MQ=255)
gctggagctgAAAGGCGGTGAAGTGATTCGCGCGAAGCTGGTGATTGGTGCCGACGGCGCAAATTCGCa > 1:3356539/1‑69 (MQ=255)
gctggagctgAAAGGCGGTGAAGTGATTCGCGCGAAGCTGGTGATTGGTGCCGACGGCGCAAATTCGCa > 1:1605574/1‑69 (MQ=255)
gctcgagctgAAAGGCGGAGAAGTGATTCGCGCGAAGCTGGTGATTCGAGCCGACgg > 1:1422457/1‑57 (MQ=255)
|
GTGTGCCAGGCTCGCTGATTGCGCTGCATCGCCATGATGATCTTCAGGAGCTGGAGCTGAAAGGCGGTGAAGTGATTCGCGCGAAGCTGGTGATTGGTGCCGACGGCGCAAATTCGCA > minE/418793‑418910
|
| 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
