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 F21 I0 R1
|
476 |
35.3 |
2812105 |
96.7% |
2719305 |
61.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,609,975 |
C→T |
68.8% |
L254L (CTG→CTA) |
yneE ← |
conserved inner membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,609,975 | 0 | C | T | 68.8%
| 58.2
/ 39.6
| 48 | L254L (CTG→CTA) | yneE | conserved inner membrane protein |
| Reads supporting (aligned to +/- strand): ref base C (7/8); new base T (24/9); total (31/17) |
| Fisher's exact test for biased strand distribution p-value = 1.08e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CAGATGGCATCCAGTGGTAAATCATTGTTTTCAGTACCGAACGGATCTTCCAGTTCTTCCGCCAGACAATCCAGCGAAATAAAAGTGTAGGAAATCAGCACAGAGATAAAAGGCGTCATGTAATGC > W3110S.gb/1609913‑1610038
|
cAGATGGCATCCAGTGGTAAATCATTGTTTTCAGTACCGAACGGATCTTCCAGTTCTTCCGCCAGACAAt < 1:1006762/70‑1 (MQ=255)
ggCATCCAGTGGTAAATCATTGTTTTCAGTACCGAACGGATCTTCCAGTTCTTCCGCTAGACAATCCAGc > 1:2415820/1‑70 (MQ=255)
ggCATCCAGTGGTAAATCATTGTTTTCAGTACCGAACGGATCTTCCAGTTCTTCCGCTAGACAATCCAGc > 1:97375/1‑70 (MQ=255)
ggCATCCAGTGGTAAATCATTGTTTTCAGTACCGAACGGATCTTCCAGTTCTTCCGCTAGACAATCCAGc > 1:577400/1‑70 (MQ=255)
ggCATCCAGTGGTAAATCATTGTTTTCAGTACCGAACGGATCTTCCAGTTCTTCCGCTAGACAATCCAGc > 1:463759/1‑70 (MQ=255)
ggCATCCAGTGGTAAATCATTGTTTTCAGTACCGAACGGATCTTCCAGTTCTTCCGCTAGACAATCCAGc > 1:384671/1‑70 (MQ=255)
gCATCCAGTGGTAAATCATTGTTTTCAGTACCGAACGGATCTTCCAGTTCTTCCGCTAGACAATCCAGCGa < 1:1442393/71‑1 (MQ=255)
gCATCCAGTGGTAAATCATTGTTTTCAGTACCGAACGGATCTTCCAGTTCTTCCGCTAGACAATCCAGCGa < 1:2200692/71‑1 (MQ=255)
cAGTGGTAAATCATTGTTTTCAGTACCGAACGGATCTTCCAGTTCTTCCGCTAGACAATCCAg > 1:1633098/1‑63 (MQ=255)
cAGTGGTAAATCATTGTTTTCAGTACCGAACGGATCTTCCAGTTCTTCCGCTAGACAATCCAg > 1:1636362/1‑63 (MQ=255)
cAGTGGTAAATCATTGTTTTCAGTACCGAACGGATCTTCCAGTTCTTCCGCTAGACAATCCAg > 1:901588/1‑63 (MQ=255)
cAGTGGTAAATCATTGTTTTCAGTACCGAACGGATCTTCCAGTTCTTCCGCTAGACAATCCAg > 1:1848313/1‑63 (MQ=255)
cAGTGGTAAATCATTGTTTTCAGTACCGAACGGATCTTCCAGTTCTTCCGCTAGACAATCCAGCGAAATa > 1:1932563/1‑70 (MQ=255)
ggTAAATCATTGTTTTCAGTACCGAACGGATCTTCCAGTTCTTCCGCTAGACAATCCAGCGAAATAAAAg > 1:450381/1‑70 (MQ=255)
gTAAATCATTGTTTTCAGTACCGAACGGATCTTCCAGTTCTTCCGCTAGACAATCCAGCGAAATAAAAgtg > 1:1760966/1‑71 (MQ=255)
gTAAATCATTGTTTTCAGTACCGAACGGATCTTCCAGTTCTTCCGCTAGACAATCCAGCGAAATAAAAgtg > 1:210858/1‑71 (MQ=255)
gTAAATCATTGTTTTCAGTACCGAACGGATCTTCCAGTTCTTCCGCCAGACAATCCAGCGaaa > 1:113703/1‑63 (MQ=255)
aaaTCATTGTTTTCAGTACCGAACGGATCTTCCAGTTCTTCCGCTAGACAATCCAGCGAAATAAAAgtg > 1:1607/1‑69 (MQ=255)
aaTCATTGTTTTCAGTACCGAACGGATCTTCCAGTTCTTCCGCTAGACAATCCAGCTAAATAAAAgtgt < 1:2748962/69‑1 (MQ=255)
aaTCATTGTTTTCAGTACCGAACGGATCTTCCAGTTCTTCCGCTAGACAATCCAGCGAAATAAAAGTGTAg > 1:2046262/1‑71 (MQ=255)
aaTCATTGTTTTCAGTACCGAACGGATCTTCCAGTTCTTCCGCCAGACAATCCAGCGAAATAAAAGTGTAg > 1:451031/1‑71 (MQ=255)
aaTCATTGTTTTCAGTACCGAACGGATCTTCCAGTTCTTCCGCCAGACAATCCAGCGAAATAAAAGTGTAg > 1:447794/1‑71 (MQ=255)
aTCATTGTTTTCAGTACCGAACGGATCTTCCAGTTCTTCCGCCAGACAATc < 1:45886/51‑1 (MQ=255)
tCATTGTTTTCAGTACCGAACGGATCTTCCAGTTCTTCCGCTAGACAATCCAGCGAAATAAAAGTGTAGGa < 1:2517906/71‑1 (MQ=255)
cATTGTTTTCAGTACCGAACGGATCTTCCAGTTCTTCCGCCAGACAATCCAGCGAAATAAAAGTGTAGGa > 1:1794498/1‑70 (MQ=255)
cATTGTTTTCAGGACCGAACGGATCTTCCAGTTCTTCCGCTAGa > 1:2704449/1‑44 (MQ=38)
aTTGTTTTCAGTACCGAACGGATCTTCCAGTTCTTCCGCCAGACAATCCAGCGAAATAAAAg > 1:942296/1‑62 (MQ=255)
aTTGTTTTCAGTACCGAACGGATCTTCCAGTTCTTCCGCCAGACAATCCAGCGAAATAAAAg > 1:2689900/1‑62 (MQ=255)
gTTTTCAGTACCGAACGGATCTTCCAGTTCTTCCGCTAGACAATCCAGCGAAATAAAAGTGTAGGAAATc < 1:2126641/70‑1 (MQ=255)
gTTTTCAGTACCGAACGGATCTTCCAGTTCTTCCGCTAGACAATCAAGCGAAATAAAAGAGTa > 1:568794/1‑63 (MQ=255)
ttttCAGTACCGAACGGATCTTCCAGTTCTTCCGCCAGAc < 1:1788412/40‑1 (MQ=255)
ttCAGTACCGAACGGATCTTCCAGTTCTTCCGCTAGACAATCCAg > 1:1225698/1‑45 (MQ=255)
ccGAACGGATCTTCCAGTTCTTCCGCCAGACAATCCAGCGAAATaaaa > 1:2159518/1‑48 (MQ=255)
aaCGGATCTTCCAGTTCTTCCGCCAGACAATCCAGCGAAATAAAAgtgt < 1:1901012/49‑1 (MQ=255)
aaCGGATCTTCCAGTTCTTCCGCCAGACAATCCAGCGAAATAAAAgtgt < 1:897929/49‑1 (MQ=255)
aCGGATCTTCCAGTTCTTCCGCCAGACAATCCAGCGAAATAAAAGTGTAGGAAATCAGCACAGAGATaaaa < 1:972930/71‑1 (MQ=255)
gATCTTCCAGTTCTTCCTCTAGACAATCCAGCGAAATaa < 1:2354807/39‑1 (MQ=37)
aTCTTCCAGTTCTTCCGCTAGACAATCCAGCGAAATAAAAGTGTAGGAAATCAGCACAGAGATaaaa < 1:2806193/67‑1 (MQ=255)
ccAGTTCTTCCGCCAGACAATCCAGCGAAATAAAAGTGTAGGAAATCAGCACAGAGATAAAAGGCGt < 1:2273069/67‑1 (MQ=255)
ccAGTTCTTCCGCCAGACAATCCAGCGAAATAAAAGTGTAGGAAATCAGCACAGAGATAAAAGGCGt < 1:1223702/67‑1 (MQ=255)
ttcttcCGCTAGACAATCCAGCGAAATAAAAGTGTAGGAAATCAGCACAGAGATaa < 1:253035/56‑1 (MQ=255)
ttcttcCGCTAGACAATCCAGCGAAATAAAAGTGTAGGAAATCAGCACAGAGATAAAAGGCGTCATGTa > 1:502612/1‑69 (MQ=255)
tcttcCGCTAGACAATCCAGCGAAATAAAAGTGTa > 1:2443588/1‑35 (MQ=255)
cttcCGCTAGACAATCCAGCGAAATAAAAGTGTAGGAAATCAGCACAGAGATaaaa > 1:2626942/1‑56 (MQ=255)
cttcCGCTAGACAATCCAGCGAAATAAAAGTGTAGGAAATCAGCACAGAGATAAAAGGCGTCATGTAATg > 1:2307182/1‑70 (MQ=255)
cttcCGCTAGACAATCCAGCGAAATAAAAGTGTAGGAAATCAGCACAGAGATAAAAGGCGTCATGTAATg > 1:134618/1‑70 (MQ=255)
cttcCGCTAGACAATCCAGCGAAATAAAAGTGTAGGAAATCAGCACAGAGATAAAAGGCGTCATGTAATg > 1:1746544/1‑70 (MQ=255)
ccGCTAGACAATCCAGCGAAATAAAAGTGTAGGAAATCAGCACAGAGATAAAAGGCGTCATGTAATGc < 1:328324/68‑1 (MQ=255)
|
CAGATGGCATCCAGTGGTAAATCATTGTTTTCAGTACCGAACGGATCTTCCAGTTCTTCCGCCAGACAATCCAGCGAAATAAAAGTGTAGGAAATCAGCACAGAGATAAAAGGCGTCATGTAATGC > W3110S.gb/1609913‑1610038
|
| 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
