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 |
|
A13 F40 I0 R1
|
17 |
35.0 |
784744 |
95.0% |
745506 |
140.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
USA300TCH1516_ALE |
2,372,484 |
A→T |
26.1% |
L431* (TTA→TAA) |
pbuG ← |
Guanine/hypoxanthine permease PbuG |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | USA300TCH1516_ALE | 2,372,484 | 0 | A | T | 26.1%
| 36.8
/ 12.9
| 23 | L431* (TTA→TAA) | pbuG | Guanine/hypoxanthine permease PbuG |
| Reads supporting (aligned to +/- strand): ref base A (9/8); new base T (3/3); total (12/11) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.84e-01 |
AATATCGCTTTATGTTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCGTTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAAAATAAATCCACACGCAATACCAGTTGCAATTGAATATGATAAAGGCATCATAATGATTGTAATGAAGGCTGGC > USA300TCH1516_ALE/2372347‑2372621
|
aataTCGCTTTATGTTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCGTTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTtata < 2:300337/141‑1 (MQ=255)
atCGCTTTATGTTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCGTTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATTGTACAATTattttat > 1:302226/1‑135 (MQ=255)
gtaagatATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCGTTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTa < 2:253789/135‑1 (MQ=255)
aTGTTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCGTTTTTTGTGTCTGAATTTAACCATGAACAAATATCAAGTACAGAATGAATATTACCATTAATACATACATAATc > 2:45248/1‑141 (MQ=255)
tGTTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCGTTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCg > 1:313525/1‑141 (MQ=255)
cGCTACTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCGTTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTAct < 1:134839/141‑1 (MQ=255)
ttATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATTATTGGCAGTCGTTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTTATACATACATTATCGGATGTACTTCTTTa > 2:178839/1‑141 (MQ=255)
aTTTGATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCGTTTTTTGTGTCTGGATTTAACCATGAACAAATATGAGGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATg < 1:109868/141‑1 (MQ=255)
tACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCGTTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTagag < 1:277695/141‑1 (MQ=255)
gtagtaaaCGTCTACCAAGCATTTGCAGTCGTTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCAtt < 2:40643/136‑1 (MQ=255)
aaaaaaaCGACTACCAATCATTGGCAGTCGTTTATTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTg < 2:15518/141‑1 (MQ=255)
aaaaaCGACTACCAATCATTGGCAGTCGTTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTTATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTa > 1:210372/1‑141 (MQ=255)
aaaaaCGACTACCAATCATTGGCAGTCGTTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTATTAGAGATAAGAATTGTa > 2:130429/1‑141 (MQ=255)
gccAATGATTGGTAGTCGTTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGa > 1:238452/2‑141 (MQ=255)
aCCAATCATTGGCAGTCGTTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTTATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGa < 1:199424/141‑1 (MQ=255)
ccAATCATTGGCAGTCGTTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGaa > 1:232316/1‑141 (MQ=255)
gTCGTTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAAAGTAAATCCacac > 1:63811/1‑141 (MQ=255)
ttttGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAAAATAAATCCACACGCAATa > 1:253046/1‑141 (MQ=255)
tgtgTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTTATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAAAATAAATCCACACGCAATACCa < 2:226063/141‑1 (MQ=255)
tGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTTATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAAAATAAATCCACACGCAATACCAGTTGCa < 1:135340/141‑1 (MQ=255)
aaCAAATATGAAGTATAGAAGGAGTGGTACCATTATAACATACATTATCAGTTGTACTTCTTTATGTTTTTTTGAGATAAGCATTGTAATTAGATAGAAAATCAATCCACACGCAATACCCGTTGCAATTGAATATGATaa < 2:319329/141‑1 (MQ=255)
atatGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAAAATAAATCCACACGCAATACCAGTTGCAATTGAATATGATAAAGGca < 1:313696/141‑1 (MQ=255)
atatGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAAAATAAATCCACACGCAATACCAGTTGCAATTGAATATGATAAAGGca > 2:15564/1‑141 (MQ=255)
aatgaatAGTACCATTTATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAAAATACCTCCACACGCAATACTAGTTGTCAACAAATATGATAAAGGCATCATAATGATTGt > 1:246553/1‑141 (MQ=255)
aTTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAAAATAAATCCACACGCAATACCAGTTGCAATTGAATATGATAAAGGCATCATAATGATTGTAATGAAGGCTGGc > 1:220410/1‑141 (MQ=255)
|
AATATCGCTTTATGTTATTTCGCTTCTTATTTTATCCTTACTTCAAAGAAAAAAACGACTACCAATCATTGGCAGTCGTTTTTTGTGTCTGGATTTAACCATGAACAAATATGAAGTACAGAATGAATAGTACCATTAATACATACATTATCGGATGTACTTCTTTATGTTTTTTAGAGATAAGCATTGTAATTGGATAGAAAATAAATCCACACGCAATACCAGTTGCAATTGAATATGATAAAGGCATCATAATGATTGTAATGAAGGCTGGC > USA300TCH1516_ALE/2372347‑2372621
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
