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 F17 I0 R2
|
276 |
45.3 |
3729697 |
93.0% |
3468618 |
60.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,714,423 |
C→T |
48.1% |
H61Y (CAC→TAC) |
atpI → |
ATP synthase, membrane‑bound accesory subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,714,423 | 0 | C | T | 48.1%
| 5.1
/ 76.7
| 54 | H61Y (CAC→TAC) | atpI | ATP synthase, membrane‑bound accesory subunit |
| Reads supporting (aligned to +/- strand): ref base C (19/9); new base T (16/10); total (35/19) |
| Fisher's exact test for biased strand distribution p-value = 7.77e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.34e-01 |
TCTGCAATAAGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCATTTGGCGAAGCTTTCAAAGT > W3110S.gb/3714357‑3714490
|
tctGCAATAAGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTc > 1:2781288/1‑67 (MQ=255)
tctGCAATAAGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTc > 1:2776762/1‑67 (MQ=255)
tctGCAATAAGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTc > 1:1986306/1‑67 (MQ=255)
tctGCAATAAGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTAc < 1:112159/69‑1 (MQ=255)
aaTAAGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCa > 1:3654310/1‑66 (MQ=255)
aGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCa < 1:983200/68‑1 (MQ=255)
aGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCa < 1:210019/68‑1 (MQ=255)
aGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCCCa < 1:1593826/68‑1 (MQ=255)
aGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGgc > 1:3020652/1‑65 (MQ=255)
cGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATa < 1:3091387/68‑1 (MQ=255)
cGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAgg < 1:2971604/62‑1 (MQ=255)
ggCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAgg < 1:2600978/58‑1 (MQ=255)
ccTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCATACACCAg > 1:2331826/1‑68 (MQ=255)
ccTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCATACACCAg > 1:3699640/1‑68 (MQ=255)
aGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCa > 1:1474735/1‑54 (MQ=255)
aGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCa < 1:2978007/54‑1 (MQ=255)
aGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCATac > 1:172020/1‑57 (MQ=255)
aGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCATac > 1:2151720/1‑57 (MQ=255)
aGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCATACACCAGCGAAAgg > 1:1579997/1‑69 (MQ=255)
aGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCATACACCAGCGAAAgg > 1:2413729/1‑69 (MQ=255)
gTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCa < 1:2656229/53‑1 (MQ=255)
tCTTTCTGCTTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGgcg > 1:449888/1‑50 (MQ=255)
tCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGgcg < 1:3457404/50‑1 (MQ=255)
tCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGgcg < 1:781097/50‑1 (MQ=255)
tCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGgcg > 1:950893/1‑50 (MQ=255)
tCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGgcg > 1:2599921/1‑50 (MQ=255)
tCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGgcg > 1:2358813/1‑50 (MQ=255)
tCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGgcg < 1:1084119/50‑1 (MQ=255)
acTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGgcg > 1:2085742/2‑50 (MQ=255)
cTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCa < 1:338071/51‑1 (MQ=255)
cTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCa < 1:1252010/51‑1 (MQ=255)
cTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCa < 1:2563638/51‑1 (MQ=255)
tttCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTc > 1:1172798/1‑40 (MQ=255)
tttCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCgg > 1:2246889/1‑69 (MQ=255)
tttCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCgg > 1:2152019/1‑69 (MQ=255)
tttCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCgg > 1:3551173/1‑69 (MQ=255)
tttCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCg > 1:3135387/1‑68 (MQ=255)
tttCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCATACACCAGCGAAAGGCCgg > 1:1419676/1‑69 (MQ=255)
tttCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCATACACCAGCGAAAGGCCgg > 1:3377650/1‑69 (MQ=255)
tttCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCATACACCAGCGAAAGGCCgg > 1:1526335/1‑69 (MQ=255)
tttCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCATACACCAGCGAAAGGCCgg > 1:3410672/1‑69 (MQ=255)
tttCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCATACACCAGCGAAAGGCCgg > 1:1144937/1‑69 (MQ=255)
tttCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCATACACCAGCGAAAGGCCgg > 1:3577427/1‑69 (MQ=255)
tttCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCATACACCAGCGAAAGGCCgg > 1:1146388/1‑69 (MQ=255)
tCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCg > 1:1225304/1‑66 (MQ=255)
tCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGt > 1:1674014/1‑69 (MQ=255)
cTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCATACACCAGCGAAAGGCCGGGTGGcc > 1:64488/1‑68 (MQ=255)
aCGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGa > 1:1171348/1‑69 (MQ=255)
ttttGTTTATGATATTTGCCTGGCGTCACCAGGCGCATACACCAGCGAAAGGCCg > 1:1614871/1‑55 (MQ=255)
ttttGTTTATGATATTTGCCTGGCGTCACCAGGCGCATACACCAGCGAAAGGCCg > 1:789441/1‑55 (MQ=255)
ttGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGaa < 1:343165/47‑1 (MQ=255)
tATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCAtt > 1:1889175/1‑69 (MQ=255)
atatTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCATTTgg > 1:1422639/1‑68 (MQ=255)
atatTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCATTTgg > 1:1304388/1‑68 (MQ=255)
atatTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCATTTgg > 1:2735231/1‑68 (MQ=255)
ggCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCATTTGGCGAAGCTTTCa < 1:2303719/69‑1 (MQ=255)
ggCGTCACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCATTTGGCGAAGCTTTCa < 1:1700428/69‑1 (MQ=255)
tCACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCATTTGGCGAAGCTTTCAAAGt < 1:403140/69‑1 (MQ=255)
|
TCTGCAATAAGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCATTTGGCGAAGCTTTCAAAGT > W3110S.gb/3714357‑3714490
|
| 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
