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 |
593,201 |
A→G |
22.2% |
F265L (TTC→CTC) |
cusS ← |
sensory histidine kinase in two‑component regulatory system with CusR, senses copper ions |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 593,201 | 0 | A | G | 22.2%
| 86.3
/ 23.8
| 45 | F265L (TTC→CTC) | cusS | sensory histidine kinase in two‑component regulatory system with CusR, senses copper ions |
| Reads supporting (aligned to +/- strand): ref base A (17/18); new base G (2/8); total (19/26) |
| Fisher's exact test for biased strand distribution p-value = 1.54e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01 |
GGGCGATTTCGGTTTGCGTTATGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGACATCCTCAATACGCTCGATCATATGGTTGAACGACAGTACCAGCTGTTC > W3110S.gb/593132‑593270
|
gggCGATTTCGGTTTGCGTTATGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGaaa > 1:1172241/1‑71 (MQ=255)
gggCGATTTCGGTTTGCGTTATGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGaaa < 1:4840279/71‑1 (MQ=255)
ggCGATTTCGGTTTGCGTTATGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGaaa < 1:3302544/70‑1 (MQ=255)
cGATTTCGGTTTGCGTTATGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTg > 1:2937057/1‑71 (MQ=255)
taggTTTGCGTTATGAGAGTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTg > 1:2220526/3‑66 (MQ=255)
tCGGTTTGCGTTATGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGa > 1:921457/1‑68 (MQ=255)
gTTTGCGTTATGAGATTCGTATTTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTg < 1:4905979/63‑1 (MQ=255)
cGTTATGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAGATTGGACTGGCGGGTaa < 1:2118947/71‑1 (MQ=255)
gTTATGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAGATTGGACTGGCGGGTaaa < 1:4350132/71‑1 (MQ=255)
tGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGACa > 1:4808994/1‑71 (MQ=255)
tGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGACa > 1:2462418/1‑71 (MQ=255)
aTTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAGATTGGACTGGCGGGTaaa < 1:1637617/63‑1 (MQ=255)
aTTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAGATTGGACTGGCGGGTAAAGACATCCt > 1:1904261/1‑71 (MQ=255)
ttCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAGATTGGACTGGCGGGTAAAGACATCCTc < 1:2487244/71‑1 (MQ=255)
cGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGACATCCTCaa > 1:580878/1‑71 (MQ=255)
gTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGACATCCTCaa < 1:4530761/70‑1 (MQ=255)
gTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGACATCCTCAAt < 1:1688735/71‑1 (MQ=255)
tAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAGATTGGACTGGCGGGTAAAGACATCCTCa > 1:1914064/1‑68 (MQ=255)
aTTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGAc > 1:3646026/1‑59 (MQ=255)
aTTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGAc > 1:1774876/1‑59 (MQ=255)
ttGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAGATTGGACTGGCGGGTAAAGACa < 1:4620077/59‑1 (MQ=255)
ttGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAGATTGGACTGGCGGGTAAAGACATCCTc < 1:2786599/64‑1 (MQ=255)
ttGGTGTGCGAATTTCGTGAGCGATATCCGCCGAGAAATTGGACTGGCGGGTAAAGACATCCTCAATACGc < 1:2510380/71‑1 (MQ=255)
ggTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGa > 1:3089083/1‑55 (MQ=255)
gtgtGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGACATCCTCAATACGCTc < 1:403191/70‑1 (MQ=255)
tgCGAATTTCGTGAGCGATATCCGCTGAGAGATTGGACTGGCGGGTAAAGACATCCTc < 1:1655904/58‑1 (MQ=255)
tgCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGTaaa < 1:4830326/49‑1 (MQ=255)
tgCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGACATCCTCAATACGCTCGAt > 1:3147644/1‑70 (MQ=255)
cGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGATATCCTCAATACGCTCGATCa < 1:1412720/70‑1 (MQ=255)
cGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGACATCCTCAATACGCTCGATCa > 1:4845088/1‑70 (MQ=255)
cGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGACATCCTCAATACGCTCGATCa < 1:1159027/70‑1 (MQ=255)
cGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGACATCCTCAATACGCTCGATCa < 1:4071598/70‑1 (MQ=255)
cGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGACATCCTCAATACGCTCGATCa > 1:2097239/1‑70 (MQ=255)
tCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGACATCCTCAATACGCTCGATCATATGGtt > 1:2101414/1‑71 (MQ=255)
tGAGCGATATCCGCTGAGAAATTGGACTGGCGGGTa < 1:490356/36‑1 (MQ=255)
tGAGCGATATCCGCTGAGAAATTGGACTGGCGGGTa < 1:2257097/36‑1 (MQ=255)
gAGCGATATCCGCTGAGAGATTGGACTGGCGGGTaaa < 1:975422/37‑1 (MQ=255)
aGCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGACATCCTCAATACGCTCGATCATATGGTTGAAc > 1:1627159/1‑70 (MQ=255)
aGCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGACATCCTCAATACGCTCGATCATATGGTTGAAc > 1:1633160/1‑70 (MQ=255)
gCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGACATCCTCAATACGCTCGATCATATGGTTGAACGa < 1:4906642/71‑1 (MQ=255)
gCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGACATCCTCAATACGCTCGATCATATGGTTGAACGa < 1:111522/71‑1 (MQ=255)
gCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGACATCCTCAATACGCTCGATCATATGGTTGAACGa < 1:4346960/71‑1 (MQ=255)
gATATCCGCTGAGAAATTGGACTGGCGGGTAAAGACATCCTCAATACGCTCGATCa < 1:780814/56‑1 (MQ=255)
tCCGCTGAGAAATTGGACTGGCGGGTAAAGACATCCTCAATACGCTCGATCATATGGTTGAACGACAGt < 1:3216528/69‑1 (MQ=255)
tCCGCTGAGAAATTGGACTGGCGGGTAAAGACATCCTCAATACGCTCGATCATATGGTTGAACGACAGTAc < 1:4630513/71‑1 (MQ=255)
ccGCTGAGAAATTGGACTGGCGGGTAAAGACATCCTCAATACGCTCGATCATATGGTTGAACGACAGTAc > 1:3942533/1‑70 (MQ=255)
cGCTGAGAAATTGGACTGGCGGGTAAAGACATCCTCAATACGCTCGATCATATGGTTGAACGACAGTAc > 1:1331769/1‑69 (MQ=255)
gaAATTTGACTGGCGTGTAAAGACATCCTCAATACGCTCGATCATATGGTTGAACGa < 1:1242784/57‑1 (MQ=255)
aaaTTGGACTGGCGGGTAAAGACATCCTCAATACGCTCGATCATATGGTTGAACGACAGTACCAGCTGTTc > 1:756635/1‑71 (MQ=255)
|
GGGCGATTTCGGTTTGCGTTATGAGATTCGTAATTGGTGTGCGAATTTCGTGAGCGATATCCGCTGAGAAATTGGACTGGCGGGTAAAGACATCCTCAATACGCTCGATCATATGGTTGAACGACAGTACCAGCTGTTC > W3110S.gb/593132‑593270
|
| 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
