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 |
2,759,004 |
C→T |
33.7% |
A180A (GCC→GCT) |
smf → |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,759,004 | 0 | C | T | 33.7%
| 55.1
/ 34.4
| 68 | A180A (GCC→GCT) | smf | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base C (22/23); new base T (3/20); total (25/43) |
| Fisher's exact test for biased strand distribution p-value = 3.86e-03 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.31e-01 |
AATGGCGTCAGCATTGCTGTATTGGGGAATGGACTTAATACCATTCATCCCCGCCGTCATGCCCGACTGGCTGCCAGTCTGCTTGAACAGGGGGGCGCTCTCGTCTCGGAATTTCCCCTCGATGTTCCAC > minE/2758942‑2759071
|
aaTGGCGTCAGCATTGCTGTATTGGGGAATGGACTTAATACCATTCATCCCCGCCGTCATGCCCGACTg < 1:3153679/69‑1 (MQ=255)
ggggAATGGACTTAATACCATTCATCCCCGCCGTCATGCCCGACTGGCTGCCAGTCTGCTTg < 1:2383181/62‑1 (MQ=255)
ggggAATGGACTTAATACCATTCATCCCCGCCGTCATGCCCGACTGGCTGCCAGTCTGCTTg > 1:673061/1‑62 (MQ=255)
ggggAATGGACTTAATACCATTCATCCCCGCCGTCATGCCCGACTGGCTGCCAGTCTGCTTg > 1:2795633/1‑62 (MQ=255)
ggggAATGGACTTAATACCATTCATCCCCGCCGTCATGCCCGACTGGCTGCCAGTCTGCTTg > 1:540318/1‑62 (MQ=255)
ggggAATGGACTTAATACCATTCATCCCCGCCGTCATGCCCGACTGGCTGCCAGTCTGCTTg > 1:1847102/1‑62 (MQ=255)
ggggAATGGACTTAATACCATTCATCCCCGCCGTCATGCCCGACTGGCTGCCAGTCTGCTTg > 1:203255/1‑62 (MQ=255)
ggggAATGGACTTAATACCATTCATCCCCGCCGTCATGCCCGACTGGCTGCCAGTCTGCTTg > 1:1200415/1‑62 (MQ=255)
gcggAATGGACTTAATACCATTCATCCCCGCCGTCATGCCCGACTGGCTGCCAGTCTGCTTg < 1:3390928/60‑1 (MQ=255)
tGGACTTAATACCATTCATCCCCGCCGTCATGCCCGACTGGCTGCCAGTCTGCTTGAACAGGGGGgcgc < 1:696860/69‑1 (MQ=255)
tGGACTTAATACCATTCATCCCCGCCGTCATGCCCGACTGGCTGCCAGTCTGCTTGAACAGGGGGgcgc < 1:3125557/69‑1 (MQ=255)
tGGACTTAATACCATTCATCCCCGCCGTCATGCCCGACTGGCTGCCAGTCTGCTTGAACAGGGGGgcgc < 1:2728480/69‑1 (MQ=255)
ggACTTAATACCATTCATCCCCGCCGTCATGCCCGACTGGCTGCCAGTCTGCTTGAACAGGGGGgcgc < 1:1012495/68‑1 (MQ=255)
ggACTTAATACCATTCATCCCCGCCGTCATGCCCGACTGGCTGCCAGTCTGCTTGAACAGGGGGGCGct < 1:1615033/69‑1 (MQ=255)
ggACTTAATACCATTCATCCCCGCCGTCATGCCCGACTGGCTGCCAGTCTGCTTGAACAGGGGGGCGct < 1:2683739/69‑1 (MQ=255)
gACTTAATACCATTCATCCCCGCCGTCATGCCCGACTGGCTGCCAGTCTGCTTGAACAGGGGGgcgc > 1:2408901/1‑67 (MQ=255)
gACTTAATACCATTCATCCCCGCCGTCATGCCCGACTGGCTGCCAGTCTGCTTGAACAGGGGGGCGctc > 1:315968/1‑69 (MQ=255)
cTTAATACCATTCATCCCCTCCGCCATGCTCCACTgg < 1:3044264/37‑1 (MQ=21)
cTTAATACCATTCATCCCCTCCGCCATGCTCCACTgg < 1:123162/37‑1 (MQ=21)
cTTAATACCATTCATCCCCGCCGCCATGCTCCACTgg < 1:2964124/37‑1 (MQ=25)
cTTAATACCATTCATCCCCGCCGCCATGCTCCACTgg < 1:3047380/37‑1 (MQ=25)
cTTAATACCATTCATCCCCGCCGCCATGCTCCACTgg < 1:356207/37‑1 (MQ=25)
cTTAATACCATTCATCCCCGCCGCCATGCTCCACTgg < 1:3336795/37‑1 (MQ=25)
cTTAATACCATTCATCCCCGCCGCCATGCTCCACTgg < 1:2082497/37‑1 (MQ=25)
cTTAATACCATTCATCCCCGCCGCCATGCTCCACTgg < 1:2244779/37‑1 (MQ=25)
cTTAATACCATTCATCCCCGCCGCCATGCTCCACTgg < 1:462623/37‑1 (MQ=25)
cTTAATACCATTCATCCCCGCCGCCATGCTCCACTgg < 1:912983/37‑1 (MQ=25)
cTTAATACCATTCATCCCCGCCGCCATGCTCCACTgg < 1:1130384/37‑1 (MQ=25)
cTTAATACCATTCATCCCCGCCGCCATGCTCCACTgg < 1:715094/37‑1 (MQ=25)
cTTAATACCATTCATCCCCGCCGCCATGCTCCACTgg < 1:133987/37‑1 (MQ=25)
cTTAATACCATTCATCCCCGCCGCCATGCTCCACTgg < 1:1532698/37‑1 (MQ=25)
cTTAATACCATTCATCCCCGCCGCCATGCTCCACTgg < 1:1613127/37‑1 (MQ=25)
cTTAATACCATTCATCCCCGCCGCCATGCTCCACTgg < 1:584798/37‑1 (MQ=25)
cTTAATACCATTCATCCCCGCCGCCATGCTCCACTgg < 1:466647/37‑1 (MQ=25)
cTTAATACCATTCATCCCCGCCGCCATGCTCCACTgg < 1:2142903/37‑1 (MQ=25)
cTTAATACCATTCATCCCCGCCGCCATGCTCCACTgg < 1:2196778/37‑1 (MQ=25)
ttAATACCATTCATCCCCGCCGCCATGCTCCACTgg < 1:298125/36‑1 (MQ=37)
aCCATTCATCCCCGCCGTCATGCCCGACTGGCTGCCAGTCTGCTTGAACAGGGGGGCGCtctcgtctc < 1:269336/68‑1 (MQ=255)
aCCATTCATCCCCGCCGTCATGCCCGACTGGCTGCCAGTCTGCTTGAACAGGGGGGCGCtctcgtctc < 1:544718/68‑1 (MQ=255)
aCCATTCATCCCCGCCGTCATGCCCGACTGGCTGCCAGTCTGCTTGAACAGGGGGGCGCtctcgtctc < 1:3376229/68‑1 (MQ=255)
aCCATTCATCCCCGCCGTCATGCCCGACTGGCTGCCAGTCTGCTTGAACAGGGGGGCGCtctcgtctc < 1:1312304/68‑1 (MQ=255)
aCCATTCATCCCCGCCGTCATGCCCGACTGGCTGCCAGTCTGCGTGAACAGGGGGGCGCtctcgtctc < 1:950022/68‑1 (MQ=255)
ccATTCATCCCCGCCGTCATGCCCGACTTGCTGCCAGTCTGCTTGAACa > 1:1307637/1‑49 (MQ=255)
ccATTCATCCCCGCCGTCATGCCCGACTGGCTGCCAGTCTGCTTGAACa > 1:480995/1‑49 (MQ=255)
ccATTCATCCCCGCCGTCATGCCCGACTGGCTGCCAGTCTGCTTGAACa > 1:2739607/1‑49 (MQ=255)
ccATTCATCCCCGCCGTCATGCCCGACTGGCTGCCAGTCTGCTTGAACa > 1:286748/1‑49 (MQ=255)
ccATTCATCCCCGCCGTCATGCCCGACTGGCTGCCAGTCTGCTTGAACa > 1:181912/1‑49 (MQ=255)
ccATTCATCCCCGCCGTCATGCCCGACTGGCTGCCAGTCTGCTTGAACa > 1:3208096/1‑49 (MQ=255)
ccATTCATCCCCGCCGTCATGCCCGACTGGCTGCCAGTCTGCTTGAACa > 1:1780298/1‑49 (MQ=255)
ccATTCATCCCCGCCGTCATGCCCGACTGGCTGCCAGTCTGCTAGa > 1:3121955/1‑46 (MQ=255)
ccATTCATCCCCGCCGTCATGCCCGACTGGCTGCCAGACTGCTTGAACa > 1:2008876/1‑49 (MQ=255)
ccATTCATCACCGCCGTCATGCCCGACTGGCTGCCAGTCTGCTTGAACa > 1:1555485/1‑49 (MQ=255)
acATTCATCCCCGCCGTCATGCCCGACTGGCTGCCAGTCTGCTTGAACa > 1:50008/2‑49 (MQ=255)
cATTCATCCCCGCCGCCATGCTCCACTGGCTGCCAGTCTACTTGAGCAAGGTGGTGCTCTCGTCTCGGa > 1:83716/1‑69 (MQ=255)
cATTCATCCCCGCCGCCATGCTCCACTGGCTGCCAGTCTACTTGAGCAAGGTGGTGCTCTCGTCTCGGa > 1:730297/1‑69 (MQ=255)
cATTCATCCCCGCCGCCATGCTCCACTGGCTGCCAGTCTACTTGAGCAAGGTGGTGCTCTCGTCTCGGa > 1:2189817/1‑69 (MQ=255)
ccccGCCGTCATGCCCGACTGGCTGCCAGTCTGCTTGAACAGGGGGGCGCTCTCGTCTCGGAATTTccc > 1:2561787/1‑69 (MQ=255)
ccccGCCGTCATGCCCGACTGGCTGCCAGTCTGCTTGAACAGGGGGGCGCTCTCGTCTCGGAATTTcc > 1:1231012/1‑68 (MQ=255)
ccccGCCGTCATGCCCGACTGGCTGCCAGTCTGATTGAACAGGGGGGCGCTCTCGTCTCGGAATTTccc > 1:3238852/1‑69 (MQ=255)
cgccgTCATGCCCGACTGGCTGCCAGTCTGCTTGAACAGGGGGGCGCTCTCGTCTCGGAATTTCCCCTc < 1:1788934/69‑1 (MQ=255)
cgccgTCATGCCCGACTGGCTGCCAGTCTGCTTGAACAGGGGGGCGCTCTCGTCTCGGAATTTCCCCTc < 1:524190/69‑1 (MQ=255)
gTCATGCCCGACTGGCTGCCAGTCTGCTTGAACAGGGGGGCGCTCTCGTCTCGGAATTTCCCCTCGATg < 1:687735/69‑1 (MQ=255)
gTCATGCCCGACTGGCTGCCAGTCTGCTTGAACAGGGGGGCGCTCTCGTCTCGGAATTTCCCCTCGATg < 1:1292359/69‑1 (MQ=255)
gTCATGCCCGACTGGCTGCCAGTCTGCTTGAACAGGGGGGCGCTCTCGTCTCGGAATTTCCCCTCGATg < 1:2678443/69‑1 (MQ=255)
gTCATGCCCGACTGGCTGCCAGTCTGCTTGAACAGGGGGGCGCTCTCGTCTCGGAATTTCCCCTCGATg < 1:3350974/69‑1 (MQ=255)
gTCATGCCCGACTGGCTGCCAGTCTGCTTGAACAGGGGGGCGCTCTCGTCTCGGAATTTCCCCTCGATg < 1:1026325/69‑1 (MQ=255)
gtGCCCGACTGGCTGCCAGTCTGCTTGAACAGGGGGGCGCTCTCGTCTCGGAATTTCCCCTCGATGTTc < 1:1086426/68‑1 (MQ=255)
aTGCCCGACTGGCTGCCAGTCTGCTTGAACAGGGGGGCGCTCTCGTCTCGGAATTTCCCCTCGATGTTc < 1:1768086/69‑1 (MQ=255)
cccGACTGGCTGCCAGTCTGCTTGAACAGGGGGGCGCTCTCGTCTCGGAATTTCCCCTCGATGTTCCAc > 1:925350/1‑69 (MQ=255)
|
AATGGCGTCAGCATTGCTGTATTGGGGAATGGACTTAATACCATTCATCCCCGCCGTCATGCCCGACTGGCTGCCAGTCTGCTTGAACAGGGGGGCGCTCTCGTCTCGGAATTTCCCCTCGATGTTCCAC > minE/2758942‑2759071
|
| 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
