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 |
|
A1 F8 I0 R2
|
422 |
46.8 |
3726540 |
94.7% |
3529033 |
61.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,581,839 |
C→T |
100% |
M222I (ATG→ATA) |
ydeM ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,581,839 | 0 | C | T | 97.2%
| 104.2
/ ‑3.9
| 36 | M222I (ATG→ATA) | ydeM | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base C (0/1); new base T (24/10); total (25/11) |
| Fisher's exact test for biased strand distribution p-value = 3.14e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
AAACTGACGGATGAAAATTTCACCCACATCGTTTTTAACCCATTGCATAAAAATGGTTGACATAAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAATGATACGGAATGTGTTCTCACTATGAC > W3110S.gb/1581779‑1581906
|
aaaCTGACGGATGAAAATTTCACCCACATCGTTTTTAACCCATTGCATAAAAATGGTTGATATAAACtt < 1:2985774/69‑1 (MQ=255)
aaCTGACGGATGAAAATTTCACCCACATCGTTTTTAACCCATTGCATAAAAATGGTTGATATAAACTTGcc < 1:3221589/71‑1 (MQ=255)
cTGACGGATGAAAATTTCACCCACATCGTTTTTAACCCATTGCATAAAAATGGTTGATATAAACTTGCCa > 1:3700569/1‑70 (MQ=255)
cGGATGAAAATTTCACCCACATCGTTTTTAACCCATTGCATAAAAATGGTTGATATAAACTTGCCATAAGc < 1:3456394/71‑1 (MQ=255)
aaaaTTTCACCCACATCGTTTTTAACCCATTGCATAAAAATGGTTGATATAAACTTGCCATAAGCCGTgg > 1:1930790/1‑70 (MQ=255)
cacaTCGTTTTTAACCCATTGCATAAAAATGGTTGATATAAACTTGCCATAAGCCGTGGGAGGCACAGaa > 1:828489/1‑70 (MQ=255)
cacaTCGTTTTTAACCCATTGCATAAAAATGGTTGATATAAACTTGCCATAAGCCGTGGGAGGCACAGaa > 1:2600817/1‑70 (MQ=255)
cacaTCGTTTTTAACCCATTGCATAAAAATGGTTGATATAAACTTGCCATAAGCCGTGGGAGGCACAGaa > 1:246452/1‑70 (MQ=255)
cacaTCGTTTTTAACCCATTGCATAAAAATGGTTGATATAAACTTGCCATAAGCCGTGGGAGGCACAGaa > 1:1890892/1‑70 (MQ=255)
cacaTCGTTTTTAACCCATTGCATAAAAATGGTTGATATAAACTTGCCATAAGCCGTGGGAGGCACAGaa > 1:1773932/1‑70 (MQ=255)
caTCGTTTTTAACCCATTGCATAAAAATGGTTGAtata < 1:3203585/38‑1 (MQ=255)
caTCGTTTTTAACCCATTGCATAAAAATGGTTGAtata < 1:959005/38‑1 (MQ=255)
caTCGTTTTTAACCCATTGCATAAAAATGGTTGAtata < 1:1596415/38‑1 (MQ=255)
caTCGTTTTTAACCCATTGCATAAAAATGGTTGAtata < 1:2601197/38‑1 (MQ=255)
caTCGTTTTTAACACATTGCATAAAAATGGTTGAtata < 1:394675/38‑1 (MQ=38)
tCGTTTTTAACCCATTGCATAAAAATGGTTGATATAAACTTGCCATAAGc < 1:3005661/50‑1 (MQ=255)
tCGTTTTTAACCCATTGCATAAAAATGGTTGATATAAACTTGCCATAAGc > 1:1639636/1‑50 (MQ=255)
tCGTTTTTAACCCATTGCATAAAAATGGTTGATATAAACTTGCCATAAGCCGTGGGAGGCACAGAAAAAt > 1:369173/1‑70 (MQ=255)
tCGTTTTTAACCCATTGCATAAAAATGGTTGATATAAACTTGCCATAAGCCGTGGGAGGCACAGAAAAAt > 1:3116485/1‑70 (MQ=255)
tCGTTTTTAACCCATTGCATAAAAATGGTTGATATAAACTTGCCATAAGCCGTGGGAGGCACAGAAAAAt > 1:2662443/1‑70 (MQ=255)
tCGTTTTTAACCCATTGCATAAAAATGGTTGATATAAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATc < 1:3596451/71‑1 (MQ=255)
gTTTTTAACCCATTGCATAAAAATGGTTGATATAAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCa < 1:202212/70‑1 (MQ=255)
tAACCCATTGCATAAAAATGGTTGATATAAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAATGAt < 1:2326670/70‑1 (MQ=255)
ccgaTTGCATAAAAATGGTTGATATAAACTTGCCATAAGCCGTGGGAGACACAGAAAAATCAATGATACgg < 1:1367824/68‑1 (MQ=255)
ttGCATAAAAATGGTTGATATAAACTTGCCATAAGCCGTgg < 1:105505/41‑1 (MQ=255)
gCATAAAAATGGTTGATATAAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAATGa > 1:76672/1‑60 (MQ=255)
gCATAAAAATGGTTGATATAAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAATGa > 1:2413272/1‑60 (MQ=255)
gCATAAAAATGGTTGATATAAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAATGa > 1:185065/1‑60 (MQ=255)
gCATAAAAATGGTTGATATAAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAATGa > 1:1057179/1‑60 (MQ=255)
cATAAAAATGGTTGACATAAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAATGATACGGAATgtgt < 1:1754753/71‑1 (MQ=255)
aaaaTGGTTGATATAAACTTGCCATAAGCCGTGGGAGGca > 1:3186433/1‑40 (MQ=255)
aaaaTGGTTGATATAAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAATGATACGGAAt > 1:2463771/1‑63 (MQ=255)
aaaaTGGTTGATATAAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAATGATACGGAATGTGtt > 1:2852540/1‑68 (MQ=255)
aaaaTGGTTGATATAAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAATGATACGGAATGTGtt > 1:2483971/1‑68 (MQ=255)
aaaaTGGTTGAAATAAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAATGATACGGAATGTGtt > 1:105625/1‑68 (MQ=255)
tGGTTGATATAAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAATGATa > 1:1898225/1‑53 (MQ=255)
gTTGATATAAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAAt < 1:2522762/47‑1 (MQ=255)
tGATATAAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAATGa > 1:3148540/1‑47 (MQ=255)
tGATATAAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAATGa > 1:2431237/1‑47 (MQ=255)
tGATATAAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAATGa > 1:1975496/1‑47 (MQ=255)
tGATATAAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAATGATACGGAATGTGTTCTCACTATGAc > 1:267340/1‑71 (MQ=255)
|
AAACTGACGGATGAAAATTTCACCCACATCGTTTTTAACCCATTGCATAAAAATGGTTGACATAAACTTGCCATAAGCCGTGGGAGGCACAGAAAAATCAATGATACGGAATGTGTTCTCACTATGAC > W3110S.gb/1581779‑1581906
|
| 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
