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 F17 I0 R2
|
162 |
60.6 |
4616657 |
98.5% |
4547407 |
62.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
406,395 |
C→T |
13.5% |
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 | 13.5%
| 161.6
/ 14.7
| 59 | intergenic (+1/‑257) | yaiA/aroM | hypothetical protein/conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base C (24/27); new base T (5/3); total (29/30) |
| Fisher's exact test for biased strand distribution p-value = 4.72e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.26e-01 |
AGTGAACATCCGACCGCTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTGCGTCACATTTTTCATAAT > W3110S.gb/406326‑406462
|
aGTGAACATCCGACCGCTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGAcc > 1:2203273/1‑71 (MQ=255)
aGTGAACATCCGACCGCTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGAcc < 1:1489116/71‑1 (MQ=255)
tGAACATCCGACCGCTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCg > 1:3340552/1‑70 (MQ=255)
gAACATCCGACCGCTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCa > 1:54380/1‑71 (MQ=255)
aaCATCCGACCGCTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCAt < 1:498175/71‑1 (MQ=255)
aCATCCGACCGCTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCAt < 1:763505/70‑1 (MQ=255)
cATCCGACCGCTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGATCGCATCa < 1:2948472/71‑1 (MQ=255)
tCCGACCGCTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGATCGCATCAGa > 1:408586/1‑71 (MQ=255)
ccGCTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGCCCGCATCAGa > 1:554242/1‑66 (MQ=255)
cTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCgg < 1:3035041/71‑1 (MQ=255)
cTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCg > 1:4593856/1‑70 (MQ=255)
tCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCgg > 1:470089/1‑70 (MQ=255)
tCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCgg > 1:4530151/1‑70 (MQ=255)
cAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCgg > 1:3480324/1‑69 (MQ=255)
cAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCgg > 1:2778385/1‑69 (MQ=255)
aGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCgg < 1:1780585/68‑1 (MQ=255)
aGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGa < 1:3821739/69‑1 (MQ=255)
cGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTc < 1:537850/71‑1 (MQ=255)
gatggatgCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCgg < 1:4492319/61‑1 (MQ=255)
gatggatgCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCt < 1:4124598/71‑1 (MQ=255)
atggatgCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCa < 1:3820773/47‑1 (MQ=255)
tggatgCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGATCGCATCAGACTGCTCGGAAGGGATTCt > 1:2959678/1‑69 (MQ=255)
tggatgCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGa < 1:2784589/71‑1 (MQ=255)
ggatgCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAgg < 1:4589952/62‑1 (MQ=255)
tgCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGAtt < 1:2166253/63‑1 (MQ=255)
tgCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCt < 1:307551/65‑1 (MQ=255)
cGAAAAAACGCTATGAGGACCCTGACAAAGAGTGATCGCATCAGAc > 1:1221863/1‑46 (MQ=255)
cGAAAAAACGCTATGAGGACCCTGACAAAGAGTGATCGCATCAGAc > 1:983427/1‑46 (MQ=255)
cGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCa > 1:1345243/1‑71 (MQ=255)
gAAAAAACGCTATGAGGACCCTGACAAAGAGTGATCGCATCAGACTGCTCCGAAGGGATTCTGAGTGCCAc > 1:167893/1‑71 (MQ=255)
gAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCAc > 1:1749690/1‑71 (MQ=255)
aaaaaaCGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGa > 1:3925801/1‑57 (MQ=255)
aaaaaaCGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCt < 1:3608934/61‑1 (MQ=255)
aaaaaaCGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTg < 1:3157016/62‑1 (MQ=255)
aaaaaaCGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTg < 1:470624/62‑1 (MQ=255)
aaaaaaCGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCa > 1:2674162/1‑69 (MQ=255)
aaaaaaCGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACt < 1:219756/71‑1 (MQ=255)
aaaaaCGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTa > 1:1291010/1‑71 (MQ=255)
aaaaaCGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTa > 1:3129678/1‑71 (MQ=255)
aaaaaCGCTATGAGGACCCTGAAAAAGAGTGACCGCATc > 1:3519500/1‑39 (MQ=255)
aaaaCGCTATGAGGACCCTGACAAAGAGTGACCGCATCa > 1:1476987/1‑39 (MQ=255)
aaCGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACaa < 1:3265574/71‑1 (MQ=255)
aCGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCt < 1:313006/56‑1 (MQ=255)
cGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAgg > 1:390342/1‑71 (MQ=255)
gCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAggg < 1:2098784/71‑1 (MQ=255)
tATGAGGACCCTGACAAAGAGTGATCGCATCAGACTGCTCgg < 1:828657/42‑1 (MQ=255)
tATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGAt > 1:295247/1‑71 (MQ=255)
tATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGAt > 1:1531807/1‑71 (MQ=255)
tGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCt < 1:852284/71‑1 (MQ=255)
aGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTg < 1:2666981/70‑1 (MQ=255)
ccTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTg < 1:3382645/44‑1 (MQ=255)
tGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGAt < 1:4587609/38‑1 (MQ=255)
aCAAAGAGTGACCGCATCAGACTGCTCGGAAGGGAtt > 1:2913287/1‑37 (MQ=255)
aCAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTc > 1:4030344/1‑38 (MQ=255)
aCAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTGCGTCACAttt < 1:263794/71‑1 (MQ=255)
aCAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTGCGTCACAttt < 1:2238962/71‑1 (MQ=255)
aCAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTGCGTCACAttt > 1:2745365/1‑71 (MQ=255)
aCAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTGCGTCACAtt < 1:2891058/70‑1 (MQ=255)
aaaGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATATGCGTCACAtttt > 1:3272875/1‑70 (MQ=255)
agTGACCGCATCAGACTGCTCGGAAGGGATTCTGAg > 1:1448400/1‑36 (MQ=255)
tGATCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTGCGTCACATTTTTCATAAt < 1:3572578/71‑1 (MQ=255)
ccGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTGCg < 1:1963950/52‑1 (MQ=255)
|
AGTGAACATCCGACCGCTCAGGAAGCGATGGATGCGAAAAAACGCTATGAGGACCCTGACAAAGAGTGACCGCATCAGACTGCTCGGAAGGGATTCTGAGTGCCACTACAAGGGATCTGCGTCACATTTTTCATAAT > W3110S.gb/406326‑406462
|
| 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
