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 |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,671,600 |
C→T |
72.0% |
P192L (CCG→CTG) |
malQ → |
4‑alpha‑glucanotransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,671,600 | 0 | C | T | 72.0%
| 29.4
/ 9.8
| 32 | P192L (CCG→CTG) | malQ | 4‑alpha‑glucanotransferase |
| Reads supporting (aligned to +/- strand): ref base C (4/5); new base T (20/3); total (24/8) |
| Fisher's exact test for biased strand distribution p-value = 2.33e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
ATGCTGGTGGATGTGGCAAAACGTGGCGGGTCGTTCATTGGCCTGAACCCGATTCATGCGCTCTATCCGGCAAATCCGGAGAGCGCCAGCCCATACAGCCCGTCTTCTCGCCGTTGGCTGAA > minE/2671533‑2671654
|
aTGCTGGTGGATGTGGCAAAACGTGGCGGGTCGTTCATTGGCCTGAACCCGATTCATGCGCTCTATcc > 1:1206531/1‑68 (MQ=255)
aTGCTGGTGGATGTGGCAAAACGTGGCGGGTCGTTCATTGGCCTGAACCCGATTCATGCGCTCTATcc > 1:2765836/1‑68 (MQ=255)
aTGCTGGTGGATGTGGCAAAACGTGGCGGGTCGTTCATTGGCCTGAACCCGATTCATGCGCTCTATcc > 1:2447002/1‑68 (MQ=255)
aTGCTGGTGGATGTGGCAAAACGTGGCGGGTCGTTCATTGGCCTGAACCCGATTCATGCGCTCTATcc > 1:2136154/1‑68 (MQ=255)
aTGCTGGTGGATGTGGCAAAACGTGGCGGGTCGTTCATTGGCCTGAACCCGATTCATGCGCTCTATcc > 1:2028016/1‑68 (MQ=255)
aTGCTGGTGGATGTGGCAAAACGTGGCGGGTCGTTCATTGGCCTGAACCCGATTCATGCGCTCTATcc > 1:446717/1‑68 (MQ=255)
aTGCTGGTGGATGTGGCAAAACGTGGCGGGTCGTTCATTGGCCTGAACCCGATTCATGCGCTCTATcc > 1:120435/1‑68 (MQ=255)
ggtggATGTGGCAAAACGTGGCGGGTCGTTCATTGGCCTGAACCCGATTCATGCGCTCTATCCGGCaaa < 1:3343184/69‑1 (MQ=255)
ggtggATGTGGCAAAACGTGGCGGGTCGTTCATTGGCCTGAACCCGATTCATGCGCTCTATCCGGCaaa < 1:927127/69‑1 (MQ=255)
ggtggATGTGGCAAAACGTGGCGGGTCGTTCATTGGCCTGAACCCGATTCATGCGCTCTATCCGGCaaa < 1:2073551/69‑1 (MQ=255)
ggtggATGTGGCAAAACGTGGCGGGTCGTTCATTGGCCTGAACCCGATTCATGCGCTCTATCCGGCaaa < 1:1462228/69‑1 (MQ=255)
gtgGCAAAACGTGGCGGGTCGTTCATTGGCCTGAACCCGATTCATGCGCTCTATCCGGCAAATCCGgag < 1:1558114/69‑1 (MQ=255)
gTTTATTGGTCTGAACCCGATTCATGCGCTCTATCTGGCAAATCCGGAAAGTGCCAGCCCGTACAGccc < 1:2123908/69‑1 (MQ=255)
gTTTATTGGTCTGAACCCGATTCATGCGCTCTATCTGGCAAATCCGGAAAGTGCCAGCCCGTACAGccc < 1:30087/69‑1 (MQ=255)
ttaTTGGTCTGAACCCGATTCATGCGCTCTATCTGGCAAATCCGGAAAGTGCCAGCCCGTACAGccc < 1:1282253/65‑1 (MQ=255)
cATTGGCCTGAACCCGATTCATGCGCTCTATCCGGCAAATCCGGAGAGCGCCAGCCCATACAGCCCGtc > 1:27020/1‑69 (MQ=255)
cATTGGCCTGAACCCGATTCATGCGCTCTATCCGGCAAATCCGGAGAGCGCCAGCCCATACAGCCCGt > 1:1349442/1‑68 (MQ=255)
tcTGAACCCGATTCATGCGCTCTATCTGGCAAATCCGgaa > 1:491205/2‑39 (MQ=255)
tcTGAACCCGATTCATGCGCTCTATCTGGCAAATCCGgaa > 1:606383/2‑39 (MQ=255)
tcTGAACCCGATTCATGCGCTCTATCTGGCAAATCCGgaa > 1:649323/2‑39 (MQ=255)
tcTGAACCCGATTCATGCGCTCTATCTGGCAAATCCGgaa > 1:758150/2‑39 (MQ=255)
tcTGAACCCGATTCATGCGCTCTATCTGGCAAATCCGgaa > 1:3335283/2‑39 (MQ=255)
tcTGAACCCGATTCATGCGCTCTATCTGGCAAATCCGgaa > 1:3330942/2‑39 (MQ=255)
tcTGAACCCGATTCATGCGCTCTATCTGGCAAATCCGgaa > 1:987190/2‑39 (MQ=255)
tcTGAACCCGATTCATGCGCTCTATCTGGCAAATCCGgaa > 1:759215/2‑39 (MQ=255)
tcTGAACCCGATTCATGCGCTCTATCTGGCAAATCCGgaa > 1:3311130/2‑39 (MQ=255)
tcTGAACCCGATTCATGCGCTCTATCTGGCAAATCCGgaa > 1:3113831/2‑39 (MQ=255)
tcTGAACCCGATTCATGCGCTCTATCTGGCAAATCCGgaa > 1:2283043/2‑39 (MQ=255)
tcTGAACCCGATTCATGCGCTCTATCTGGCAAATCCGgaa > 1:2276538/2‑39 (MQ=255)
tcTGAACCCGATTCATGCGCTCTATCTGGCAAATCCGgaa > 1:218584/2‑39 (MQ=255)
tcTGAACCCGATTCATGCGCTCTATCTGGCAAATCCGgaa > 1:1979817/2‑39 (MQ=255)
tcTGAACCCGATTCATGCGCTCTATCTGGCAAATCCGgaa > 1:1968167/2‑39 (MQ=255)
tcTGAACCCGATTCATGCGCTCTATCTGGCAAATCCGgaa > 1:1966171/2‑39 (MQ=255)
tcTGAACCCGATTCATGCGCTCTATCTGGCAAATCCGgaa > 1:1953555/2‑39 (MQ=255)
tcTGAACCCGATTCATGCGCTCTATCTGGCAAATCCGgaa > 1:1940829/2‑39 (MQ=255)
tcTGAACCCGATTCATGCGCTCTATCTGGCAAATCCGgaa > 1:1813485/2‑39 (MQ=255)
tcTGAACCCGATTCATGCGCTCTATCTGGCAAATCCGgaa > 1:1349451/2‑39 (MQ=255)
tCATGCGCTCTATCCGGCAAATCCGGAGAGCGCCAGCCCa > 1:921919/1‑40 (MQ=255)
tCATGCGCTCTATCCGGCAAATCCGGAGAGCGCCAGCCCATACAGCCCGTCTTCTCGCCGTTGGCTGaa > 1:1473120/1‑69 (MQ=255)
|
ATGCTGGTGGATGTGGCAAAACGTGGCGGGTCGTTCATTGGCCTGAACCCGATTCATGCGCTCTATCCGGCAAATCCGGAGAGCGCCAGCCCATACAGCCCGTCTTCTCGCCGTTGGCTGAA > minE/2671533‑2671654
|
| 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
