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 |
745,073 |
C→T |
32.7% |
intergenic (+133/‑267) |
ycfP → / → ndh |
conserved hypothetical protein/respiratory NADH dehydrogenase 2/cupric reductase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 745,073 | 0 | C | T | 32.7%
| 52.7
/ 30.9
| 64 | intergenic (+133/‑267) | ycfP/ndh | conserved hypothetical protein/respiratory NADH dehydrogenase 2/cupric reductase |
| Reads supporting (aligned to +/- strand): ref base C (4/39); new base T (14/7); total (18/46) |
| Fisher's exact test for biased strand distribution p-value = 4.18e-06 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.88e-01 |
AGGCGTCCACGCCGCATCCGACAGTCGAGCATCAATGCCTGATGCGCTTCTTATCAGGCCTACCGAACGCCCTGCATACACCCCTCACTCTATATCACTCTCACAAATTCGCTCAAATAATAAAC > minE/745006‑745130
|
aGGCGTCCACGCCGCATCCGACAGTCGAGCATCAATGCCTGATGCGCTTCTTATCAGGCCTACCGAACg < 1:1460074/69‑1 (MQ=255)
aGGCGTCCACGCCGCATCCGACAGTCGAGCATCAATGCCTGATGCGCTTCTTATCAGGCCTACCGAACg < 1:2384987/69‑1 (MQ=255)
gCGTCCACGCCGCATCCGACAGTCGAGCATCAATGCCTGATGCGCTTCTTATCAGGCCTACCGAACGcc < 1:2908361/69‑1 (MQ=255)
gCGTCCACGCCGCATCCGACAGTCGAGCATCAATGCCTGATGCGCTTCTTATCAGGCCTACCGAACGcc < 1:1878002/69‑1 (MQ=255)
gCGTCCACGCCGCATCCGACAGTCGAGCATCAATGCCTGATGCGCTTCTTATCAGGCCTACCGAACGcc < 1:1152572/69‑1 (MQ=255)
gCGTCCACGCCGCATCCGACAGTCGAGCATCAATGCCTGATGCGCTTCTTATCAGGCCTACCGAACGcc < 1:1881942/69‑1 (MQ=255)
gCGTCCACGCCGCATCCGACAGTCGAGCATCAATGCCTGATGCGCTTCTTATCAGGCCTACCGAACGcc < 1:1313805/69‑1 (MQ=255)
cACGCCGCATCCGACAGTCGAGCATGAATGCCTGATGTGCTTCTTATCAGGCCTACCGAACGCCCTGCa < 1:3170313/69‑1 (MQ=255)
cACGCCGCATCCGACAGTCGAGCATCAATGCCTGATGTGCTTCTTATCAGGCCTACCGAACGCCCTGCa < 1:1267154/69‑1 (MQ=255)
cACGCCGCATCCGACAGTCGAGCATCAATGCCTGATGTGCTTCTTATCAGGCCTACCGAACGCCCTGCa < 1:122114/69‑1 (MQ=255)
cACGCCGCATCCGACAGTCGAGCATCAATGCCTGATGTGCTTCTTATCAGGCCTACCGAACGCCCTGCa < 1:3010651/69‑1 (MQ=255)
cgccgcATCCGACAGTCGAGCATCAATGCCTGATGCGCTTCTTATCAGGCCTACCGAACGCCCTGCATa < 1:2171373/69‑1 (MQ=255)
cgccgcATCCGACAGTCGAGCATCAATGCCTGATGCGCTTCTTATCAGGCCTACCGAACGCCCTGCATa < 1:440980/69‑1 (MQ=255)
cgccgcATCCGACAGTCGAGCATCAATGCCTGATGCGCTTCTTATCAGGCCTACCGAACGCCCTGCATa < 1:1205216/69‑1 (MQ=255)
cgccgcATCCGACAGTCGAGCATCAATGCCTGATGCGCTTCTTATCAGGCCTACCGAACGCCCTGCATa < 1:767147/69‑1 (MQ=255)
cgccgcATCCGACAGTCGAGCATCAATGCCTGATGCGCTTCTTATCAGGCCTACCGAACGCCCTGCATa < 1:1458066/69‑1 (MQ=255)
cgccgcATCCGACAGTCGAGCATCAATGCCTGATGCGCTTCTTATCAGGCCTACCGAACGCCCTGCATa < 1:632879/69‑1 (MQ=255)
gcATCCGACAGTCGAGCATCAATGCCTGATGCGCCTCTTATCAGGCCTACCGAATGCCCTCCATacaca > 1:2400509/1‑68 (MQ=38)
gcATCCGACAGTCGAGCATCAATGCCTGATGCGCCTCTTATCAGGCCTACCGAATGCCCTCCATacaca > 1:37517/1‑68 (MQ=38)
gcATCCGACAGTCGAGCATCAATGCCTGATGCGCCTCTTATCAGGCCTACCGAATGCCCTCCATacaca > 1:3181768/1‑68 (MQ=38)
gcATCCGACAGTCGAGCATCAATGCCTGATGCGCCTCTTATCAGGCCTACCGAATGCCCTCCATacaca > 1:2307458/1‑68 (MQ=38)
gcATCCGACAGTCGAGCATCAATGCCTGATGCGCCTCTTATCAGGCCTACCGAATGCCCTCCATacaca > 1:2384500/1‑68 (MQ=38)
gcATCCGACAGTCGAGCATCAATGCCTGATGCGCCTCTTATCAGGCCTACCGAATGCCCTCCATacaca > 1:725454/1‑68 (MQ=38)
gcATCCGACAGTCGAGCATCAATGCCTGATGCGCCTCTTATCAGGCCTACCGAATGCCCTCCATacaca > 1:1441345/1‑68 (MQ=38)
gcATCCGACAGTCGAGCATCAATGCCTGATGCGCCTCTTATCAGGCCTACCGAATGCCCTCCATacaca > 1:2698100/1‑68 (MQ=38)
gcATCCGACAGTCGAGCATCAATGCCTGATGCGCCTCTTATCAGGCCTACCGAATGCCCTCCATacaca > 1:1347711/1‑68 (MQ=38)
gcATCCGACAGTCGAGCATCAATGCCTGATGCGCCTCTTATCAGGCCTACCGAATGCCCTCCATacaca > 1:1251182/1‑68 (MQ=38)
gcATCCGACAGTCGAGCATCAATGCCTGATGCGCCTCTTATCAGGCCTACCGAATGCCCTCCATacaca > 1:1132169/1‑68 (MQ=38)
gcATCCGACAGTCGAGCATCAATGCCTGATGCGCCTCTTATCAGGCCTACCGAATGCCCTCCATacaca > 1:2830414/1‑68 (MQ=38)
gcATCCGACAGTCGAGCATCAATGCCTGATGCGCCTCTTATCAGGCCTACCGAATGCCCTCCATacac > 1:1327001/1‑68 (MQ=38)
gcATCCGACAGTCGAGCATCAATGCCTGATGCGCCTCTTATCAGGCCTACCGAATGCCCTCCATacac > 1:1025343/1‑68 (MQ=38)
cAGTCGAGCATCAATGCCTGATGCGCTTCTTATCAGGCCTACCGAACGCCCTGCATACACCCCTCActc < 1:549887/69‑1 (MQ=255)
cAGTCGAGCATCAATGCCTGATGCGCTTCTTATCAGGCCTACCGAACGCCCTGCATACACCCCTCActc < 1:2906240/69‑1 (MQ=255)
tCGAGCATCAATGCCTGATGCGCTTCTTATCAGGCCTACCGAACGCCCTGCATACACCCCTCActc < 1:1204271/66‑1 (MQ=255)
tCGAGCATCAATGCCTGATGCGCTTCTTATCAGGCCTACCGAACGCCCTGCATACACCCCTCACTCtat < 1:2869593/69‑1 (MQ=255)
cGAGCATCAATGCCTGATGCGCTTCTTATCAGGCCTACCGAACGCCCTGCATACACCCCTCACTCtat < 1:1001204/68‑1 (MQ=255)
gCATCAATGCCTGATGCGCTTCTTATCAGGCCTACCGAACGCCCTGCa < 1:2971018/48‑1 (MQ=255)
cATCAATGCCTGATGCGCTTCTTATCAGGCCTACCGAACGCCCTGCATACACCCCTCACTCTATATCAc > 1:3404765/1‑69 (MQ=255)
cATCAATGCCTGATGCGCTTCTTATCAGGCCTACCGAACGCCCTGCATACACCCCTCACTCTATATCAc > 1:535170/1‑69 (MQ=255)
ccTGATGCGCTTCTTATCAGGCCTACCGAACGCCCTGCATACACCCCTCACTCTATATCACTCTCACaa > 1:1814275/1‑69 (MQ=255)
ccTGATGCGCTTCTTATCAGGCCTACCGAACGCCCTGCATACACCCCTCACTCTATATCACTCTCACaa > 1:1375572/1‑69 (MQ=255)
tGCTCTTCTTATCAGGCCTACCGAACGCCCTGCATACACCCCTCACTCTATATCActct < 1:3309866/59‑1 (MQ=255)
tGCGCTTCTTATCAGGCCTACCGAACGCCCTGCATACACCCCTCACTCTATATCActct < 1:795516/59‑1 (MQ=255)
tGCGCTTCTTATCAGGCCTACCGAACGCCCTGCATACACCCCTCACTCTATATCActct < 1:1004564/59‑1 (MQ=255)
tGCGCTTCTTATCAGGCCTACCGAACGCCCTGCATACACCCCTCACTCTATATCActct < 1:2468715/59‑1 (MQ=255)
tGCGCTTCTTATCAGGCCTACCGAACGCCCTGCATACACCCCTCACTCTATATCActct < 1:226736/59‑1 (MQ=255)
tGCGCTTCTTATCAGGCCTACCGAACGCCCTGCATACACCCCTCACTCTATATCActct < 1:18435/59‑1 (MQ=255)
tGCGCTTCTTATCAGGCCTACCGAACGCCCTGCATACACCCCTCACTCTATATCActct < 1:14381/59‑1 (MQ=255)
tGCGCTTCTTATCAGGCCTACCGAACGCCCTGCATACACCCCTCACTCTATATCActct < 1:1767813/59‑1 (MQ=255)
ttATCATGACTACCGAACGCCCTGCATACACCCCTCActc < 1:641559/40‑1 (MQ=255)
aGGCCTACCGAACGCCCTGCATACACCCCTCACTCTATATCACTCTCACAAATTCGCTCAAATaataaa < 1:2516337/69‑1 (MQ=255)
aGGCCTACCGAACGCCCTGCATACACCCCTCACTCTATATCACTCTCACAAATTCGCTCAAATaataaa < 1:886163/69‑1 (MQ=255)
aGGCCTACCGAACGCCCTGCATACACCCCTCACTCTATATCACTCTCACAAATTCGCTCAAATaataaa < 1:140745/69‑1 (MQ=255)
aGGCCTACCGAACGCCCTGCATACACCCCTCACTCTATATCACTCTCACAAATTCGCTCAAATaataaa < 1:2055170/69‑1 (MQ=255)
aGGCCTACCGAACGCCCTGCATACACCCCTCACTCTATATCACTCTCACAAATTCGCTCAAATaataaa < 1:2049674/69‑1 (MQ=255)
aGGCCTACCGAACGCCCTGCATACACCCCTCACTCTATATCACTCTCACAAATTCGCTCAAATaataaa < 1:1936844/69‑1 (MQ=255)
ggCCTACCGAACGCCGTGCATACACCGCTCTCTCTATATCACTCTCACAAATTCGCTCAAATaataaa < 1:1861257/68‑1 (MQ=255)
gCCTACCGAATGCCCTCCATACACACCTCACTCTATATCACTCTCACAAATCAGCTCAAATaataaac < 1:932385/68‑1 (MQ=255)
gCCTACCGAATGCCCTCCATACACACCTCACTCTATATCACTCTCACAAATCAGCTCAAATaataaac < 1:2619117/68‑1 (MQ=255)
gCCTACCGAATGCCCTCCATACACACCTCACTCTATATCACTCTCACAAATCAGCTCAAATaataaac < 1:1597807/68‑1 (MQ=255)
gCCTACCGAATGCCCTCCATACACACCTCACTCTATATCACTCTCACAAATCAGCTCAAATaataaac < 1:598571/68‑1 (MQ=255)
gCCTACCGAATGCCCTCCATACACACCTCACTCTATATCACTCTCACAAATCAGCTCAAATaataaac < 1:2187524/68‑1 (MQ=255)
gCCTACCGAATGCCCTCCATACACACCTCACTCTATATCACTCTCACAAATCAGCTCAAATaataaac < 1:2340632/68‑1 (MQ=255)
gCCTACCGAATGCCCTCCATACACACCTCACTCTATATCACTCTCACAAATCAGCTCAAATaataaac < 1:2567040/68‑1 (MQ=255)
|
AGGCGTCCACGCCGCATCCGACAGTCGAGCATCAATGCCTGATGCGCTTCTTATCAGGCCTACCGAACGCCCTGCATACACCCCTCACTCTATATCACTCTCACAAATTCGCTCAAATAATAAAC > minE/745006‑745130
|
| 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
