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 |
|
A5 F21 I0 R2
|
316 |
65.6 |
5147759 |
97.4% |
5013917 |
60.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,841,531 |
G→A |
40.4% |
R57* (CGA→TGA) |
hycI ← |
protease involved in processing C‑terminal end of HycE |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,841,531 | 0 | G | A | 40.4%
| 36.6
/ 59.2
| 52 | R57* (CGA→TGA) | hycI | protease involved in processing C‑terminal end of HycE |
| Reads supporting (aligned to +/- strand): ref base G (7/24); new base A (11/10); total (18/34) |
| Fisher's exact test for biased strand distribution p-value = 3.87e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.74e-01 |
TCATCCGGGTCGATGATGCGGATCTCGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTACCGCCGTCAATCAC > W3110S.gb/2841461‑2841594
|
tcatcCGGGTCGATGATGCGGATCTCGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCg > 1:64323/1‑71 (MQ=255)
catcCGGGTCGATGATGCGGATCTCGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCgt > 1:1631469/1‑71 (MQ=255)
atcCGGGTCGATGATGCGGATCTCGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCgt < 1:4471854/70‑1 (MQ=255)
cGGGTCGATGATGCGGATCTCGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCGTGTCg < 1:4763366/71‑1 (MQ=255)
cGGGTCGATGATGCGGATCTCGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCATGTc < 1:3340050/70‑1 (MQ=255)
cGATGATGCGGATCTCGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCATGTCGGgcg > 1:3389535/1‑70 (MQ=255)
gatgatGCGGATCTCGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCGTGTCGGgcgc < 1:2639061/70‑1 (MQ=255)
gatgatGCGGATCTCGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCGTGTCGGgcgc < 1:2295953/70‑1 (MQ=255)
tgatgCGGATCTCGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGt < 1:1744159/71‑1 (MQ=255)
tgCGGATCTCGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCa < 1:2023848/71‑1 (MQ=255)
gCGGATCTCGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCATGTCGGGCGCAGTTCa < 1:1174454/70‑1 (MQ=255)
cGGATCTCGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCGGTCATGTCGGGCGCAGTTCAc < 1:1679918/70‑1 (MQ=255)
aTCTCGGCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCGTGTc < 1:3039740/54‑1 (MQ=255)
aTCTCGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCGTGTc < 1:4408288/54‑1 (MQ=255)
aTCTCGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCGTGTc < 1:2133700/54‑1 (MQ=255)
tctcGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCATGTCGGGCGCAGTTCACGGa > 1:486467/1‑69 (MQ=255)
tctcGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCATGTCGGGCGCAGTTCACGGa > 1:1602685/1‑69 (MQ=255)
ctcGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCGTGTc < 1:1310145/52‑1 (MQ=255)
tcGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCATGTCGGGCGCAGtac > 1:1644613/1‑60 (MQ=255)
gCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGc < 1:4096928/69‑1 (MQ=255)
ccGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCATGTCGGGCGCAGTTCACGGATAGcgac < 1:3642732/71‑1 (MQ=255)
ccGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCATGTCGGGCGCAGTTCACGGATAGcgac < 1:2505502/71‑1 (MQ=255)
ggTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCGTGTCGGgcgc < 1:1304958/50‑1 (MQ=255)
tttAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCgt < 1:113255/39‑1 (MQ=255)
tttAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCgt < 1:2017202/39‑1 (MQ=255)
tttAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGcgacg < 1:1954087/66‑1 (MQ=255)
tAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCg < 1:797457/70‑1 (MQ=255)
tAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCATGTCGGGCGCAGTTCACGGATAGCGACGATGTCGt > 1:2385564/1‑71 (MQ=255)
cccATATCCGTGGCGTCGACAATCAGCAGTCATGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTc > 1:5033050/1‑71 (MQ=255)
atatCCGTGGCGTCGACAATCAGCAGTCATGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTcc < 1:3537108/69‑1 (MQ=255)
tatCCGTGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCa > 1:904175/1‑44 (MQ=255)
tCCGTGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTgc > 1:3604345/1‑71 (MQ=255)
tCCGTGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTgc > 1:4818536/1‑71 (MQ=255)
tCCGTGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTg > 1:4135273/1‑70 (MQ=255)
tCCGTGGCGTCGACAATCAGCAGTCATGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTcc > 1:3411626/1‑66 (MQ=255)
tCCGTGGCGTCGACAATCAGCAGTCATGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTcc > 1:1204658/1‑66 (MQ=255)
tCCGTGGCGTCGACAATCAGCAGTCATGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTg < 1:846568/70‑1 (MQ=255)
cGTGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTgcgc < 1:1552481/71‑1 (MQ=255)
cGTGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTgcgc < 1:1230839/71‑1 (MQ=255)
cGTGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATCTCGTTTTCCGGTgcgc < 1:1887421/71‑1 (MQ=255)
cGTGGCGTCGACAATCAGCAGTCATGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTgcgc < 1:2646089/71‑1 (MQ=255)
tGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAg < 1:353720/45‑1 (MQ=255)
tGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAg < 1:4092136/45‑1 (MQ=255)
tGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCTCTa < 1:3746088/71‑1 (MQ=255)
tGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTa < 1:459481/71‑1 (MQ=255)
gCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTAc > 1:4720766/1‑70 (MQ=255)
gTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACg < 1:2296331/36‑1 (MQ=255)
tCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTAccgc > 1:3690384/1‑70 (MQ=255)
tCGACAATCAGCAGTCATGTCGGGCGCAGTTCACGGATAGcgac < 1:3098505/44‑1 (MQ=255)
gACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGa > 1:2780198/1‑35 (MQ=255)
aCAATCAGCAGTCATGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTcc > 1:4216922/1‑54 (MQ=255)
aCAATCAGCAGTCATGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCgg > 1:1295283/1‑56 (MQ=255)
aCAATCAGCAGTCATGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCgg > 1:4092195/1‑56 (MQ=255)
cAATCAGCAGTCATGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTACCGCCGTCa < 1:367736/71‑1 (MQ=255)
aaTCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGcgac < 1:4944953/39‑1 (MQ=255)
tCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTACCGCCGTCAATc < 1:3877607/71‑1 (MQ=255)
agcagTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTACCGCCGTCAATcac < 1:3290157/71‑1 (MQ=255)
|
TCATCCGGGTCGATGATGCGGATCTCGCCGGGGTTTAGCCCCATATCCGTGGCGTCGACAATCAGCAGTCGTGTCGGGCGCAGTTCACGGATAGCGACGATGTCGTTTTCCGGTGCGCTACCGCCGTCAATCAC > W3110S.gb/2841461‑2841594
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
