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 F8 I0 R2
|
296 |
77.6 |
4260404 |
88.1% |
3753415 |
61.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,892,019:1 |
+GC |
100% |
intergenic (‑437/+54) |
gudP ← / ← ygdL |
predicted D‑glucarate transporter/conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,892,019 | 1 | . | G | 97.9%
| 159.6
/ ‑3.4
| 47 | intergenic (‑437/+54) | gudP/ygdL | predicted D‑glucarate transporter/conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base G (21/25); total (22/25) |
| Fisher's exact test for biased strand distribution p-value = 4.68e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| 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. |
| * | minE | 1,892,019 | 2 | . | C | 97.9%
| 158.6
/ ‑3.7
| 47 | intergenic (‑437/+54) | gudP/ygdL | predicted D‑glucarate transporter/conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base C (21/25); total (22/25) |
| Fisher's exact test for biased strand distribution p-value = 4.68e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| 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. |
CTGGCATTTGCCTGAAAAGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATAT‑CA‑‑TAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGACCTGATTGTTTAACC > minE/1891951‑1892078
||
cTGGCTTTTGCCTGAAAAGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATAT‑Cag < 1:3162540/70‑2 (MQ=255)
tGAAAAGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATAT‑CAGCTAAGCACAGAAc > 1:3022377/1‑71 (MQ=255)
tGAAAAGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATAT‑CAGCTAAGCACAGAAc > 1:3547098/1‑71 (MQ=255)
gAAAAGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATAT‑CAGCTAAGCACAGAAcc > 1:135972/1‑71 (MQ=255)
aaaaGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATAT‑CAGCTAAGCACAGAAcc < 1:876678/70‑1 (MQ=255)
aaaaGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATAT‑CAGCTAAGCACAGAACCg > 1:336944/1‑71 (MQ=255)
aaaGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATAT‑CAGCTAAGCACAGAACCgg < 1:3582697/71‑1 (MQ=255)
aaaGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATAT‑CAGCTAAGCACAGAACCgg > 1:3092738/1‑71 (MQ=255)
aaGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATAT‑CAGCTAAGCACAGAACCggg > 1:4124870/1‑71 (MQ=255)
aaGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATAT‑CAGCTAAGCACAGAACCggg > 1:1467700/1‑71 (MQ=255)
aaGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATAT‑CAGCTAAGCACAGAACCggg > 1:2025014/1‑71 (MQ=255)
aaGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATAT‑CAGCTAAGCACAGAACCggg > 1:3404617/1‑71 (MQ=255)
aaGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATAT‑CAGCTAAGCACAGAACCggg > 1:1203488/1‑71 (MQ=255)
aaGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATAT‑CAGCTAAGCACAGAACCgg < 1:3750739/70‑1 (MQ=255)
gattcAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATAT‑CAGCTAAGCACAGAACCGGGTCGGATa < 1:1502913/71‑1 (MQ=255)
gattcAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATAT‑CAGCTAAGCACAGAACCGGGTCGGATa < 1:1775677/71‑1 (MQ=255)
attcAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATAT‑CAGCTAAGCACAGAACCGGGTCGGATa < 1:873904/70‑1 (MQ=255)
cAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATAT‑CAGCTAAGCACAGAACCGGGTCGGATAAGa < 1:387865/70‑1 (MQ=255)
cAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATAT‑CAGCTAAGCACAGAACCGGGTCGGATAAGa < 1:1152587/70‑1 (MQ=255)
aGCACCGCTAAAACGACATTTACCGCTCGCTGAACATAT‑CAGCTAAGCACAGa < 1:717044/53‑1 (MQ=255)
aGCACCGCTAAAACGACATTTACCGCTCGCTGAACATAT‑CAGCTAAGCACAGa < 1:3512737/53‑1 (MQ=255)
aGCACCGCTAAAACGACATTTACCGCTCGCTGAACATAT‑CAGCTAAGCACAGa < 1:2647261/53‑1 (MQ=255)
aGCACCGCTAAAACGACATTTACCGCTCGCTGAACATAT‑CAGCTAAGCACAGa < 1:2845215/53‑1 (MQ=255)
aGCACCCCTAAAACGACATTTACCGCTCGCTGAACATAT‑CAGCTAAGCACAGa < 1:2282030/53‑1 (MQ=255)
cACCGCTAAAACGACATTTACCGCTCGCTGAACATAT‑CAGCTAAGCACAGAACCGGGTCGGATAAGACGtt > 1:36675/1‑71 (MQ=255)
ccGCTAAAACGACATTTACCGCTCGCTGAACATAT‑CAGCTAAGCACAGaa > 1:1064891/1‑50 (MQ=255)
ccGCTAAAACGACATTTACCGCTCGCTGAACATAT‑CAGCTAAGCACAGaa > 1:2592759/1‑50 (MQ=255)
gCTAAAACGACATTTACCGCTCGCTGAACATAT‑CAGCTAAGCACAGAACCGGGTCGGATAAGACGTTcgcg > 1:566275/1‑71 (MQ=255)
tAAAACGACATTTACCGCTCGCTGAACATAT‑CAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGt < 1:3734112/70‑1 (MQ=255)
aaaaCGACATTTACCGCTCGCTGAACATATAGC‑‑TAAGCACAGAACCg > 1:1243749/1‑47 (MQ=255)
aaaaCGACATTTACCGCTCGCTGAACATAT‑CAGCTAAGCACAGAACCg > 1:467656/1‑48 (MQ=255)
aaaCGACATTTACCGCTCGCTGAACATAT‑CAGCTAAGCACAGAACCGGGTCGTATAAGACGTTCGCGtc < 1:1413482/69‑1 (MQ=255)
aaCGACATTTACCGCTCGCTGAACATAT‑CAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGtc < 1:3072304/68‑1 (MQ=255)
gACATTTACCGCTCGCTGAACATAT‑CAGCTAAGCACAGAACCGGGTCgg < 1:1357234/49‑1 (MQ=255)
cATTTACCGCTCGCTGAACATAT‑CAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCg < 1:2517524/70‑1 (MQ=255)
tttACCGCTCGCTGAACATAT‑CAGCTAAGCACAGAACCGGGTCGGATaa < 1:2044171/49‑1 (MQ=255)
tttACCGCTCGCTGAACATAT‑CAGCTAAGCACAGAACCGGGTCGGATaa < 1:1816954/49‑1 (MQ=255)
tttACCGCTCGCTGAACATAT‑CAGCTAAGCACAGAACCGGGTCGGATaa < 1:4079426/49‑1 (MQ=255)
tttACCGCTCGCTGAACATAT‑CAGCTAAGCACAGAACCGGGTCGGATaa < 1:3086344/49‑1 (MQ=255)
tACCGCTCGCTGAACATAT‑CAGCTAAGCACAGAACCGGGTCGGATaa > 1:1440787/1‑47 (MQ=255)
tACCGCTCGCTGAACATAT‑CAGCTAAGCACAGAACCGGGTCGGATaa > 1:2562933/1‑47 (MQ=255)
tACCGCTCGCTGAACATAT‑CAGCTAAGCACAGAACCGGGTCGGATaa > 1:2063704/1‑47 (MQ=255)
aCCGCTCGCTGAACATAT‑CAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGACCTg < 1:2150612/70‑1 (MQ=255)
cgctcgctGAACATAT‑CAGCTAAGCACAGAACCGGGTCGGATAAGACGTTcgc < 1:2637422/53‑1 (MQ=255)
cgctcgctGAACATAT‑CAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGACCTGAtt > 1:3970011/1‑71 (MQ=255)
cgctcgctGAACATAT‑CAGCTAAGCACAGAACCGGGTCGGATAAGACGTTAGCGtct > 1:2518707/1‑57 (MQ=255)
gctGAACATAT‑CAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGACCTGATTGttt < 1:1240862/70‑1 (MQ=38)
gAACATAT‑CAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGACCTGATTGTTTAAcc > 1:2494156/1‑71 (MQ=255)
||
CTGGCATTTGCCTGAAAAGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATAT‑CA‑‑TAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGACCTGATTGTTTAACC > minE/1891951‑1892078
|
| 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
