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 |
|
A5 F21 I0 R2
|
316 |
65.6 |
5147759 |
97.4% |
5013917 |
60.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
406,395 |
C→T |
28.1% |
intergenic (+1/‑257) |
yaiA → / → aroM |
hypothetical protein/conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 406,395 | 0 | C | T | 28.1%
| 93.1
/ 40.9
| 57 | intergenic (+1/‑257) | yaiA/aroM | hypothetical protein/conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base C (22/19); new base T (7/9); total (29/28) |
| Fisher's exact test for biased strand distribution p-value = 5.65e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.86e-01 |
GAACATCCGACCGCTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTGCGTCACATTTTTCATAATTC > W3110S.gb/406329‑406464
|
gAACATCCGACCGCTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCa > 1:2230138/1‑71 (MQ=255)
cATCCGACCGCTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCAt > 1:1496570/1‑69 (MQ=255)
cATCCGACCGCTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCAt > 1:3335679/1‑69 (MQ=255)
ccGACCGCTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGATCGCATCAGAc > 1:4268905/1‑71 (MQ=255)
cGACCGCTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACt > 1:4996319/1‑71 (MQ=255)
gCTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCg < 1:4529339/71‑1 (MQ=255)
cTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCgg < 1:4871632/71‑1 (MQ=255)
cTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCgg < 1:2887327/71‑1 (MQ=255)
cTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCgg < 1:2163211/71‑1 (MQ=255)
cTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCgg < 1:1858293/71‑1 (MQ=255)
cTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCg > 1:2426589/1‑70 (MQ=255)
cTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCACACTGCTCgg < 1:450169/71‑1 (MQ=255)
ggAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACAGCATCAGACTGCTCGGaa > 1:2649339/1‑69 (MQ=255)
gAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCa < 1:2877218/56‑1 (MQ=255)
gAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAgg > 1:4551520/1‑70 (MQ=255)
aGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGa > 1:4148489/1‑56 (MQ=255)
gatggatgCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGATCGCATCAGACTGCTCGGAAGGGATTCt > 1:4305868/1‑71 (MQ=255)
gatggatgCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGATCGCATCAGACTGCTCGGAAGGGATTCt > 1:735928/1‑71 (MQ=255)
gatggatgCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGa > 1:4155490/1‑53 (MQ=255)
atggatgCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTg < 1:3665002/71‑1 (MQ=255)
atggatgCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTg < 1:294938/71‑1 (MQ=255)
tggatgCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGATCGCATCAGACTGCTCGGAAGGGATTCt > 1:3391006/1‑69 (MQ=255)
tggatgCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGa > 1:1578619/1‑65 (MQ=255)
gatgCGAAAAAACTCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGt < 1:796828/71‑1 (MQ=255)
tgCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGATCGCATCAGACTGCTCGGAAGGGATTCTg < 1:4638354/66‑1 (MQ=255)
gCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGAt < 1:3881648/61‑1 (MQ=255)
cGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCa > 1:323977/1‑71 (MQ=255)
gAAAAAACGCTATGAGGACCCTGACAAAGAGTGATCGCATCAGACTGCTCgg < 1:4703070/52‑1 (MQ=255)
gAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCAc > 1:4223808/1‑71 (MQ=255)
aaaaaaCGCTATGAGGACCCTGACAAAGAGTGATCGCATCAGACTGCTCGGAAGGGATTCt < 1:1898985/61‑1 (MQ=255)
cGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTTAGTGCCACTACAAgg > 1:1113661/1‑71 (MQ=255)
cGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAgg > 1:4994520/1‑71 (MQ=255)
gCTATGAGGACCCTGACAAAGAGTGATCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAggg < 1:5004918/71‑1 (MQ=255)
gCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAgg > 1:2614577/1‑70 (MQ=255)
tATGAGGACCCTGACAAAGAGTGATCGCATCAGACTGCTCGGaa < 1:4762953/44‑1 (MQ=255)
tATGAGGACCCTGACAAAGAGTGATCGCATCAGACTGCTCGGaa < 1:3457249/44‑1 (MQ=255)
aGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTGc > 1:4754137/1‑71 (MQ=255)
aGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTGc > 1:1759449/1‑71 (MQ=255)
ggACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTGCg < 1:560433/71‑1 (MQ=255)
cTGACAAAGAGTGATCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTAc < 1:1669769/54‑1 (MQ=255)
cTGACAAAGAGTGACCGCATCAGACTGCTCGGAAgg < 1:3049101/36‑1 (MQ=255)
cTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTGCGTcaca > 1:3124444/1‑71 (MQ=255)
tGACAAAGAGTGATCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTGCGTCACAt > 1:218751/1‑71 (MQ=255)
tGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTGCGTCACAt > 1:507782/1‑71 (MQ=255)
gACAAAGAGTGATCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACt < 1:2996264/50‑1 (MQ=255)
gACAAAGAGTGATCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTGCGTCACAtt > 1:1394184/1‑71 (MQ=255)
gACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTGCGTCACAtt > 1:3968564/1‑71 (MQ=255)
cAAAGAGTGATCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACaa > 1:1743630/1‑52 (MQ=255)
aaaGAGTGATCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTGCGTCACAttttt < 1:44460/71‑1 (MQ=255)
aaaGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTg > 1:1253731/1‑38 (MQ=255)
aaGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTGCGTCACATTTTTc < 1:4289607/71‑1 (MQ=255)
agagTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTGCGTCACATTTTTCa < 1:1782525/71‑1 (MQ=255)
agagTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTGCGTCACATTTTTCa < 1:229089/71‑1 (MQ=255)
gagTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTGCGTCACATTTTTCAt < 1:1909039/71‑1 (MQ=255)
gagTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTGCGTCACATTTTTCAt < 1:1475025/71‑1 (MQ=255)
aCCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTGCGTCACATTTTTCATAAtt > 1:369301/1‑70 (MQ=255)
aCCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTGCGTCACATTTTTCATAATTc < 1:1822057/71‑1 (MQ=255)
|
GAACATCCGACCGCTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTGCGTCACATTTTTCATAATTC > W3110S.gb/406329‑406464
|
| 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
