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 |
2,594,104 |
G→A |
100% |
H138Y (CAT→TAT) |
ypfI ← |
predicted hydrolase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,594,104 | 0 | G | A | 95.3%
| 191.0
/ 1.0
| 64 | H138Y (CAT→TAT) | ypfI | predicted hydrolase |
| Reads supporting (aligned to +/- strand): ref base G (1/2); new base A (16/45); total (17/47) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.62e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
GAGAATGGCTGGTTTTGCCGCCAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATGCTGGACAAAATGCGGCGTCGCAATAGGGTCAGGGCAATCACTCCAGCGCAGCGAGTCGGCAT > W3110S.gb/2594040‑2594166
|
gagaATGGCTGGTTTTGCCGCCAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGAc < 1:1520683/71‑1 (MQ=255)
gaATGGCTGGTTTTGCCGCCAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACaa < 1:3142222/71‑1 (MQ=255)
gaATGGCTGGTTTTGCCGCCAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACaa < 1:3129916/71‑1 (MQ=255)
gaATGGCTGGTTTTGCCGCCAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACaa < 1:3327686/71‑1 (MQ=255)
gaATGGCTGGTTTTGCCGCCAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACaa < 1:2869041/71‑1 (MQ=255)
gaATGGCTGGTTTTGCCGCCAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACaa < 1:2262519/71‑1 (MQ=255)
gaATGGCTGGTTTTGCCGCCAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACaa < 1:2207869/71‑1 (MQ=255)
tGGCTGGTTTTGCCGCCAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAAt < 1:3262092/71‑1 (MQ=255)
tGGCTGGTTTTGCCGCCAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAAt > 1:1870888/1‑71 (MQ=255)
gCTGGTTTTGGCGCCAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATgc < 1:3347621/71‑1 (MQ=255)
gCTGGTTTTGCCGCCAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATgc < 1:3178730/71‑1 (MQ=255)
gCTGGTTTTGCCGCCAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATgc < 1:767635/71‑1 (MQ=255)
gCTGGTTTTGCCGCCAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATgc < 1:1585679/71‑1 (MQ=255)
gCTGGTTTTGCCGCCAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATgc < 1:2397289/71‑1 (MQ=255)
tttGCCGCCAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATGCTGGACAAAATGCGGCGt > 1:3052258/1‑70 (MQ=255)
ttGCCGCCAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCg > 1:2635380/1‑71 (MQ=255)
ttGCCGCCAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCg > 1:119239/1‑71 (MQ=255)
ttGCCGCCAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCg > 1:1617171/1‑71 (MQ=255)
gccgccAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGc < 1:733572/70‑1 (MQ=255)
gccgccAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGc < 1:3642526/70‑1 (MQ=255)
gccgccAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGc < 1:3706076/70‑1 (MQ=255)
gccgccAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGGTTGAGATACTGGACAAAATGCGGCGTCGc < 1:397223/70‑1 (MQ=255)
ccgccAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGCaa < 1:334341/71‑1 (MQ=255)
ccgccAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGCaa < 1:587869/71‑1 (MQ=255)
ccgccAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGCaa < 1:1731641/71‑1 (MQ=255)
ccgccAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATG‑GGCGTCGCAAt < 1:3093168/71‑1 (MQ=255)
cgccAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATGCTGGACAAAATGCGGCGTCGCAAt < 1:2770303/71‑1 (MQ=255)
cgccAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATGCTGGACAAAATGCGGCGTCGCAAt < 1:1982493/71‑1 (MQ=255)
cgccAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGCAAt < 1:1756223/71‑1 (MQ=255)
cAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGCAATAgg < 1:3002098/71‑1 (MQ=255)
cAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGCAATAgg < 1:3187539/71‑1 (MQ=255)
cAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGCAATAgg < 1:2617594/71‑1 (MQ=255)
cAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGCAATAgg < 1:3368553/71‑1 (MQ=255)
cAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGCAATAgg < 1:2621940/71‑1 (MQ=255)
cAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGCAATAgg < 1:753864/71‑1 (MQ=255)
cAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGCAATAgg < 1:1799059/71‑1 (MQ=255)
ggATAGCCTCGTTATCCGCCGTAAGTACGCGTTTTAGATACTGGACAAAATGCGGCGTCGCAATa < 1:1952803/65‑1 (MQ=255)
ggATAGCCTCGTTATCCGCCGTAAGTACGCGTTTTAGATACTGGACAAAATGCGGCGTCGCAATa < 1:1948475/65‑1 (MQ=255)
ggATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGCAATa < 1:2436552/65‑1 (MQ=255)
ggATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGCAATa < 1:1191250/65‑1 (MQ=255)
gATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGCAATAGGGTCAg > 1:716421/1‑71 (MQ=255)
aTAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGCAATa < 1:734603/63‑1 (MQ=255)
aTAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGCAATa < 1:919149/63‑1 (MQ=255)
aTAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGCAATa < 1:1649670/63‑1 (MQ=255)
aTAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGCAATa < 1:1849857/63‑1 (MQ=255)
aTAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGCAATa < 1:2477031/63‑1 (MQ=255)
tAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGCAATAGGGTCAggg > 1:467205/1‑71 (MQ=255)
tAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGCAATAGGGTCAggg > 1:1086144/1‑71 (MQ=255)
tAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGCAATAGGGTCAggg > 1:2899247/1‑71 (MQ=255)
aGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGCAATAGGGTCAggg > 1:2189642/1‑70 (MQ=255)
gCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGCAATAGGGTCAGGGc < 1:3574693/70‑1 (MQ=255)
gCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGCAATAGGGTCAGGGc < 1:2115345/70‑1 (MQ=255)
gCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGCAATAGGGTCAGGGc < 1:2627835/70‑1 (MQ=255)
tCGTTATCCGCCGTAAGTACGCGTTTGAGATACTGGAc < 1:1943663/38‑1 (MQ=255)
cGTTATCCGCCGTCAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGCAATAGGGTCAGGGc < 1:558434/66‑1 (MQ=255)
tCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGCAATAGGGTCAGGGCAATCACTc > 1:1732651/1‑69 (MQ=255)
tCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGCAATAGGGTCAGGGCAATCACTc > 1:113513/1‑69 (MQ=255)
tCCGCCGTAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGCAATAGGGTCAGGGCAATCACTc > 1:3056420/1‑69 (MQ=255)
tAAGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGCAATAGGGTCAGGGCAATCACTCcagcgcagc < 1:766939/71‑1 (MQ=255)
aGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGCAATAg > 1:3553828/1‑43 (MQ=255)
aGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGCAATAg > 1:2043104/1‑43 (MQ=255)
aGTACGCGTTTGAGATACTGGACAAAATGCGGCGTCGCAATAg > 1:647732/1‑43 (MQ=255)
cgTTTGATATACTGGACAAAATGCGGCGTCGCAATAGGGTCAGGGc < 1:2621972/46‑1 (MQ=255)
tGAGATACTGGACAAAATGCGGCGTCGCAATAGGGTAAGGGCAATCACTCCAGCGCAGCGAGTCGGCAt > 1:3202693/1‑69 (MQ=255)
|
GAGAATGGCTGGTTTTGCCGCCAGAGGATAGCCTCGTTATCCGCCGTAAGTACGCGTTTGAGATGCTGGACAAAATGCGGCGTCGCAATAGGGTCAGGGCAATCACTCCAGCGCAGCGAGTCGGCAT > W3110S.gb/2594040‑2594166
|
| 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
