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 F8 I0 R2
|
422 |
46.8 |
3726540 |
94.7% |
3529033 |
61.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,035,868:1 |
+T |
100% |
intergenic (‑247/‑320) |
yedR ← / → yedS |
predicted inner membrane protein/ECK1962:JW5319:b1964; hypothetical protein, N‑ter fragment |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,035,868 | 1 | . | T | 91.7%
| 58.4
/ 1.2
| 24 | intergenic (‑247/‑320) | yedR/yedS | predicted inner membrane protein/ECK1962:JW5319:b1964; hypothetical protein, N‑ter fragment |
| Reads supporting (aligned to +/- strand): ref base . (0/2); new base T (9/13); total (9/15) |
| Fisher's exact test for biased strand distribution p-value = 5.11e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.34e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. |
ATGCTTCCGTTATTAGCCTTTTATCGTCTTGTTTATATTTTTTGGGCCGGCATGATGCCGGC‑TTTTTTTTATGCCTTCATTAATGTGCGCCTGATCACACCAGCCGTTTGGCGCAACAATCATTGA > W3110S.gb/2035807‑2035932
|
atgCTTCCGTTATTAGCCTTTTATCGTCTTGTTTATATTTTTTGGGCCGGCATGATGCCGGC‑tttttttt < 1:3182216/70‑1 (MQ=255)
tgCTTCCGTTATTAGCCTTTTATCGTCTTGTTTATATTTTTTGGGCCGGCATGATGCCGGC‑tttttttt < 1:737391/69‑1 (MQ=255)
tgCTTCCGTTATTAGCCTTTTATCGTCTTGTTTATATTTTTTGGGCCGGCATGATGCCGGC‑tttttttt < 1:3587364/69‑1 (MQ=255)
gCTTCCGTTATTAGCCTTTTATCGTCTTGTTTATATTTTTTGGGCCGGCATGATGCCGGC‑tttttttttat > 1:1112550/1‑68 (MQ=255)
cTTCCGTTATTAGCCTTTTATCGTCTTGTTTATATTTTTTGGGCCGGCATGATGCCGGC‑tttttttttat < 1:2529544/70‑4 (MQ=255)
gCCTTTTATCGTCTTGTTTATATTTTTTGGGCCGGCATGATGCCGGCTTTTTTTTTATGCCTTCa < 1:1001608/65‑1 (MQ=255)
gCCTTTTATCGTCTTGTTTATATTTTTTGGGCCGGCATGATGCCGGCTTTTTTTTTATGCCTTCATTAAtg < 1:1482530/71‑1 (MQ=255)
cTTTTATCGTCTTGTTTATATTTTTTGGGCCGGCATGATGCCGGCTTTTTTTTTATGCCTTCATTAAtgtg > 1:2972680/1‑71 (MQ=255)
cTTTTATCGTCTTGTTTATATTTTTTGGGCCGGCATGATGCCGGCTTTTTTTTTATGCCTTCATTAAtgtg > 1:7290/1‑71 (MQ=255)
ttttATCGTCTTGTTTATATTTTTTGGGCCGGCATGATGCCGGC‑tttttttt < 1:1188883/52‑1 (MQ=255)
ttATCGTCTTGTTTATATTTTTTGGGCCGGCATGATGCCGGC‑ttttttttta > 1:60939/1‑50 (MQ=255)
tCGTCTTGTTTATATTTTTTGGGCCGGCATGATGCCGGCTTTTTTTTTATGCCTTCATTAATGTGCGCCt < 1:1292535/70‑1 (MQ=255)
tCGTCTTGTTTATATTTTTTGGGCCGGCATGATGCCGGCTTTTTTTTTATGCCTTCATTAATGTGCGCCt < 1:1211168/70‑1 (MQ=255)
cGTCTTGTTTATATTTTTTGGGCCGGCATGATGCCGGCTTTTTTTTTATGCCTTCATTAATGTGCGCCt < 1:3090284/69‑1 (MQ=255)
ttGTTTATATTTTTTGGGCCGGCATGATGCCGGCTTTTTTTTTATGCCTTCATTaa > 1:3545167/1‑56 (MQ=255)
ttttttGGGCCGGCATGATGCCGGCTTTTTTTTTATGCCTTCATTAATGTGCGCCTGATca > 1:2974475/1‑61 (MQ=255)
ggCCGGCATGATGCCGGCTTTTTTTTTATGCCTTCATTAATGTGCGCCTGATCACACCAGCCGTTTGgcgc < 1:402668/71‑1 (MQ=255)
gCCGGCATGATGCCGGCTTTTTTTTTATGCCTTCATTAATGTGCGCCTGATCACACCAGCCGTTTGGCGca < 1:1318812/71‑1 (MQ=255)
gCCGGCATGATGCCGGCTTTTTTTTTATGCCTTCATTAATGTGCGCCTGATCACACCAGCCGTTTGGCGca < 1:3413016/71‑1 (MQ=255)
ggCATGATGCCGGCTTTTTTTTTATGCCTTCATTAATGTGCGCCt < 1:1046316/45‑1 (MQ=38)
atgatgCCGGCTTTTTTTTTATGCCTTCATTAATGTGCGCCTGATCACACCAGCCGTTTGGCGCAACAAt > 1:322308/1‑70 (MQ=255)
atgatgCCGGC‑TTTTTTTTATGCCTTCATTAATGTGCGCCTGATCACACCAGCCGTTTGGCGCAACAATCa < 1:1982535/71‑1 (MQ=255)
tgatgCCGGCTTTTTTTTTATGCCTTCATTAATGTGCGCCTGATcaca > 1:2556498/1‑48 (MQ=39)
tgatgCCGGCTTTTTTTTTATGCCTTCATTAATGTGCGCCTGATCACACCAGCCGTTTGGCGCAACAATCa > 1:575822/1‑71 (MQ=255)
atgCCGGCTTTTTTTTTATGCCTTCATTAATGTGCGCCTGATCACACCAGCCGTTTGGCGCAACAATCAtt < 1:3243033/71‑1 (MQ=255)
atgCCGGCTTTTTTTTTATGCCTTCATTAATGTGCGCCTGATCACACCAGCCGTTTGGCGCAACAATCAtt < 1:2322582/71‑1 (MQ=255)
atgCCGGCTTTTTTTTTATGCCTTCATTAATGTGCGCCTGATCACACCAGCCGTTTGGCGCAACAATCAtt < 1:3595712/71‑1 (MQ=255)
atgCCGGCTTTTTTTTTATGCCTTCATTAATGTGCGCCTGATCACACCAGCCGTTTGGCGCAACAATCAtt > 1:1542211/1‑71 (MQ=255)
tgCCGGCTTTTTTTTTATGCCTTCATTAATGTGCGCCTGATCACACCAGCCGTTTGGCGCAACAATCATTg < 1:941771/71‑1 (MQ=255)
gCCGGCTTTTTTTTTATGCCTTCATTAATGTGCGCCTGATCACACCAGCCGTTTGGCGCAACAATCATTGa > 1:1617877/1‑71 (MQ=255)
gC‑TTTTTTTTATGCCTTCATTAATGTGCGCCTGATCACACCAGCCGTTTGGCGCAACAATCAtt < 1:1916815/64‑1 (MQ=255)
|
ATGCTTCCGTTATTAGCCTTTTATCGTCTTGTTTATATTTTTTGGGCCGGCATGATGCCGGC‑TTTTTTTTATGCCTTCATTAATGTGCGCCTGATCACACCAGCCGTTTGGCGCAACAATCATTGA > W3110S.gb/2035807‑2035932
|
| 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
