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 F1 I0 R2
|
532 |
47.8 |
3863072 |
94.9% |
3666055 |
61.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
598,515 |
C→T |
20.6% |
P193P (CCC→CCT) |
cusA → |
copper/silver efflux system, membrane component |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 598,515 | 0 | C | T | 20.6%
| 74.0
/ 14.5
| 39 | P193P (CCC→CCT) | cusA | copper/silver efflux system, membrane component |
| Reads supporting (aligned to +/- strand): ref base C (13/17); new base T (3/5); total (16/23) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.31e-01 |
CATCCCTGACGTTGCGGAAGTGGCGTCGGTGGGCGGTGTGGTGAAAGAGTATCAGGTGGTTATCGATCCCCAGCGCCTGGCGCAGTATGGCATCAGTCTCGCCGAAGTAAAAAGCGCGCTGGATGCTTCAAACCAGG > W3110S.gb/598446‑598582
|
cATCCCTGACGTTGCGGAAGTGGCGTCGGTGGGCGGTGTGGTGAAAGAGTATCAGGTGGTTATCGATcccc < 1:2371575/71‑1 (MQ=255)
ccTGACGTTGCGGAAGTGGCGTCGGTGGGCGGTGTGGTGAAAGAGTATCAGGTGGTTATCGATCCTCAgcg > 1:722619/1‑71 (MQ=255)
ccTGACGTTGCGGAAGTGGCGTCGGTGGGCGGTGTGGTGAAAGAGTATCAGGTGGTTATCGATCCTCAgcg > 1:3566737/1‑71 (MQ=255)
ccTGACGTTGCGGAAGTGGCGTCGGTGGGCGGTGTGGTGAAAGAGTATCAGGTGGTTATCGATCCTCAgcg > 1:1312753/1‑71 (MQ=255)
aCGTTGCGGAAGTGGCGTCGGTGGGCGGTGTGGTGAAAGAGTATCAGGTGGTTATCGATCCCCAGCGcc < 1:1338883/69‑1 (MQ=255)
aCGTTGCGGAAGTGGCGTCGGTGGGCGGTGTGGTGAAAGAGTATCAGGTGGTTATCGATCCCCAGCGcc < 1:3408104/69‑1 (MQ=255)
aCGTTGCGGAAGTGGCGTCGGTGGGCGGTGTGGTGAAAGAGTATCAGGTGGTTATCGATCCCCAGCGCCTg > 1:307577/1‑71 (MQ=255)
ttGCGGAAGTGGCGTCGGTGGGCGGTGTGGTGAAAGAGTATCAGGTGGTTATCGATCCTCAGCGCCTg < 1:1094556/68‑1 (MQ=255)
ttGCGGAAGTGGCGTCGGTGGGCGGTGTGGTGAAAGAGTATCAGGTGGTTATCGATCCTCAGCGCCTg < 1:3387212/68‑1 (MQ=255)
ttGCGGAAGTGGCGTCGGTGGGCGGTGTGGTGAAAGAGTATCAGGTGGTTATCGATCCTCAGCGCCTg < 1:2452000/68‑1 (MQ=255)
ttGCGGAAGTGGCGTCGGTGGGCGGTGTGGTGAAAGAGTATCAGGTGGTTATCGATCCTCAGCGCCTg < 1:1481321/68‑1 (MQ=255)
ttGCGGAAGTGGCGTCGGTGGGCGGTGTGGTGAAAGAGTATCAGGTGGTTATCGATCCTCAGCGCCTg < 1:1500327/68‑1 (MQ=255)
gCGGAAGTGGCGTCGGTGGGCGGTGTGGTGAAAGAGTATCAGGTGGTTATCGATCCCCAGCGCCTGgcgc < 1:2900097/70‑1 (MQ=255)
gCGGAAGTGGCGTCGGTGGGCGGTGTGGTGAAAGAGTATCAGGTGGTTATCGATCCCCAGCGCCTGgcg > 1:408761/1‑69 (MQ=255)
cGGAAGTGGCGTCTGTGGGCGGTGTGGTGAAAGAGTATCAGGTGGTTATCGATCCCCAGCGCCTGGCGCAg < 1:1863802/71‑1 (MQ=255)
cGGAAGTGGCGTCGGTGGGCGGTGTGGTGAAAGAGTATCAGGTGGTTATCGATCCCCAGCGCCTGGCGCAg < 1:2148581/71‑1 (MQ=255)
ggAAGTGGCGTCGGTGGGCGGTGTGGTGAAAGAGTATCAGGTGGTTATCGATCCCCAGCGCCTGGCGCAGt < 1:1747445/71‑1 (MQ=255)
gCGTCGGTGGGCGGTGTGGTGAAAGAGTATCAGGTGGTTATCGATCCCCAGCGCCTGGCGCAGTATGGCAt < 1:2247116/71‑1 (MQ=255)
gTGGGCGGTGTGGTGAAAGAGTATCAGGTGGTTATCGATCCCCAGCGCCTGGCGCAGTATGGCATCAGtct < 1:3564344/71‑1 (MQ=255)
ggCGGTGTGGTGAAAGAGTATCAGGTGGTTATCGATCCCCAGCGCCTGGCGCAGTATGGCATCa > 1:1037119/1‑64 (MQ=255)
tggtgAAAGAGTATCAGGTGGTTATCGATCCCCAGCGCCTGGCGCAGTa > 1:2493034/1‑49 (MQ=255)
tggtgAAAGAGTATCAGGTGGTTATCGATCCCCAGCGCCTGGCGCAGTa > 1:1206774/1‑49 (MQ=255)
ggtgAAAGAGTATCAGGTGGTTATCGATCCCCAGCGCCTGGCGCa < 1:1961896/45‑1 (MQ=255)
ggtgAAAGAGTATCAGGTGGTTATCGATCCCCAGCGCCTGGCGCAGTATGGCa < 1:1589248/53‑1 (MQ=255)
gtgAAAGAGTATCAGGTGGTTATCGATCCCCAGCGCCTGGCGCAGTATGGCATCAGTCTCGCCGAAGTaaa < 1:2284437/71‑1 (MQ=255)
gtgAAAGAGTATCAGGTGGTTATCGATCCCCAGCGCCTGGCGCAGTATGGCATCAGTCTCGCCGAAGTaa < 1:3572841/70‑1 (MQ=255)
gtgAAAGAGTATCAGGTGGTTATCGATCCCCAGCGCCTGGCGCAGTATGGCATCAGTCTCGCCGAAGTaa > 1:174313/1‑70 (MQ=255)
tgAAAGAGTATCAGGTGGTTATCGATCCCCAGCGCCTGGCGCAGTATGGCATCAGTCTCGCCGAAGTaaaa < 1:2779090/71‑1 (MQ=255)
gAAAGAGTATCAGGTGGTTATCGATCCCCAGCGCCTGGCGCAGTa > 1:880380/1‑45 (MQ=255)
aaaGAGTATCAGGTGGTTATCGATCCCCAGCGCCTGGCGCAGTATGGCATCAGTCTCGCCGAAGTaaaaa < 1:3466843/70‑1 (MQ=255)
agagTATCAGGTGGTTATCGATCCCCAGCGCCTGGCGCAGTa > 1:2805142/1‑42 (MQ=255)
agagTATCAGGTGGTTATCGATCCCCAGCGCCTGGCGCAGTa > 1:2680833/1‑42 (MQ=255)
agTATCAGGTGGTTATCGATCCCCAGCGCCTGGCGCAGTATGGCATCAGTCTCGCCGAAGTAAAAAgcgcg > 1:282527/1‑71 (MQ=255)
tCAGGTGGTTATCGATCCCCAGCGCCTGGCGCAGTa > 1:3703168/1‑36 (MQ=255)
tCAGGTGGTTATCGATCCCCAGCGCCTGGCGCAGTATGGCATCAGTCTCGCCGAAGTAAAAAGCGCGCTg < 1:2764803/70‑1 (MQ=255)
gtggtTATCGATCCCCAGCGCCTGGCGCAGTATGGCATCAGTCTCGCCGAAGTAAAAAGCGCGCTGGATGc > 1:1476622/1‑71 (MQ=255)
gATCCCCAGCGCCTGGCGCAGTATGGCATCAGTCTCGCCGaa > 1:2273824/1‑42 (MQ=255)
aTCCCCAGCGCCTGGCGCAGTATGGCATCAGTCTCGCCGAAGt < 1:1372063/43‑1 (MQ=255)
aTCCCCAGCGCCTGGCGCAGTATGGCATCAGTCTCGCCGAAGt < 1:1493904/43‑1 (MQ=255)
aTCCACAGCGCCTGGCGCAGTATGGCATCAGTCTCGCCGAAGt < 1:1563467/43‑1 (MQ=255)
ccccAGCGCCTGGCGCAGTATGGCATCAGTCTCGCCGAAGTAAAAAGCGCGCTGGATGCTTCAAACCAgg > 1:3328802/1‑70 (MQ=255)
|
CATCCCTGACGTTGCGGAAGTGGCGTCGGTGGGCGGTGTGGTGAAAGAGTATCAGGTGGTTATCGATCCCCAGCGCCTGGCGCAGTATGGCATCAGTCTCGCCGAAGTAAAAAGCGCGCTGGATGCTTCAAACCAGG > W3110S.gb/598446‑598582
|
| 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
