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 |
|
A6 F21 I0 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,493,694 |
T→G |
20.4% |
intergenic (+76/‑299) |
gyrB → / → ibpA |
DNA gyrase, subunit B/heat shock chaperone |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,493,694 | 0 | T | G | 20.4%
| 106.3
/ 29.3
| 54 | intergenic (+76/‑299) | gyrB/ibpA | DNA gyrase, subunit B/heat shock chaperone |
| Reads supporting (aligned to +/- strand): ref base T (20/23); new base G (5/6); total (25/29) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01 |
GCGTGCCTGATGCGCTACGCTTATCAGGCCTACGAAAATCTTGCAATGTATTGAATTTTCATGATTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAAGAAGCTATAAGAAAAGGGCG > minE/2493636‑2493759
|
gCGTGCCTGATGCGCTACGCTTATCAGGCCTACGAAAATCTTGCAATGTATTGAATTTTCATGATTTTg > 1:177543/1‑69 (MQ=255)
gCGTGCCTGATGCGCTACGCTTATCAGGCCTACGAAAATCTTGCAATGTATTGAATTTTCATGATTTTGTa < 1:928018/71‑1 (MQ=255)
aatGCCTGATGCGCTCCGCTTATCAGGCCTACGAAAATTCTGCAATGTATTGAATTTGCACGATTTTGTAg > 1:2701367/3‑71 (MQ=14)
atGCCTGATGCGCTCCGCTTATCAGGCCTACGAAAATTCTGCAATGTATTGAATTTGCACGATTTTGTAgg < 1:1678206/70‑1 (MQ=14)
ccTGATGCGCTACGCTTATCAGGCCTACGAAAATCTTGCAATGTATTGAATTTTCATGATTTTGTAGGCCg > 1:741336/1‑71 (MQ=255)
cTGATGCGCTACGCTTATCAGGCCTACGAAAATCTTGCAATGTATTGAAtttt < 1:1089963/53‑1 (MQ=255)
cTGATGCGCTACGCTTATCAGGCCTACGAAAATCTTGCAATGTATTGAATTTTCATGATTTTGTAGGCCg > 1:229203/1‑70 (MQ=255)
gATGCGCTCCGCTTATCAGGCCTACGAAAATTCTGCAATGTATTGAATTTGCACGATTTTGTAGGCCGGa > 1:277434/1‑70 (MQ=14)
aTGCGCTCCGCTTATCAGGCCTACGAAAATTCTGCAATGTATTGAATTTGCACGATTTTGTAGGCCGGAt < 1:1366568/70‑1 (MQ=14)
aTGCGCTACGCTTATCAGGCCTACGAAAATCTTGCAATGTATTGAATTTTCATGATTTTGTAGGCCGGAt < 1:1127597/70‑1 (MQ=255)
aTGCGCTACGCTTATCAGGCCTACGAAAATCTTGCAATGTATTGAATTTTCATGATTTTGTAGGCCGGAt > 1:1751399/1‑70 (MQ=255)
tGCGCTCCGCTTATCAGGCCTACGAAAATTCTGCAGTGTATTGAATTTGCACGATTTTGTAGGCCGGAt > 1:3531496/1‑69 (MQ=14)
tGCGCTACGCTTATCAGGCCTACGAAAATCTTGCAATGTATTGAATTTTCATGATTTTGTAGGCCGGAt > 1:3830590/1‑69 (MQ=255)
cgcTCCGCTTATCAGGCCTACGAAAATTCTGCAATGTATTGAATTTGCACGATTTTGTAGGCCGGATAAg < 1:1473834/70‑1 (MQ=14)
cgcTACGCTTATCAGGCCTACGAAAATCTTGCAATGTATTGAATTTTCATGATTTTGTAGGCCGGATAAgg < 1:1981069/71‑1 (MQ=255)
gcTACGCTTATCAGGCCTACGAAAATCTTGCAATGTATTGAATTTTCATGAtttt < 1:2128235/55‑1 (MQ=255)
gcTACGCTTATCAGGCCTACGAAAATCTTGCAATGTATTGAATTTTCATGATTTTg > 1:2761066/1‑56 (MQ=255)
cTACGCTTATCAGGCCTACGAAAATCTTGCAATGTATTGAATTTTCATGAt < 1:1709508/51‑1 (MQ=255)
cTACGCTTATCAGGCCTACGAAAATCTTGCAATGTATTGAATTTTCATGAt < 1:1559875/51‑1 (MQ=255)
cTACGCTTATCAGGCCTACGAAAATCTTGCAATGTATTGAATTTTCATGAt < 1:2565870/51‑1 (MQ=255)
cTACGCTTATCAGGCCTACGAAAATCTTGCAATGTATTGAATTTTCATGATTTTGTAGGCCg < 1:3240778/62‑1 (MQ=255)
tACGCTTATCAGGCCTACGAAAATCTTGCAATGTATTGAATTTTCATGATTTTGTAGGCCGGATAAGGCGt > 1:1674431/1‑71 (MQ=255)
cGCTTATCAGGCCTACGAAAATTCTGCAATGTATTGAATTTGCACGATTTTGTAGGCCGGATAAGGCGtt > 1:981727/1‑70 (MQ=14)
cTTATCAGGCCTACGAAAATCTTGCAATGTATTGAATTTTCATGATTTTGTAGGCCGGATAAGGCGTTCAc < 1:3193602/71‑1 (MQ=255)
tATCAGGCCTACGAAAATCTTGCAATGTATTGAATTTTCATGATTTTg < 1:354434/48‑1 (MQ=255)
tATCAGGCCTACGAAAATCTTGCAATGTATTGAATTTTCATGATTTTGTAGGCCGGATAAGGCGTTCAcgc > 1:3533810/1‑71 (MQ=255)
tCAGGCCTACGAAAATCTTGCAATGTATTGAATTTTCATGATTTTGTa > 1:1000507/1‑48 (MQ=255)
ggCCTACGAAAATTCTGCAATGTATTGAATTTGCACGATTTTGTAGGCCGGATAAGGCGTTAACGCCGCAt < 1:1782256/71‑1 (MQ=14)
ggCCTACGAAAATCTTGCAATGTATTGAATTTTCATGATTTTGTAGGCCGGATAAGGCGTTCACGCCGCAt < 1:3135301/71‑1 (MQ=255)
ggCCTACGAAAATCTTGCAATGTATTGAATTTTCATGATTTTGTAGGCCGGATAAGGCGTTCACGCCGCAt > 1:3576027/1‑71 (MQ=255)
gCCTACGAAAATTCTGCAATGTATTGAATTTGCACGATTTTGTAGGCCGGATAAGGCGTTAACGCCGCATc < 1:3501910/71‑1 (MQ=11)
gCCTACGAAAATCTTGCAATGTATTGAATTTTCATGATTTTGTAGGCCGGATAAGGCGTTCACGCCGCATc < 1:1685497/71‑1 (MQ=255)
gCCTACGAAAATCTTGCAATGTATTGAATTTTCATGATTTTGTAGGCCGGATAAGGCGTTAACGCCGCATc < 1:893433/71‑1 (MQ=255)
ccTACGAAAATTCTGCAATGTATTGAATTTGCACGATTTTGTAGGCCGGATAAGGCGTTAACGCCGCATcc < 1:1653805/71‑1 (MQ=11)
cTACGAAAATTCTGCAATGTATTGAATTTGCACGATTTTGTa > 1:3602198/1‑42 (MQ=14)
tACGAAAATCTTGCAATGTATTGAATTTTCATGAtttt < 1:258896/38‑1 (MQ=255)
aCGAAAATCTTGCAATGTATTGAATTTTCATGATTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCgg > 1:3912605/1‑70 (MQ=255)
gAAAATCTTGCAATGTATTGAATTTTCATGATTTTg < 1:989866/36‑1 (MQ=255)
gAAAATCTTGCAATGTATTGAATTTTCATGATTTTGTAGGCCGGATaa < 1:3297536/48‑1 (MQ=255)
gAAAATCTTGCAATGTATTGAATTTTCATGATTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCaa < 1:1248346/71‑1 (MQ=255)
aaaTCTTGCAATGTATTGAATTTTCATGATTTTGTa > 1:1134761/1‑36 (MQ=255)
aaaTCTTGCAATGTATTGAATTTTCATGATTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCaag < 1:1423851/70‑1 (MQ=255)
aaTCTTGCAATGTATTGAATTTTCATGATTTTGTAGGCCGGATa < 1:3883058/44‑1 (MQ=255)
aTCTTGCAATGTATTGAATTTTCATGATTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCaagaag > 1:1047723/1‑71 (MQ=255)
tCTTGCAATGTATTGAATTTTCATGATTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAAGAAGc > 1:1307273/1‑71 (MQ=255)
ttGCAATGTATTGAATTTTCATGATTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAAGAAGCta > 1:1279665/1‑71 (MQ=255)
ttGCAATGTATTGAATTTTCATGATTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAAGAAGCt > 1:1898855/1‑70 (MQ=255)
tGCAATGTATTGAATTTTCATGATTTTGTAGGCCGGATAAGGc < 1:1741457/43‑1 (MQ=255)
tGTATTGAATTTTCATGATTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAAGAAGCTATAAGa > 1:2040879/1‑70 (MQ=255)
gTATTGAATTTTCATGATTTTGTAGGCCGGATAAGGCGTTCAcg < 1:2719292/44‑1 (MQ=255)
tATTGAATTTTCATGATTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAAGAAGCTATAAGaa > 1:470627/1‑69 (MQ=255)
gtaTTTTCATGATTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAAGAAGCTATAAGaa < 1:3753821/63‑1 (MQ=255)
gAATTTTCATGATTTTGTAGGCCGGATAAGGCGTTCa < 1:632819/37‑1 (MQ=40)
aaTTTTCATGATTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAAGAAGCTATAAGAAAAGGGCg > 1:1847341/1‑71 (MQ=255)
aTTTTCATGATTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAAGAAGCtata > 1:2484319/1‑59 (MQ=255)
ttttCATGATTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAAGAAGCTATAAGaa < 1:1399217/62‑1 (MQ=255)
|
GCGTGCCTGATGCGCTACGCTTATCAGGCCTACGAAAATCTTGCAATGTATTGAATTTTCATGATTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAAGAAGCTATAAGAAAAGGGCG > minE/2493636‑2493759
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
