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 |
|
A2 F3 I0 R2
|
232 |
76.3 |
4135488 |
90.9% |
3759158 |
60.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,249,490 |
G→A |
29.8% |
S227N (AGC→AAC) |
thiF → |
thiamin (thiazole moiety) biosynthesis protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,249,490 | 0 | G | A | 29.8%
| 83.5
/ 44.4
| 57 | S227N (AGC→AAC) | thiF | thiamin (thiazole moiety) biosynthesis protein |
| Reads supporting (aligned to +/- strand): ref base G (31/9); new base A (8/9); total (39/18) |
| Fisher's exact test for biased strand distribution p-value = 3.23e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.89e-01 |
GAAGCCATTAAGTTATTAAGCGGTATAGAGACACCTGCGGGAGAACTCCGACTGTTCGACGGTAAATCGAGCCAGTGGCGCAGCCTGGCGTTGCGCCGCGCCAGTGGTTGCCCGGTATGCGGAGGAAGCAATGCA > minE/2249420‑2249554
|
gAAGCCATTAAGTTATTAAGCGGTATAGAGACACCTGCGGGAGAACTCCGACTGTTCGACGGTAAATCGAg > 1:800639/1‑71 (MQ=255)
aGCCATTAAGTTATTAAGCGGTATAGAGACACCTGCGGGAGAACTCCGACTGTTCGACGGTAAATCGAGcc < 1:1242389/71‑1 (MQ=255)
aaGTTATTAAGCGGTATAGAGACACCTGCGGGAGAACTCCGACTGTTCGACGGTAAATCGAGCCAGTGgcg > 1:2940655/1‑71 (MQ=255)
aaGTTATTAAGCGGTATAGAGACACCTGCGGGAGAACTCCGACTGTTCGACGGTAAATCGAGCCAGTGgcg > 1:1619564/1‑71 (MQ=255)
aaGTTATTAAGCGGTATAGAGACACCTGCGGGAGAACTCCGACTGTTCGACGGTAAATCGAGCCAGAGgcg > 1:2879636/1‑71 (MQ=255)
tattaAGCGGTATAGAGACACCTGCGGGAGAACTCCGACTGTTCGACGGTAAATCGAGCCAGTGgcg > 1:3939839/1‑67 (MQ=255)
aGCGGTATAGAGACACCTGCGGGAGAACTCCGACTGTTCGACGGTAAATCGAGCCAGTGGCGCAGCCTgg < 1:1189929/70‑1 (MQ=255)
tataGAGACACCTGCGGGAGAACTCCGACTGTTCGACGGTAAATCGAGCCAGTGGCGCAGCCTGGCGTTgc > 1:1538765/1‑71 (MQ=255)
tataGAGACACCTGCGGGAGAACTCCGACTGTTCGACGGTAAATCGAGCCAGTGGCGCAGCCTGGCGTTgc > 1:2374717/1‑71 (MQ=255)
ataGAGACACCTGCGGGAGAACTCCGACTGTTCGACGGTAAATCGAGCCAGTGGCGCAGCCTGGCGTTgcg > 1:3698205/1‑71 (MQ=255)
taGAGACACCTGCGGGAGAACTCCGACTGTTCGACGGTAAATCGAGCCAg > 1:3200704/1‑50 (MQ=255)
taGAGACACCTGCGGGAGAACTCCGACTGTTCGACGGTAAATCGAGCCAGTGGCGCAGCCTGGCGTTgcg > 1:579832/1‑70 (MQ=255)
gagaCACCTGCGGGAGAACTCCGACTGTTCGACGGTAAATCGAGCCAGTGGCGCAGCCTGGCGTTgcgccg > 1:1202680/1‑71 (MQ=255)
gagaCACCTGCGGGAGAACTCCGACTGTTCGACGGTAAATCGAGCCAGTGGCGCAGCCTGGCGTTgcgccg > 1:620530/1‑71 (MQ=255)
gagaCACCTGCGGGAGAACTCCGACTGTTCGACGGTAAATCGAGCCAGTGGCGCAGCCTGGCGTTgcgccg > 1:2363839/1‑71 (MQ=255)
gagaCACCTGCGGGAGAACTCCGACTGTTCGACGGTAAATCGAGCCAGTGGCGCAGCCTGGCGTTgcgccg > 1:1448986/1‑71 (MQ=255)
acacCTGCGGGAGAACTCCGACTGTTCGACGGTAAATCGAGCCAGTGGCGCAGc > 1:907753/1‑54 (MQ=255)
acacCTGCGGGAGAACTCCGACTGTTCGACGGTAAATCGAGCCAGTGGCGCAGc > 1:91485/1‑54 (MQ=255)
acCTGCGGGAGAACTCCGACTGTTCGACGGTAAATCGAGCCa > 1:889954/1‑42 (MQ=255)
acCTGCGGGAGAACTCCGACTGTTCGACGGTAAATCGAGCCAg > 1:581286/1‑43 (MQ=255)
acCTGCGGGAGAACTCCGACTGTTCGACGGTAAATCGAGCCAg > 1:2505715/1‑43 (MQ=255)
acCTGCGGGAGAACTCCGACTGTTCGACGGTAAATCGAGCCAg > 1:556058/1‑43 (MQ=255)
acCTGCGGGAGAACTCCGACTGTTCGACGGTAAATCGAGCCAg > 1:435813/1‑43 (MQ=255)
acCTGCGGGAGAACTCCGACTGTTCGACGGTAAATCGAGCCAg > 1:3752037/1‑43 (MQ=255)
acCTGCGGGAGAACTCCGACTGTTCGACGGTAAATCGAGCCAGTGGCGCAGCCTGGCGTTgcgccgcgc > 1:1899072/1‑69 (MQ=255)
tGCGGGAGAACTCCGACTGTTCGACGGTAAATCGAACCAGTGGCGCAGCCTGGCGTTGCGCCGCGCCAg > 1:586482/1‑69 (MQ=255)
tGCGGGAGAACTCCGACTGTTCGACGGTAAATCGAACCAGTGGCGCAGCCTGGCGTTGCGCCGCGCCAGTg > 1:2519579/1‑71 (MQ=255)
tGCGGGAGAACTCCGACTGTTCGACGGTAAATCGAACCAGTGGCGCAGCCTGGCGTTGCGCCGCGCCAGTg > 1:3730850/1‑71 (MQ=255)
gCGGGAGAACTCCGACTGTTCGACGGTAAATCGAACCAGTGGCGCAGCCTGGCGTTGCGCCGCGCCAGTgg > 1:1561940/1‑71 (MQ=255)
gCGGGAGAACTCCGACTGTTCGACGGTAAATCGAACCAGTGGCGCAGCCTGGCGTTGCGCCGCGCCAGTg > 1:659880/1‑70 (MQ=255)
cGGGAGAACTCCGACTGTTCGACGGTAAATCGAACCAGTGGCGCAGCCTGGCGTTGCGCCGCGCCAGTg < 1:986630/69‑1 (MQ=255)
cGGGAGAACTCCGACTGTTCGACGGTAAATCGAACCAGTGGCGCAGCCTGGCGTTGCGCCGCGCCAGTg < 1:3456196/69‑1 (MQ=255)
cGGGAGAACTCCGACTGTTCGACGGTAAATCGAACCAGTGGCGCAGCCTGGCGTTGCGCCGCGCCAGTg < 1:1857575/69‑1 (MQ=255)
cGGGAGAACTCCGACTGTTCGACGGTAAATCGAACCAGTGGCGCAGCCTGGCGTTGCGCCGCGCCAGTg < 1:3269659/69‑1 (MQ=255)
cGGGAGAACTCCGACTGTTCGACGGTAAATCGAACCAGTGGCGCAGCCTGGCGTTGCGCCGCGCCAGTg < 1:2839795/69‑1 (MQ=255)
ggAGAACTCCGACTGTTCGACGGTAAATCGAGCCAGTGGCGCAGCCTGGCGTTGCGCCGCGCCAGTGGtt < 1:492464/70‑1 (MQ=255)
gaACTCCGACTGTTCGACGGTAAATCGAGCCAGTGGCGCAGCCTGGCGTTGCGCCGCGCCAGTGGTTGccc > 1:699873/1‑71 (MQ=255)
gaACTCCGACTGTTCGACGGTAAATCGAGCCAGTGGCGCAGCCTGGCGTTGCGCCGCGCCAGTGGTTGccc > 1:526737/1‑71 (MQ=255)
gaACTCCGACTGTTCGACGGTAAATCGAGCCAGTGGCGCAGCCTGGCGTTGCGCCGCGCCAGTGGTTGccc > 1:2730287/1‑71 (MQ=255)
gaACTCCGACTGTTCGACGGTAAATCGAACCAGTGGCGCAGCCTGGCGTTGCGCCGCGCCAGTGGTTGccc > 1:1845310/1‑71 (MQ=255)
gaACTCCGACTGTTCGACGGTAAATCGAACCAGTGGCGCAGCCTGGCGTTGCGCCGCGCCAGTGGTTGccc > 1:3452757/1‑71 (MQ=255)
aCTCCGACTGTTCGACGGTAAATCGAGCCAGTGGCGCAGCCTGGCGTTGCGCCGCGCCAGTGGTTGCCCgg > 1:4112232/1‑71 (MQ=255)
aCTCCGACTGTTCGACGGTAAATCGAGCCAGTGGCGCAGCCTGGCGTTGCGCCGCGCCAGTGGTTGCCCg < 1:196199/70‑1 (MQ=255)
ccGACTGTTCGACGGTAAATCGAGCCAGTGGCGCAGCCTGGCGTTGCGCCGCGCCAGTGGTTGCCCGGTAt > 1:2400959/1‑71 (MQ=255)
tGTTCGACGGTAAATCGAGCCAGTGGCGCAGCCTGGCGTTGCGCCGCGCCAGTGGTTGCCCGGTATGCg > 1:1240899/1‑69 (MQ=255)
aCGGTAAATCGAGCCAGTGGCGCAGCCTTGCGTTGCGCCGCGCCAGTGGTTGCCCGGTATGCGGAGGAAGc < 1:202373/71‑1 (MQ=255)
aCGGTAAATCGAGCCAGTGGCGCAGCCTGGCGTTGCGCCGCGCCAGTGGTTGCCCGGTATGCGGAGGAAGc < 1:392705/71‑1 (MQ=255)
aCGGTAAATCGAGCCAGTGGCGCAGCCTGGCGTTGCGCCGCGCCAGTGGTTGCCCGGTATGCGGAGGAAGc < 1:2371750/71‑1 (MQ=255)
aCGGTAAATCGAGCCAGTGGCGCAGCCTGGCGTTGCGCCGCGCCAGTGGTTGCCCGGTATGCGGAGGAAGc < 1:341566/71‑1 (MQ=255)
aCGGTAAATCGAACCAGTGGCGCAGCCTGGCGTTGCGCCGCGCCAGTGGTTGCCCGGTATGCGGAGGAAGc < 1:3053499/71‑1 (MQ=255)
aCGGTAAATCGAACCAGTGGCGCAGCCTGGCGTTGCGCCGCGCCAGTGGTTGCCCGGTATGCGGAGGAAGc < 1:3389814/71‑1 (MQ=255)
gTAAATCGAGCCAGTGGCGCAGCCTGGCGTTGCGCCGCGCCAGt > 1:2714338/1‑44 (MQ=255)
tAAATCGAGCCAGTGGCGCAGCCTGGCGTTGCGCCGCGCCAGTGGTTGCCCGGTATGCGGAGGAAGCAATg < 1:2537701/71‑1 (MQ=255)
aaaTCGAGCCAGTGGCGCAGCCTGGCGTTGCGCCGCGCCAGTGGTTGCCCGGTATGCGGAGGAAGCAATg > 1:2193259/1‑70 (MQ=255)
aaaTCGAGCCAGTGGCGCAGCCTGGCGTTGCGCCGCGCCAGTGGTTGCCCGGTATGCGGAGGAAGCAATg > 1:3348016/1‑70 (MQ=255)
aaaTCGAACCAGTGGCGCAGCCTGGCGTTGCGCCGCGCCAGTGGTTGCCCGGTATGCGGAGGAAGCAATg > 1:2389810/1‑70 (MQ=255)
aaTCGAACCAGTGGCGCAGCCTGGCGTTGCGCCGCGCCAGTGGTTGCCCGGTATGCGGAGGAAGCAATGCa < 1:3917283/71‑1 (MQ=255)
aaTCGAACCAGTGGCGCAGCCTGGCGTTGCGCCGCGCCAGTGGTTGCCCGGTATGCGGAGGAAGCAATGCa < 1:324774/71‑1 (MQ=255)
|
GAAGCCATTAAGTTATTAAGCGGTATAGAGACACCTGCGGGAGAACTCCGACTGTTCGACGGTAAATCGAGCCAGTGGCGCAGCCTGGCGTTGCGCCGCGCCAGTGGTTGCCCGGTATGCGGAGGAAGCAATGCA > minE/2249420‑2249554
|
| 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
