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 F21 I0 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,790,674 |
G→T |
24.3% |
intergenic (+69/‑706) |
pgi → / → ubiC |
glucosephosphate isomerase/chorismate pyruvate lyase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,790,674 | 0 | G | T | 24.3%
| 92.7
/ 15.0
| 37 | intergenic (+69/‑706) | pgi/ubiC | glucosephosphate isomerase/chorismate pyruvate lyase |
| Reads supporting (aligned to +/- strand): ref base G (15/13); new base T (7/2); total (22/15) |
| Fisher's exact test for biased strand distribution p-value = 2.62e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.57e-01 |
CGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCGTATTCGGCAATTAAT > minE/2790610‑2790734
|
cgtcgATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGTTGCGACGCGGTc < 1:1892250/68‑1 (MQ=255)
gtcgATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTcgcg > 1:2580379/1‑70 (MQ=255)
gATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCt > 1:447588/1‑70 (MQ=255)
ttcgTAGGACGGATAAGGCGTTTACGCCGCATCCGGCAACAGATGCCTGATGCGACGCTACCGCGTCTTAt < 1:382514/68‑1 (MQ=11)
tatGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTAt < 1:3247193/71‑1 (MQ=255)
tGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATc < 1:1509578/70‑1 (MQ=255)
tAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAgg < 1:380818/71‑1 (MQ=255)
tAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAg > 1:1369066/1‑70 (MQ=255)
aGGACGGATAAGGCGTTTACGCCGCATCCGGCAACAGATGCCTGATGCGACGCTACCGCGTATTATCa > 1:2394589/1‑68 (MQ=14)
ggCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGAcgcg < 1:2896853/53‑1 (MQ=255)
gacGGATAAGGCGTTTACGCTGCATCCGGCAACCTATGCCTGATGCGACGCTGAAGCGTCTTATCATGcc > 1:1671754/3‑70 (MQ=11)
gCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGcc > 1:1719234/1‑70 (MQ=255)
gCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCt < 1:612785/71‑1 (MQ=255)
ccGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTcgc > 1:661493/1‑56 (MQ=255)
acGGATAAGGCGTTTACGCTGCATCCGGCAACCTATGCCTGATGCGACGCTGAAGCGTCTTATCATGCCTa < 1:1830808/70‑1 (MQ=11)
acGGATAAGGCGTTTACGCTGCATCCGGCAACCTATGCCTGATGCGACGCTGAAGCGTCTTATCATGCCTa > 1:3894761/2‑71 (MQ=11)
cGGATAAGGCGTTTACGCTGCATCCGGCAACCTATGCCTGATGCGACGCTGAAGCGTCTTATCATGCCTa > 1:2182873/1‑70 (MQ=11)
ggATAAGGCGTTTACGCTGCATCCGGCAACCTATGCCTGATGCGACGCTGAAGCGTCTTATCATGCCTACa > 1:1131528/1‑71 (MQ=11)
tAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGt > 1:2354780/1‑71 (MQ=255)
aGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTc < 1:1910216/70‑1 (MQ=255)
cGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGa > 1:219223/1‑69 (MQ=255)
cGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGAt > 1:1458042/1‑70 (MQ=255)
ttCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTc < 1:2689770/65‑1 (MQ=255)
ttCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGcc > 1:3530579/1‑71 (MQ=255)
ttaCGCCGCATCCGGCAACAGATGCCTGATGCGACGCTACCGCGTCTTATCAGGCCTAc > 1:950418/3‑59 (MQ=14)
aCGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGa > 1:3225327/1‑70 (MQ=255)
tcgcATCCGACAACCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGc > 1:1412351/2‑50 (MQ=9)
ccgcATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATg < 1:2916010/71‑1 (MQ=255)
cgcATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATg > 1:2280855/1‑70 (MQ=255)
cATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTa > 1:623416/1‑70 (MQ=255)
tCCGGCAACCGATGCCTGATGCGACGCGGTTGCGTATTATCAGGCCTACATGTCGATGCCGATATGTACa < 1:1736647/70‑1 (MQ=25)
tCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTa > 1:641935/1‑68 (MQ=255)
ccGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATc > 1:3087224/1‑40 (MQ=255)
ccGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATc > 1:3133815/1‑71 (MQ=255)
cGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCGTATTCgg < 1:2558409/71‑1 (MQ=255)
aTGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCGTATTCGGCa < 1:3787538/71‑1 (MQ=255)
cTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCGTa < 1:2117652/60‑1 (MQ=255)
aTGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCGTATTCGGCAATTAAt < 1:1337355/70‑1 (MQ=255)
cgcgGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCGTAt > 1:2174376/1‑52 (MQ=255)
|
CGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCGTATTCGGCAATTAAT > minE/2790610‑2790734
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
