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 F1 I0 R1
|
2892 |
75.3 |
5698161 |
66.1% |
3766484 |
59.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,773,670 |
Δ1 bp |
25.5% |
intergenic (+59/‑124) |
aceA → / → aceK |
isocitrate lyase/isocitrate dehydrogenase kinase/phosphatase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,773,670 | 0 | T | . | 25.5%
| 102.0
/ 45.9
| 51 | intergenic (+59/‑124) | aceA/aceK | isocitrate lyase/isocitrate dehydrogenase kinase/phosphatase |
| Reads supporting (aligned to +/- strand): ref base T (17/21); new base . (5/8); total (22/29) |
| Fisher's exact test for biased strand distribution p-value = 7.55e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AGTTCTAAGCAACAACAACCGTTGCTGACTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAATCGGTGCACGA‑TGCCTGATGCGACGC‑TTGCGCGTCTTATCATGCCTACAGCCGTTGCCGAACGTAG > minE/2773604‑2773735
|
aGTTCTAAGCAACAACAACCGTTGCTGACTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAATCgg < 1:2431421/70‑1 (MQ=255)
cTAAGCAACAACAACAGTTGCTGACTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAATCGGTGCAc > 1:2642731/1‑71 (MQ=255)
gCAACAACAACCGTTGCTGACTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAATCGGTGCACGA‑Tg > 1:2750278/1‑71 (MQ=255)
gCAACAACAACCGTTGCTGACTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAATCGGTGCACGA‑Tg > 1:4513233/1‑71 (MQ=255)
gCAACAACAACCGTTGCTGACTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAATCGGTGCACGA‑Tg > 1:1488604/1‑71 (MQ=255)
gCAACAACAACCGTTGCTGACTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAATCGGTGCACGA‑Tg > 1:4473628/1‑71 (MQ=255)
gCAACAACAACCGTTGCTGACTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAATCGGTGCACGA‑Tg > 1:2082521/1‑71 (MQ=255)
acaacaacCGTTGCTGACTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAATCGGTGCAc < 1:651087/64‑1 (MQ=255)
acaacaacCGTTGCTGACTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAATCGGTGCACGA‑TGCCt < 1:551396/71‑1 (MQ=255)
caacaacCGTTGCTGACTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAATCGGTGCACGA‑TGCCt > 1:5141301/1‑70 (MQ=255)
caacaacCGTTGCTGACTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAATCGGTGCACGA‑TGCCTg < 1:1795518/71‑1 (MQ=255)
aacaacCGTTGCTGACTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAATCGGTGCACGA‑TGCCTGa > 1:2894040/1‑71 (MQ=255)
aacaacCGTTGCTGACTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAATCGGTGCACGA‑TGCCTGa > 1:3714733/1‑71 (MQ=255)
acaacCGTTGCTGACTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAATCGGTGCACGA‑TGCCTGAt > 1:499976/1‑71 (MQ=255)
cTGACTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAAt < 1:2311645/43‑1 (MQ=255)
gACTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAATCGGTGCACGA‑TGCCTGATGCGACGC‑TTgcg > 1:5337156/1‑71 (MQ=255)
cTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAATCGGTGCACGA‑TGCCTGATGCGACGC‑TTGcgcg > 1:4337777/1‑71 (MQ=255)
cTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAATCGGTGCACGA‑TGCCTGATGCGACGC‑TTGcgcg < 1:310363/71‑1 (MQ=255)
aGGCCGGATAAGGCGTTCACGCCGCATCCGGCAATCGGTGCACGA‑TGCCTGATGCGACGC‑TTGCGCGTCt > 1:4861730/1‑70 (MQ=255)
ggCCGGATAAGGCGTTTACGCCGCATCCGGCAA‑CGGTGC‑CGACTGCCTGATGCGACGC‑TTGCGCGTCTTa < 1:2980922/70‑1 (MQ=11)
ggCCGGATAAGGCGTTCACGCCGCATCCGGCAATCGGTGCACGA‑TGCCTGATGc < 1:1754404/54‑1 (MQ=255)
ggCCGGATAAGGCGTTCACGCCGCATCCGGCAATCGGTGCACGA‑TGCCTGATGCGACGC‑TTGCGCGTCtt < 1:702953/70‑1 (MQ=255)
gaccGGATAAGGCGTTCACGCCGCATCCGGCAGTC‑GTGCGCCA‑TGCCTGATGCGACGCTTTGCGCGTCtt < 1:3613819/68‑1 (MQ=1)
gaccGGATAAGGCGTTCACGCCGCATCCGGCAGTC‑GTGCGCCA‑TGCCTGATGCGACGCTTTGCGCGTCTTa < 1:3007464/69‑1 (MQ=11)
gaccGGATAAGGCGTTCACGCCGCATCCGGCAGTC‑GTGCGCCA‑TGCCTGATGCGACGCTTTGCGCGTCTTa < 1:895741/69‑1 (MQ=11)
gaccGGATAAGGCGTTCACGCCGCATCCGGCAGTC‑GTGCGCCA‑TGCCTGATGCGACGCTTTGCGCGTCTTa < 1:3307294/69‑1 (MQ=11)
agCCGGATAAGGCGCTCGCGCCGCATCCGGCAA‑CGGTGCCAGA‑TGCCTGATGCGACGC‑TTGCGCGTCTTAt < 1:1428683/70‑1 (MQ=14)
gCCGGATAAGGCGTTTACGCCGCATCCGGCAA‑CGGTGC‑CGACTGCCTGATGCGACGC‑TTGCGCGTCTTAt < 1:4359086/70‑1 (MQ=11)
gCCGGATAAGGCGTTCACGCCGCATCCGGCAATCGGTGCACGA‑TGCCTGATGCGACGC‑TTGCGCGTCTTAt < 1:1913176/71‑1 (MQ=255)
gCCGGATAAGGCGTTCACGCCGCATCCGGCAATCGGTGCACGA‑TGCCTGATGCGACGC‑TTGCGCGTCTTAt < 1:2817935/71‑1 (MQ=255)
accGGATAAGGCGTTCACGCCGCATCCGGCAGTC‑GTGCGCCA‑TGCCTGATGCGACGCTTTGCGCGTCTTAt < 1:1166876/70‑1 (MQ=11)
ccGGATAAGGCGTTTACGCCGCATCCGGCAA‑CGGTGC‑CGACTGCCTGATGCGACGC‑TTGCGCGTCTTATCa < 1:3793475/71‑1 (MQ=11)
ccGGATAAGGCGTTCACGCCGCATCCGGCAGTC‑GTGCGCCA‑TGCCTGATGCGACGCTTTGCGCGTCTTATc < 1:4271156/71‑1 (MQ=11)
cGGATAAGGCGCTCGCGCCGCATCCGGCAA‑CGGTGCCAGA‑TGCCTGATGCGACGC‑TTGCGCGTCTTATCag > 1:1015364/1‑70 (MQ=14)
ggATAAGGCGTTTACGCCGCATCCGGCAA‑CGGTGC‑CGACTGCCTGATGCGACGC‑TTGCGCGTCTTAt < 1:5187437/67‑1 (MQ=11)
ggATAAGGCGTTCACGCCGCATCCGGCAGTC‑GTGCGCCA‑TGCCTGATGCGACGCTTTGCGCGTCTTATCag > 1:455277/1‑70 (MQ=1)
aTAAGGCGTTTACGCCGCATCCGGCAA‑CGGTGC‑CGACTGCCTGATGCGACGC‑TTGCGCGTCTTATCAGGcc > 1:3814546/1‑71 (MQ=11)
aaGGCGTTTACGCCGCATCCGGCAA‑CGGTGC‑CGACTGCCTGATGCGACGC‑TTGCGCGTCTTATCAGGCCTa > 1:234268/1‑71 (MQ=11)
aGGCGTTCACGCCGCATCCGGCAATCGGTGCACGA‑TGCCTGATGCGACGC‑TTGCGCGTCTTATCATGCCt < 1:3737784/70‑1 (MQ=255)
ggCGTTTACGCCGCATCCGGCAA‑CGGTGC‑CGACTGCCTGATGCGACGC‑TTGCGCGTCTTATCAGGCCTa > 1:3284257/1‑69 (MQ=11)
ggCGTTTACGCCGCATCCGGCAA‑CGGTGC‑CGACTGCCTGATGCGACGC‑TTGCGCGTCTTATCAGGCCTACa < 1:3713134/71‑1 (MQ=11)
ggCGTTTACGCCGCATCCGGCAA‑CGGTGC‑CGACTGCCTGATGCGACGC‑TTGCGCGTCTTATCAGGCCTACa < 1:169435/71‑1 (MQ=11)
ggCGTTCACGCCGCATCCGGCAATCGGTGCACGA‑TGCCTGATGCGACGC‑TTGCGCGTCTTATCATGCCTAc < 1:423264/71‑1 (MQ=255)
cGTTTACGCCGCATCCGGCAA‑CGGTGC‑CGACTGCCTGATGCGACGC‑TTGCGCGTCTTAt > 1:4935700/1‑59 (MQ=11)
ttCACGCCGCATCCGGCAATCGGTGCACGA‑TGCCTGATGc < 1:214201/40‑1 (MQ=40)
ttCACGCCGCATCCGGCAATCGGTGCACGA‑TGCCTGATGCGACGC‑TTGCGCGTCTTATCATGCCTACAGcc > 1:4729389/1‑71 (MQ=255)
ttCACGCCGCATCCGGCAATCGGTGCACGA‑TGCCTGATGCGACGC‑TTGCGCGTCTTATCATGCCTACAGcc < 1:5093041/71‑1 (MQ=255)
aCGCCGCATCCGGCAATCGGTGCACGA‑TGCCTGATGCGACGC‑TTGCGCGTCTTATCATGCCTACAGCCGtt > 1:4200124/1‑71 (MQ=255)
aCGCCGCATCCGGCAATCGGTGCACGA‑TGCCTGATGCGACGC‑TTGCGCGTCTTATCATGCCTACAGCCGtt > 1:27977/1‑71 (MQ=255)
cgccgcATCCGGCAA‑CGGTGC‑CGACTGCCTGATGCGACGC‑TTGCGCGTc < 1:4656924/49‑1 (MQ=11)
cGGCAATCGGTGCACGA‑TGCCTGATGCGACGC‑TTGCGCGTCTTATCATGCCTACAGCCGTTGCCGAACGt < 1:2852359/70‑1 (MQ=255)
gCAATCGGTGCACGA‑TGCCTGATGCGACGC‑TTGCGCGTCTTATCATGCCTACAGCCGTTGCCGAACGTAg < 1:1052830/70‑1 (MQ=255)
|
AGTTCTAAGCAACAACAACCGTTGCTGACTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAATCGGTGCACGA‑TGCCTGATGCGACGC‑TTGCGCGTCTTATCATGCCTACAGCCGTTGCCGAACGTAG > minE/2773604‑2773735
|
| 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
