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 |
1,210,070 |
C→T |
36.6% |
S121F (TCC→TTC) |
ymfS → |
hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,210,070 | 0 | C | T | 36.6%
| 36.4
/ 39.9
| 41 | S121F (TCC→TTC) | ymfS | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base C (14/12); new base T (8/7); total (22/19) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.52e-01 |
AAGAAGATGAGCTGAAACAATATAATTTGTGGCTGGATTATCTGGAAGCACTGGAACTGGTTGATACATCCAGTGCGCCAGATATTGAATGGCCTACGCCTCCGGCAGTTCAGGCCAGATGACATCCGGCGCGGTGC > W3110S.gb/1210001‑1210137
|
aagaagATGAGCTGAAACAATATAATTTGTGGCTGGATTATCTGGAAGCACTGGAACTGGTTGATACATcc < 1:2410296/71‑1 (MQ=255)
agaagaTGAGCTGAAACAATATAATTTGTGGCTGGATTATCTGGAAGCACTGGAACTGGTTGATACATTCa < 1:435118/71‑1 (MQ=255)
gaagaTGAGCTGAAACAATATAATTTGTGGCTGGATTATCTGGAAGCACTGGAACTGGTTGATACATTCAg < 1:2078893/71‑1 (MQ=255)
gaagaTGAGCTGAAACAATATAATTTGTGGCTGGATTATCTGGAAGCACTGGAACTGGTTGATACATTCAg < 1:3479544/71‑1 (MQ=255)
tGAAACAATATAATTTGTGGCTGGATTATCTGGAAGCACTGGAACTGGTTGATACATcc < 1:4633456/59‑1 (MQ=255)
aaaCAATATAATTTGTGGCTGGATTATCTGGAAGCACTGGAACTGGTTGATACATTCAGTGCGCCAGatat > 1:4520934/1‑71 (MQ=255)
aaaCAATATAATTTGTGGCTGGATTATCTGGAAGCACTGGAACTGGTTGATACATTCAGTGCGCCAGatat > 1:2400465/1‑71 (MQ=255)
aaaCAATATAATTTGTGGCTGGATTATCTGGAAGCACTGGAACTGGTTGATACATCCAGTGCGCCAGata < 1:1632692/70‑1 (MQ=255)
aaaCAATATAATTTGTGGCTGGATTATCTGGAAGCACTGGAACTGGTTGATACATCCAGTGCGCCAGata < 1:40075/70‑1 (MQ=255)
cAATATAATTTGTGGCTGGATTATCTGGAAGCACTGGAACTGGTTGATACATTCAGTGCGCCAGATATTg > 1:429701/1‑70 (MQ=255)
taATTTGTGGCTGGATTATCTGGAAGCACTGGAACTGGTTGATACATTCAGTGCGCCAGATATTGAATGGc < 1:4425266/71‑1 (MQ=255)
aTTTGTGGCTGGATTATCTGGAAGCACTGGAACTGGTTGATACATCCAGTGCGCCAGATATTGAATGGcc > 1:827595/1‑70 (MQ=255)
aTTTGTGGCTGGATTATCTGGAAGCACTGGAACTGGTTGATACATCCAGTGCGCCAGATATTGAATGGcc > 1:4754843/1‑70 (MQ=255)
tgtgGCTGGATTATCTGGAAGCACTGGAACTGGTTGATACATTCAGTgcg > 1:351350/1‑50 (MQ=255)
tgtgGCTGGATTATCTGGAAGCACTGGAACTGGTTGATACATTCAGTGCGCCAGATATTGa > 1:1017382/1‑61 (MQ=255)
tgtgGCTGGATTATCTGGAAGCACTGGAACTGGTTGATACATTCAGTGCGCCAGATATTGa > 1:4596789/1‑61 (MQ=255)
tgGCTGGATTATCTGGAAGCACTGGAACTGGTTGATACATc < 1:649533/41‑1 (MQ=255)
tgGCTGGATTATCTGGAAGCACTGGAACTGGTTGATACATc < 1:1051375/41‑1 (MQ=255)
tgGCTGGATTATCTGGAAGCACTGGAACTGGTTGATACATc < 1:1488810/41‑1 (MQ=255)
ggATTATCTGGAAGCACTGGAACTGGTTGATACATCCAGTGCGCCAGATATTGAATGGCCTACGCCTCCgg > 1:4842515/1‑71 (MQ=255)
aTTATCTGGAAGCACTGGAACTGGTTGATACATCCAGTGCGCCAGATATTGAATGGCCTACGCCTCCgg > 1:3778017/1‑69 (MQ=255)
aTTATCTGGAAGCACTGGAACTGGTTGATACATCCAGTGCGCCAGATATTGAATGGCCTACGCCTCCgg > 1:2018081/1‑69 (MQ=255)
tGGAAGCACTGGAACTGGTTGATACATCCAGTGCGCCAGATATTGAATGGCCTACGCCTCCGGCAGTTCAg > 1:3198529/1‑71 (MQ=255)
gCACTGGAACTGGTTGATACATCCAGTGCGCCAGATATTGAATGGCCTACGCCTCCGGCACTTCAGGc > 1:2404082/1‑68 (MQ=255)
cACTGGAACTGGGTGATACATTCAGTGCGCCAGATATTGAAT‑GCCTACGCCTCCGGCAGTTCAGGCCAGAt < 1:574316/71‑1 (MQ=17)
cTGGAACTGGTTGATACATTCAGTGCGCCAGATATTg < 1:1212832/37‑1 (MQ=255)
cTGGAACTGGTTGATACATCCAGTGCGCCAGATATTGAATGGCCTACGCCTCCGGCAGTTCAGGCCAGAt > 1:2648504/1‑70 (MQ=255)
tGGAACTGGTTGATACATCCAGTGCGCCAGATATTGAAt < 1:1033484/39‑1 (MQ=255)
tGGAACTGGTTGATACATCCAGTGCGCCAGATATTGAAt < 1:787696/39‑1 (MQ=255)
tGGAACTGGTTGATACATCCAGTGCGCCAGATATTGAAt < 1:562268/39‑1 (MQ=255)
tGGAACTGGTTGATACATCCAGTGCGCCAGATATTGAATGGcc < 1:3045870/43‑1 (MQ=255)
tGGAACTGGTTGATACATCCAGTGCGCCAGATATTGAATGGCCTACGCCTCCGGCAGTTCAGGCCAGa < 1:3484404/68‑1 (MQ=255)
gAACTGGTTGATACATCCAGTGCGCCAGATATTGAATGGCCTACGCCTCCGGCAGTTCAGGCCAGATGACa < 1:2507845/71‑1 (MQ=255)
aCTGGTTGATACATTCAGTGCGCCAGATATTGAATGGCCTACGCCTCCGGCAGTTCAGGCCAGATGACATc < 1:2264520/71‑1 (MQ=255)
cTGGTTGATACATCCAGTGCGCCAGATATTGAATGGCCTACGCCTCCGGCAGTTCAGGCCa < 1:4809006/61‑1 (MQ=255)
ggTTGATACATCCAGTGCGCCAGATATTGAATGGCCTACGCCTCCGGCAGTTCAGGCCAGa > 1:3707526/1‑61 (MQ=255)
gTTGATACATCCAGTGCGCCAGATATTGAATGGCCTACGCCTCCGGCAGTTCAGGCCAGATg < 1:2365723/62‑1 (MQ=255)
gTTGATACATCCAGTGCGCCAGATATTGAATGGCCTACGCCTCCGGCAGTTCAGGCCAGATGACATCCGgc > 1:3188091/1‑71 (MQ=255)
ttGATACATCCAGTGCGCCAGATATTGAATGGCCTACGCCTCCGGCAGTTCAGGCCAGATg < 1:608126/61‑1 (MQ=255)
tGATACATTCAGTGCGCCAGATATTGAATGGCCTACGCCTCCGGCAGTTCAGGCCAGATGACATCCGgcgc > 1:1250942/1‑71 (MQ=255)
tGATACATCAAGTGCGCCAGATATTGAATGGCCTACGCCTCCGGCAGTTCAGGCCAGATGAc > 1:5033270/1‑62 (MQ=255)
gATACATCCAGTGCGCCAGATATTGAATGGCCTACGCATACGGCAGTTCAGGCCAGa > 1:643684/1‑57 (MQ=14)
cATTCAGTGCGCCAGATATTGAATGGCCTACGCCTCCGGCAGTTCAGGcc > 1:575083/1‑50 (MQ=255)
cATCCAGTGCGCCAGATATTGAATGGCCTACGCCTCCGGCAGTTCAGGCCAGATGACATCCGGCGCGGTGc < 1:2852232/71‑1 (MQ=38)
cATCCAGTGCGCCAGATATTGAATGGCCTACGCCTCCGGCAGTTCAGGCCAGATGACATCCCgcgc > 1:3263633/1‑66 (MQ=255)
tCCAGTGCGCCAGATATTGAATGGCCTACGCCTCCGGCAGTTCAGGCCAGATGAc > 1:558496/1‑55 (MQ=35)
|
AAGAAGATGAGCTGAAACAATATAATTTGTGGCTGGATTATCTGGAAGCACTGGAACTGGTTGATACATCCAGTGCGCCAGATATTGAATGGCCTACGCCTCCGGCAGTTCAGGCCAGATGACATCCGGCGCGGTGC > W3110S.gb/1210001‑1210137
|
| 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
