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 F28 I3 R2
|
122 |
64.1 |
3058059 |
97.6% |
2984665 |
63.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
minE |
1,827,842 |
Δ1 bp |
coding (1085/2562 nt) |
mutS → |
methyl‑directed mismatch repair protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,827,840 | 0 | C | . | 98.1%
| 211.8
/ ‑1.0
| 53 | coding (1083/2562 nt) | mutS | methyl‑directed mismatch repair protein |
| Reads supporting (aligned to +/- strand): ref base C (0/1); new base . (23/29); total (23/30) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.74e-01 |
ACAGCCGGTACTGCGTCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCGCCCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTGCCGGAGCTGCGTGCGCAGTTAGA > minE/1827771‑1827905
|
aCAGCCGGTACTGCGTCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCGc > 1:2887799/1‑70 (MQ=255)
aCAGCCGGTACTGCGTCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCGc > 1:2097595/1‑70 (MQ=255)
cAGCCGGTACTGCGTCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCGc < 1:2943074/69‑1 (MQ=255)
cGGTACTGCGTCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCAcgcg < 1:1041886/71‑1 (MQ=255)
cGGTACTGCGTCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCAcgcg < 1:1932999/71‑1 (MQ=255)
gTACTGCGTCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGAt < 1:651444/71‑1 (MQ=255)
tACTGCGTCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATc < 1:1225313/71‑1 (MQ=255)
aCTGCGTCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATc < 1:3230/70‑1 (MQ=255)
aCTGCGTCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCt > 1:2781206/1‑71 (MQ=255)
cTGCGTCAGGTCGGCGTCCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTg < 1:2773051/71‑1 (MQ=255)
cTGCGTCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTg > 1:716059/1‑71 (MQ=255)
tCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCg > 1:2575562/1‑71 (MQ=255)
tCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCg > 1:182459/1‑71 (MQ=255)
cAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCg > 1:1706150/1‑70 (MQ=255)
aGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTa > 1:1546038/1‑71 (MQ=255)
aGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTa > 1:32450/1‑71 (MQ=255)
aGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTa > 1:974963/1‑71 (MQ=255)
ggTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTAt < 1:2567353/71‑1 (MQ=255)
cGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCt > 1:1264378/1‑59 (MQ=255)
cGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATgcg > 1:1918158/1‑71 (MQ=255)
cGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATgcg > 1:1571352/1‑71 (MQ=255)
cGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATgcg > 1:604141/1‑71 (MQ=255)
gACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCAc > 1:102930/1‑71 (MQ=255)
aCCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACg < 1:730964/71‑1 (MQ=255)
catGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGc > 1:2471490/3‑71 (MQ=255)
cTGGAACGTATTCTGGCACGTCTGGCTTTACGAGCTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCt < 1:1035297/71‑1 (MQ=255)
cTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCt < 1:533173/71‑1 (MQ=255)
cTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCt < 1:1880766/71‑1 (MQ=255)
gAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTc < 1:2479882/71‑1 (MQ=255)
gAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTc > 1:1358133/1‑71 (MQ=255)
gAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTc < 1:1117271/71‑1 (MQ=255)
aaCGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTc < 1:2838416/70‑1 (MQ=255)
aCGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATc > 1:2767782/1‑46 (MQ=255)
cGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCtt > 1:2403979/1‑66 (MQ=255)
gTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGc < 1:2606384/71‑1 (MQ=255)
gTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGc < 1:1282672/71‑1 (MQ=255)
tATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCa < 1:664009/71‑1 (MQ=255)
ttCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCaa < 1:1819741/70‑1 (MQ=255)
ggCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATg > 1:1830290/1‑48 (MQ=255)
gCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTGc < 1:2250316/69‑1 (MQ=255)
cGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTGCCGGAg < 1:239516/71‑1 (MQ=255)
tCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTGCCGGAGCt < 1:2711377/71‑1 (MQ=255)
gCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTGCCGGAGCtgcgt > 1:780706/1‑71 (MQ=255)
gCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTGCCGGAGCtgc < 1:3048827/69‑1 (MQ=255)
tttACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCAACGCTTTCCAGCAACTGCCGGAGCtgcgtg > 1:775398/1‑70 (MQ=255)
ttACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTGCCGGAGCtgcgtg < 1:1971184/69‑1 (MQ=255)
aCGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTGCCGGAGCtgcgtgcg > 1:356316/1‑69 (MQ=255)
aCGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTGCCGGAGCtgcgtgcg > 1:397155/1‑69 (MQ=255)
aCGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTGCCGGAGCTGCGTgcgc < 1:2512174/70‑1 (MQ=255)
cGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTGCCGGAGCTGCGTGCGCa < 1:1185564/70‑1 (MQ=255)
gAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTGCCGGAGCTGCGTGCGCAGt < 1:2729936/71‑1 (MQ=255)
aaCTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTGCCGGAGCTGCGTGCGCAGtt < 1:715991/71‑1 (MQ=255)
aCTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCtt < 1:2572966/39‑1 (MQ=38)
aCTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTg > 1:1812230/1‑50 (MQ=39)
aCTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTGCCGGAGCTGCGTGCGCAGTTa < 1:153865/71‑1 (MQ=255)
cTCGCCCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTGCCGGAGCTGCGTGCGCAGTTAGa < 1:998564/70‑1 (MQ=255)
|
ACAGCCGGTACTGCGTCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCGCCCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTGCCGGAGCTGCGTGCGCAGTTAGA > minE/1827771‑1827905
|
| 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
