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 |
1,386,629 |
C→T |
50.9% |
A311A (GCG→GCA) |
lysP ← |
lysine transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,386,629 | 0 | C | T | 50.9%
| ‑5.3
/ 49.3
| 55 | A311A (GCG→GCA) | lysP | lysine transporter |
| Reads supporting (aligned to +/- strand): ref base C (20/7); new base T (11/17); total (31/24) |
| Fisher's exact test for biased strand distribution p-value = 1.43e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GCGCTTTACCGTCACACGCCAGGGTGTACAGCATACGAGTAGACGCATACATACCGGAGTTACCCGCTGACAGCACCGCCGTCAGAATAACTGCGTTCATCACCGCCGCCGCAGAGAGCAG > minE/1386565‑1386685
|
gcgcTTTACCGTCACACGCCAGGGTGTACAGCATACGAGTAGACGCATACATACCGGAGTTACCCGCt < 1:2616761/68‑1 (MQ=255)
tgtACAGCATACGAGTAGACGCATACATACCGGAGTTACCCGCTGACAGCACCGCCGTCAGAAt > 1:340349/1‑64 (MQ=255)
tgtACAGCATACGAGTAGACGCATACATACCGGAGTTACCCGCTGACAGCACCGCCGTCAGAAt > 1:1440601/1‑64 (MQ=255)
tgtACAGCATACGAGTAGACGCATACATACCGGAGTTACCCGCTGACAGCACCGCCGTCAGAAt > 1:1515281/1‑64 (MQ=255)
tataGCATACGAGTAGACGCATACATACCGGAGTTACCTGCTGACAGCACCGCCGTCAGAATAACTGCg < 1:869288/66‑1 (MQ=255)
tACAGCATACGAGTAGACTCATACATACCGGAGTTACCCGCTGACAGCACCGCCGTCAGAATAACTGCg > 1:944023/1‑69 (MQ=255)
tACAGCATACGAGTAGACGCATACATACCGGAGTTACCTGCTGACAGCACCGCCGTCAGAATAACTGCg < 1:11327/69‑1 (MQ=255)
tACAGCATACGAGTAGACGCATACATACCGGAGTTACCTGCTGACAGCACCGCCGTCAGAATAACTGCg < 1:631562/69‑1 (MQ=255)
tACAGCATACGAGTAGACGCATACATACCGGAGTTACCTGCTGACAGCACCGCCGTCAGAATAACTGCg < 1:579493/69‑1 (MQ=255)
tACAGCATACGAGTAGACGCATACATACCGGAGTTACCTGCTGACAGCACCGCCGTCAGAATAACTGCg < 1:3398644/69‑1 (MQ=255)
tACAGCATACGAGTAGACGCATACATACCGGAGTTACCTGCTGACAGCACCGCCGTCAGAATAACTGCg < 1:3346008/69‑1 (MQ=255)
tACAGCATACGAGTAGACGCATACATACCGGAGTTACCTGCTGACAGCACCGCCGTCAGAATAACTGCg < 1:2772308/69‑1 (MQ=255)
tACAGCATACGAGTAGACGCATACATACCGGAGTTACCTGCTGACAGCACCGCCGTCAGAATAACTGCg < 1:2245024/69‑1 (MQ=255)
tACAGCATACGAGTAGACGCATACATACCGGAGTTACCTGCTGACAGCACCGCCGTCAGAATAACTGCg < 1:1656436/69‑1 (MQ=255)
tACAGCATACGAGTAGACGCATACATACCGGAGTTACCTGCTGACAGCACCGCCGTCAGAATAACTGCg < 1:1612293/69‑1 (MQ=255)
tACAGCATACGAGTAGACGCATACATACCGGAGTTACCTGCTGACAGCACCGCCGTCAGAATAACTGCg < 1:1087778/69‑1 (MQ=255)
tACAGCATACGAGTAGACGCATACATACCGGAGTTACCTGCTGACAGCACCGCCGTCAGAATAACTGCg < 1:1254054/69‑1 (MQ=255)
tACAGCATACGAGTAGACGCATACATACCGGAGTTACCTGCTGACAGCACCGCCGTCAGAATAACTGCg < 1:1300566/69‑1 (MQ=255)
tACAGCATACGAGTAGACGCATACATACCGGAGTTACCTGCTGACAGCACCGCCGTCAGAATAACTGCg < 1:1528322/69‑1 (MQ=255)
tACAGCATACGAGTAGACGCATACATACCGGAGTTACCTGCTGAAAGCACCGCCGTCAGAATAACTGCg < 1:2141481/69‑1 (MQ=255)
tACAGCATACGAGTAGACGCATACATACCGGAGTTACCTACTGACAGCACCGCCGTCAGAATAACTGCg < 1:1577415/69‑1 (MQ=255)
tACAGCATACGAGTAGACGCATACATACCGGAGTTACCCGCTGACAGCACCGCCGTCAGAATAACTGc > 1:8533/1‑68 (MQ=255)
tACAGCATACGAGTAGACGCATACATACCGGAGTTACCCGCTGACAGCACCGCCGTCAGAATAACTGCg > 1:1761185/1‑69 (MQ=255)
tACAGCATACGAGTAGACGCATACATACCGGAGTTACCCGCTGACAGCACCGCCGTCAGAATAACTGCg > 1:972956/1‑69 (MQ=255)
tACAGCATACGAGTAGACGCATACATACCGGAGTTACCCGCTGACAGCACCGCCGTCAGAATAACTGCg > 1:859285/1‑69 (MQ=255)
tACAGCATACGAGTAGACGCATACATACCGGAGTTACCCGCTGACAGCACCGCCGTCAGAATAACTGCg > 1:3095636/1‑69 (MQ=255)
tACAGCATACGAGTAGACGCATACATACCGGAGTTACCCGCTGACAGCACCGCCGTCAGAATAACTGCg > 1:2826576/1‑69 (MQ=255)
cAGCATACGAGTAGACGCATACATACCGGAGTTACCCGCTGACAGCACCGCCGTCAGAATAACTGCGtt > 1:29640/1‑69 (MQ=255)
cAGCATACGAGTAGACGCATACATACCGGAGTTACCCGCTGACAGCACCGCCGTCAGAATAACTGCGtt > 1:2907677/1‑69 (MQ=255)
cATACGAGTAGACGCATACATACCGGAGTTACCCGCTGACAGCACCGCCGTCAGAATAACTGCGTtcat > 1:621653/1‑69 (MQ=255)
cATACGAGTAGACGCATACATACCGGAGTTACCCGCTGACAGCACCGCCGTCAGAATAACTGCGTtcat < 1:767356/69‑1 (MQ=255)
cATACGAGTAGACGCATACATACCGGAGTTACCCGCTGACAGCACCGCCGTCAGAATAACTGCGTtcat < 1:787702/69‑1 (MQ=255)
cATACGAGTAGACGCATACATACCGGAGTTACCCGCTGACAGCACCGCCGTCAGAATAACTGCGTtcat < 1:1669448/69‑1 (MQ=255)
cATACGAGTAGACGCATACATACCGGAGTTACCCGCTGACAGCACCGCCGTCAGAATAACTGCGTtcat < 1:1605475/69‑1 (MQ=255)
cATACGAGTAGACGCATACATACCGGAGTTACCCGCTGACAGCACCGCCGTCAGAATAACTGCGTtcat < 1:2344754/69‑1 (MQ=255)
aTACGAGTAGACGCATACATACCGGAGTTACCCGCTGACAGCACCGCCGTCAGAATAACTGCGTtcat < 1:151556/68‑1 (MQ=255)
cGAGTAGACGCATACATACCGGAGTTACCCGCTGACAGCACCGCCGTCAGAATAAc > 1:2962812/1‑56 (MQ=255)
cGAGTAGACGCATACATACCGGAGTTACCCGCTGACAGCACCGCCGTCAGAATAACTGCGTTCATCAcc > 1:1159957/1‑69 (MQ=255)
cGAGTAGACGCATACATACCGGAGTTACCCGCTGACAGCACCGCCGTCAGAATAACTGCGTTCATCAcc > 1:2403907/1‑69 (MQ=255)
cGAGTAGACGCATACATACCGGAGTTACCCGCTGACAGCACCGCCGTCAGAATAACTGCGTTCATCAcc > 1:2408100/1‑69 (MQ=255)
cGAGTAGACGCATACATACCGGAGTTACCCGCTGACAGCACCGCCGTCAGAATAACTGCGTTCATCAc > 1:504885/1‑68 (MQ=255)
catacCGGAGTTACCCGCTGACAGCACCGCCGTCAGAATAACTGCGTTCATCACCGCCGCCGCagag > 1:3133221/1‑67 (MQ=255)
catacCGGAGTTACCCGCTGACAGCACCGCCGTCAGAATAACTGCGTTCATCACCGCCGCCGCagag > 1:1328351/1‑67 (MQ=255)
acCGGAGTTACCTGCTGACAGCACCGCCGTCAGAATAACTGCGTTCATCAccgc > 1:1533742/1‑54 (MQ=255)
acCGGAGTTACCTGCTGACAGCACCGCCGTCAGAATAACTGCGTTCATCACCGCCGCCGCAGAGAGCAg > 1:2539630/1‑69 (MQ=255)
acCGGAGTTACCTGCTGACAGCACCGCCGTCAGAATAACTGCGTTCATCACCGCCGCCGCAGAGAGCAg > 1:2019566/1‑69 (MQ=255)
acCGGAGTTACCTGCTGACAGCACCGCCGTCAGAATAACTGCGTTCATCACCGCCGCCGCAGAGAGCAg > 1:759739/1‑69 (MQ=255)
acCGGAGTTACCTGCTGACAGCACCGCCGTCAGAATAACTGCGTTCATCACCGCCGCCGCAGAGAGCAg > 1:687513/1‑69 (MQ=255)
acCGGAGTTACCTGCTGACAGCACCGCCGTCAGAATAACTGCGTTCATCACCGCCGCCGCAGAGAGCAg > 1:2500240/1‑69 (MQ=255)
acCGGAGTTACCTGCTGACAGCACCGCCGTCAGAATAACTGCGTTCATCACCGCCGCCGCAGAGAGCAg > 1:2982274/1‑69 (MQ=255)
acCGGAGTTACCTGCTGACAGCACCGCCGTCAGAATAACTGCGTTCATCACCGCCGCCGCAGAGAGCAg > 1:592008/1‑69 (MQ=255)
acCGGAGTTACCTGCTGACAGCACCGCCGTCAGAATAACTGCGTTCATCACCGCCGCCGCAGAGAGCAg > 1:2544199/1‑69 (MQ=255)
acCGGAGTTACCTGCTGACAGCACCGCCGTCAGAATAACTGCGTTCATCACCGCCGCCGCAGAGAGCAg > 1:3421366/1‑69 (MQ=255)
acCGGAGTTACCTGCTGACAGCACCGCCGTCAGAATAACTGCGTTCATCACCGCCGCCGCAGAGAGCAg > 1:3073442/1‑69 (MQ=255)
aGTTACCTGCTGACAGCACCGCCGTCAGAATAACTGCg < 1:2388154/38‑1 (MQ=255)
|
GCGCTTTACCGTCACACGCCAGGGTGTACAGCATACGAGTAGACGCATACATACCGGAGTTACCCGCTGACAGCACCGCCGTCAGAATAACTGCGTTCATCACCGCCGCCGCAGAGAGCAG > minE/1386565‑1386685
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
