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 |
1,371,319 |
G→T |
30.1% |
L149L (CTG→CTT) |
cdd → |
cytidine/deoxycytidine deaminase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,371,319 | 0 | G | T | 30.1%
| 69.9
/ 28.3
| 53 | L149L (CTG→CTT) | cdd | cytidine/deoxycytidine deaminase |
| Reads supporting (aligned to +/- strand): ref base G (26/11); new base T (8/8); total (34/19) |
| Fisher's exact test for biased strand distribution p-value = 2.15e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GCCTTGTGGTCACTGCCGTCAGTTTATGAATGAACTGAACAGCGGTCTGGATCTGCGTATTCATCTGCCGGGCCGCGAGGCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGATCTG > minE/1371253‑1371382
|
gCCTTGTGGTCACTGCCGTCAGTTTATGAATGAACTGAACAGCGGTCTGGATCTGCGTATTCATCTGcc > 1:1249508/1‑69 (MQ=255)
gCCTTGTGGTCACTGCCGTCAGTTTATGAATGAACTGAACAGCGGTCTGGATCTGCGTATTCATCTGc > 1:2637934/1‑68 (MQ=255)
cACTGCCGTCAGTTTATGAATGAACTGAACAGCGGTCTGGATCTGCGTATTCATCTGCCGGGCCGCGa > 1:2021095/1‑68 (MQ=255)
cACTGCCGTCAGTTTATGAATGAACTGAACAGCGGTCTGGATCTGCGTATTCATCTGCCGGGCCGCGa > 1:394804/1‑68 (MQ=255)
cACTGCCGTCAGTTTATGAATGAACTGAACAGCGGTCTGGATCTGCGTATTCATCTGCCGGGCCGCGa > 1:237727/1‑68 (MQ=255)
cACTGCCGTCAGTTTATGAATGAACTGAACAGCGGTCTGGATCTGCGTATTCATCTGCCGGGCCGCGa > 1:3189283/1‑68 (MQ=255)
cACTGCCGTCAGTTTATGAATGAACTGAACAGCGGTCTGGATCTGCGTATTCATCTGCCGGGCCGCGa > 1:2964917/1‑68 (MQ=255)
cACTGCCGTCAGTTTATGAATGAACTGAACAGCGGTCTGGATCTGCGTATTCATCTGCCGGGCCGCGa > 1:2121725/1‑68 (MQ=255)
cACTGCCGTCAGTTTATGAATGAACTGAACAGCGGTCTGGATCTGCGTATTCATCTGCCGGGCCGCGa > 1:1460910/1‑68 (MQ=255)
cACTGCCGTCAGTTTATGAATGAACTGAACAGCGGTCTGGATCTGCGTATTCATCTGCCGGGCCGCGa > 1:124764/1‑68 (MQ=255)
cACTGCCGTCAGTTTATGAATGAACTGAACAGCGGTCTGGATCTGCGTATTCATCTGCCGGGCCGCGa > 1:2789765/1‑68 (MQ=255)
tGCCGTCAGTTTATGAATGAACTGAACAGCGGTCTGGATCTGCGTATTCATCTGCCGGGCCGCGAGGca < 1:1933089/69‑1 (MQ=255)
accGTCAGTTTATGAATGAACTGAACAGCGGTCTGGATCTGCGTATTCATCTGCCGGGCCGCGAGGcac < 1:1206842/68‑1 (MQ=255)
ccGTCAGTTTATGAATGAACTGAACAGCGGTCTGGATCTGCGTATTCATCTGCCGGGCCGCGAGGcaca > 1:2954334/1‑69 (MQ=255)
ccGTCAGTTTATGAATGAACTGAACAGCGGTCTGGATCTGCGTATTCATCTGCCGGGCCGCGAGGcaca > 1:3274045/1‑69 (MQ=255)
ccGTCAGTTTATGAATGAACTGAACAGCGGTCTGGATCTGCGTATTCATCTGCCGGGCCGCGAGGcaca > 1:413956/1‑69 (MQ=255)
aGTTTATGAATGAACTGAACAGCGGTCTGGATCTGCGTATTCATCTGCCGGGCCGCGAGGCACAcgcg > 1:3223052/1‑68 (MQ=255)
aGTTTATGAATGAACTGAACAGCGGTCTGGATCTGCGTATTCATCTGCCGGGCCGCGAGGCACACgcgc > 1:22437/1‑69 (MQ=255)
aGTTTATGAATGAACTGAACAGCGGTCTGGATCTGCGTATTCATCTGCCGGGCCGCGAGGCACACgcgc > 1:988578/1‑69 (MQ=255)
ttATGAATGAACTGAACAGCGGTCTGGATCTGCGTATTCATCTGCCGGGCCGCGAGGCACACGCGCTGc > 1:2543153/1‑69 (MQ=255)
ttATGAATGAACTGAACAGCGGTCTGGATCTGCGTATTCATCTGCCGGGCCGCGAGGCACACGCGCTGc > 1:2662391/1‑69 (MQ=255)
ttATGAATGAACTGAACAGCGGTCTGGATCTGCGTATTCATCTGCCGGGCCGCGAGGCACACGCGCTGc > 1:2856219/1‑69 (MQ=255)
ttATGAATGAACTGAACAGCGGTCTGGATCTGCGTATTCATCTGCCGGGCCGCGAGGCACACGCGCTGc > 1:3234174/1‑69 (MQ=255)
ttATGAATGAACTGAACAGCGGTCTGGATCTGCGTATTCATCTGCCGGGCCGCGAGGCACACGCGCTGc > 1:1888161/1‑69 (MQ=255)
ttATGAATGAACTGAACAGCGGTCTGGATCTGCGTATTCATCTGCCGGGCCGCGAGGCACACGCGCTGc > 1:642256/1‑69 (MQ=255)
ttATGAATGAACTGAACAGCGGTCTGGATCTGCGTATTCATCTGCCGGGCCGCGAGGCACACGCGCTGc > 1:68303/1‑69 (MQ=255)
tATGAATGAACTGAACAGCGGTCTGGATCTGCGTATTCATCTGCCGGGCCGCGAGGCACACGCGCTGc > 1:1017094/1‑68 (MQ=255)
cAGCGGTCTGGATCTGCGTATTCATCTGCCGGGCCGCGAGGCACACGCGCTGCGTGACTATCTGCCa < 1:1528345/67‑1 (MQ=255)
tCTGCGTATTCATCTTCCGGGACGCGAGGCACACGCGCTGCGTGACTATCTACCGGATGCCTTTggg < 1:410967/67‑1 (MQ=255)
tCTGCGTATTCATCTTCCGGGACGCGAGGCACACGCGCTGCGTGACTATCTACCGGATGCCTTTggg < 1:447380/67‑1 (MQ=255)
tCTGCGTATTCATCTTCCGGGACGCGAGGCACACGCGCTGCGTGACTATCTACCGGATGCCTTTggg < 1:940694/67‑1 (MQ=255)
tCTGCGTATTCATCTTCCGGGACGCGAGGCACACGCGCTGCGTGACTATCTACCGGATGCCTTTggg < 1:108341/67‑1 (MQ=255)
tCTGCGTATTCATCTTCCGGGACGCGAGGCACACGCGCTGCGTGACTATCTACCGGATGCCTTTggg < 1:2759026/67‑1 (MQ=255)
tCTGCGTATTCATCTTCCGGGACGCGAGGCACACGCGCTGCGTGACTATCTACCGGATGCCTTTggg < 1:2243955/67‑1 (MQ=255)
tCTGCGTATTCATCTTCCGGGACGCGAGGCACACGCGCTGCGTGACTATCTACCGGATGCCTTTggg < 1:1813608/67‑1 (MQ=255)
tCTGCGTATTCATCTTCCGGGACGCGAGGCACACGCGCTGCGTGACTATCTACCGGATGCCTTTggg < 1:1626343/67‑1 (MQ=255)
tGCGTATTCATCTGCCGGGCCGCGAGGCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGcc > 1:2176163/1‑67 (MQ=255)
aTTCATCTGTCGGGCCGCGAGGCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGAt < 1:64799/69‑1 (MQ=255)
aTTCATCTGCCGGGCCGCGAGGCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGAt < 1:2478277/69‑1 (MQ=255)
aTTCATCTGCCGGGCCGCGAGGCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGAt < 1:2063675/69‑1 (MQ=255)
aTTCATCTGCCGGGCCGCGAGGCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGAt < 1:355729/69‑1 (MQ=255)
aTTCATCTGCCGGGCCGCGAGGCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGAt < 1:1961022/69‑1 (MQ=255)
aTTCATCTGCCGGGCCGCGAGGCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGAt < 1:948735/69‑1 (MQ=255)
aTTCATCTGCCGGGCCGCGAGGCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGAt < 1:1251363/69‑1 (MQ=255)
aTTCATCTGCCGGGCCGCGAGGCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGAt < 1:811982/69‑1 (MQ=255)
aTCTTCCGGGACGCGAGGCACACGCGCTGCGTGACTATCTACCGGATGCCtttc > 1:351830/1‑53 (MQ=37)
aTCTTCCGGGACGCGAGGCACACGCGCTGCGTGACTATCTACCGGATGCCTTTg > 1:663541/1‑54 (MQ=37)
aTCTTCCGGGACGCGAGGCACACGCGCTGCGTGACTATCTACCGGATGCCTTTGGGCCGATAGAtgaa > 1:2598403/1‑65 (MQ=255)
aTCTTCCGGGACGCGAGGCACACGCGCTGCGTGACTATCTACCGGATGCCTTTGGGCCGAAAGAtgaa > 1:802633/1‑65 (MQ=255)
aTCTTCCGGGACGCGAGGCACACGCGCTGCGTGACTATCTACCGGATGCCTTTGGGCCGAAAGAtgaa > 1:1705631/1‑65 (MQ=255)
aTCTTCCGGGACGCGAGGCACACGCGCTGCGTGACTATCTACCGGATGCCTTTGGGCCGAAAGAtgaa > 1:1957893/1‑65 (MQ=255)
aTCTTCCGGGACGCGAGGCACACGCGCTGCGTGACTATCTACCGGATGCCTTTGGGCCGAAAGAtgaa > 1:1168612/1‑65 (MQ=255)
aTCTTCCGGGACGCGAGGCACACGCGCTGCGTGACTATATACCGGATg > 1:1541863/1‑48 (MQ=21)
|
GCCTTGTGGTCACTGCCGTCAGTTTATGAATGAACTGAACAGCGGTCTGGATCTGCGTATTCATCTGCCGGGCCGCGAGGCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGATCTG > minE/1371253‑1371382
|
| 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
