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 |
|
A4 F1 I0 R1
|
70 |
84.3 |
4123603 |
97.0% |
3999894 |
62.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,344,483 |
C→A |
23.5% |
G383G (GGC→GGA) |
glnG → |
fused DNA‑binding response regulator in two‑component regulatory system with GlnL, nitrogen regulator I (NRI) |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,344,483 | 0 | C | A | 23.5%
| 186.2
/ 28.6
| 68 | G383G (GGC→GGA) | glnG | fused DNA‑binding response regulator in two‑component regulatory system with GlnL, nitrogen regulator I (NRI) |
| Reads supporting (aligned to +/- strand): ref base C (27/25); new base A (10/6); total (37/31) |
| Fisher's exact test for biased strand distribution p-value = 5.70e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.65e-01 |
GAAAACACCTGCCGCTGGCTAACGGTGATGGCCGCCGGGCAGGAAGTGTTGATTCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTCGCAAATGCAACCGGACAGCTG > minE/2344415‑2344539
|
gAAAACACCTGCCGCTGGCTAACGGTGATGGCCGCCGGGCAGGAAGTGTTGATTCAGGATTTGCCCGGCg < 1:1638890/70‑1 (MQ=255)
agacCTGCCGCTGGCTAACGGTGATGGCCGCCGGGCAGGAAGTGTTGATTCAGGATTTGCCCGGCGAACTg > 1:3385180/3‑71 (MQ=255)
gCCGCTGGCTAACGGTGATGGCCGCCGGGCAGGAAGTGTTGATTCAGGATTTGCCCGGCGAACTg > 1:2673510/1‑65 (MQ=255)
gCCGCTGGCTAACGGTGATGGCCGCCGGGCAGGAAGTGTTGATTCAGGATTTGCCCGGCGAACTGTTTGaa > 1:1094965/1‑71 (MQ=255)
ccGCTGGCTAACGGTGATGGCCGCCGGGCAGGAAGTGTTGATTCAGGATTTGCCCGGCGAACTGTTTGAAt < 1:2571337/71‑1 (MQ=255)
gCTAACGGTGATGGCCGCCGGGCAGGAAGTGTTGATTCAGGATTTGCCCGGCGAACTGTTTGAATCAAc < 1:2525010/69‑1 (MQ=255)
tAACGGTGATGGCCGCCGGGCAGGAAGTGTTGATTCAGGATTTGCCCGGCGAACTGTTTGa < 1:813123/61‑1 (MQ=255)
aaCGGTGATGGCCGCCGGGCAGGAAGTGTTGATTCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGtt > 1:3732849/1‑70 (MQ=255)
aaCGGTGATGGCCGCCGGGCAGGAAGTGTTGATTCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGtt > 1:629252/1‑70 (MQ=255)
aaCGGTGATGGCCGCCGGGCAGGAAGTGTTGATTCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGtt > 1:1196459/1‑70 (MQ=255)
aaCGGTGATGGCCGCCGGGCAGGAAGTGTTGATTCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTg > 1:2677997/1‑71 (MQ=255)
aaCGGTGATGGCCGCCGGGCAGGAAGTGTTGATTCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTg > 1:2561977/1‑71 (MQ=255)
aaCGGTGATGGCCGCCGGGCAGGAAGTGTTGATTCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTg > 1:1150433/1‑71 (MQ=255)
aaCGGTGATGGCCGCCGGGCAGGAAGTGTTGATTCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTg > 1:1599513/1‑71 (MQ=255)
aaCGGTGATGGCCGCCGGGCAGGAAGTGTTGATTCAGGATTTGCCCGGAGAACTGtt > 1:2972102/1‑57 (MQ=255)
aaCGGTGATGGCCGCCGGGCAGGAAGTGTTGATTCAGGATTTGCCCGGAGAACTGtt > 1:962422/1‑57 (MQ=255)
cGGTGATGGCCGCCGGGCAGGAAGTGTTGATTCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTGCg > 1:1366611/1‑71 (MQ=255)
tGATGGCCGCCGGGCAGGAAGTGTTGATTCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTGCg < 1:646433/68‑1 (MQ=255)
tGATGGCAGCCGGGCAGGAAGTGTTGATTCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTGCg > 1:548735/1‑68 (MQ=255)
ggCCGCCGGGCAGGAAGTGTTGATTCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTGCGGAGAGTa > 1:377426/1‑71 (MQ=255)
gccgGGCAGGAAGTGTTGATTCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTc < 1:457268/71‑1 (MQ=255)
cgGGCAGGAAGTGTTGATTCAGGATTTGCCCGGCGCACTGTTTGAATCAACGGTTGCGGAGAGTACTTCg > 1:2990214/1‑70 (MQ=255)
cgGGCAGGAAGTGTTGATTCAGGATTTGCCCGGCGAACTGTTTGa > 1:2653006/1‑45 (MQ=255)
cgGGCAGGAAGTGTTGATTCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTCg > 1:2030540/1‑70 (MQ=255)
gggCAGGAAGTGTTGATTCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTCGCa < 1:189541/71‑1 (MQ=255)
gggCAGGAAGTGTTGATTCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTCGCa < 1:1450631/71‑1 (MQ=255)
gggCAGGAAGTGTTGATTCAGGATTTGCCCGGAGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTCGCa < 1:3831962/71‑1 (MQ=255)
ggCAGGAAGTGTTGATTCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTCGCa > 1:1330376/1‑70 (MQ=255)
ggCAGGAAGTGTTGATTCAGGATTTGCCCGGAGAACTGTTTGAATCAACGGTTGCGGagag < 1:802940/61‑1 (MQ=255)
gCAGGAAGTGTTGATTCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTCGCaaa < 1:1413903/71‑1 (MQ=255)
gCAGGAAGTGTTGATTCAGGATTTGCCCGGAGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTCGCaa < 1:1486536/70‑1 (MQ=255)
cAGGAAGTGTTGATTCAGGATTTGCCCGGAGAACTGTTTGAATCAACGGTTGCGGAGAGTa > 1:3332550/1‑61 (MQ=255)
ggAAGTGTTGATTCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTCGCAAATGc < 1:2473387/71‑1 (MQ=255)
ggAAGTGTTGATTCAGGATTTGCCCGGAGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTCGCaaa > 1:411947/1‑68 (MQ=255)
gtgtTGATTCAGGATTTGCCCGGAGAACTGTTTGAATCAACGGTTGct < 1:1333150/48‑2 (MQ=39)
tgtTGATTCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTGCGgag < 1:2561725/50‑1 (MQ=255)
tgtTGATTCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTGCGgag < 1:333547/50‑1 (MQ=255)
tgtTGATTCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTGCGgag < 1:3640450/50‑1 (MQ=255)
tgtTGATTCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTCGCAAATGCAACCg < 1:3934263/71‑1 (MQ=255)
tgtTGATTCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTCGCAAATGCAACCg < 1:884892/71‑1 (MQ=255)
gtTGATTCAGGATTTGCCCGGCGAACTGTTTGAATCAACg < 1:2227567/40‑1 (MQ=255)
gtTGATTCAGGATTTGCCCGGAGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTc > 1:619174/1‑57 (MQ=255)
gtTGATTCAGGATTTGCCCGGAGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTc > 1:2352303/1‑57 (MQ=255)
ttGATTCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTGCGga < 1:3805592/47‑1 (MQ=255)
ttGATTCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTGCGga < 1:1955884/47‑1 (MQ=255)
ttGATTCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTCGCAAAt > 1:3238741/1‑62 (MQ=255)
ttGATTCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTCGCAAATGCAACCGGa > 1:985650/1‑71 (MQ=255)
tGATTCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTc > 1:1087247/1‑55 (MQ=255)
tGATTCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTCGCAAATGCAACCGGa > 1:792862/1‑70 (MQ=255)
gATTCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTCGCAAATGCAACCGGa > 1:4068833/1‑69 (MQ=255)
gATTCAGGATTTGCCCGGAGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTCGCaa < 1:946626/58‑1 (MQ=255)
ttCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTCGCaa < 1:3007342/56‑1 (MQ=255)
ttCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTCGCAAATGCAACCGGACAg < 1:3297955/70‑1 (MQ=255)
ttCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTCGCAAATGCAACCGGACAGc < 1:3007057/71‑1 (MQ=255)
tCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTCGCAAATGc < 1:2267561/59‑1 (MQ=255)
tCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGTT‑CGGAGAGTACTTCGCAAATGc < 1:1222586/58‑1 (MQ=255)
ctggATTTGCCCGGCGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTCGCAAATg > 1:22312/3‑57 (MQ=255)
cAGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTCGCAAATg > 1:3414430/1‑57 (MQ=255)
aGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTGCGgaga > 1:1503232/1‑42 (MQ=255)
aGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTCGCAAATGCaa > 1:322368/1‑59 (MQ=255)
aGGATTTGCCCGGAGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTCGCAAATGCAACCGGACAGCTg > 1:2478542/1‑70 (MQ=255)
ggATTTGCCCGGCGAACTGTTTGAATCAACGGTTGCGGagag < 1:3413460/42‑1 (MQ=255)
ggATTTGCCCGGAGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTCGCAAATGCAACCGGACAGCTg < 1:3457969/69‑1 (MQ=255)
tttGCCCGGCGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTCg < 1:1511029/46‑1 (MQ=255)
tttGCCCGGAGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTCGCaaa > 1:2598599/1‑50 (MQ=255)
tttGCCCGGAGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTCGCaaa > 1:2833514/1‑50 (MQ=255)
tttGCCCGGAGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTCGCaaa > 1:2027608/1‑50 (MQ=255)
tGCCCGGCGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTCGCa > 1:2545823/1‑46 (MQ=255)
|
GAAAACACCTGCCGCTGGCTAACGGTGATGGCCGCCGGGCAGGAAGTGTTGATTCAGGATTTGCCCGGCGAACTGTTTGAATCAACGGTTGCGGAGAGTACTTCGCAAATGCAACCGGACAGCTG > minE/2344415‑2344539
|
| 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
