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 |
|
A0 F0 I1 R1
|
149 |
26.7 |
2337422 |
87.5% |
2045244 |
105.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AM260479 |
1,076,499 |
C→T |
P267L (CCG→CTG) |
cpaF3 → |
flp pilus assembly ATPase CpaF |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 1,076,499 | 0 | C | T | 100.0%
| 121.4
/ NA
| 32 | P267L (CCG→CTG) | cpaF3 | flp pilus assembly ATPase CpaF |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (15/17); total (15/17) |
AGGACGAGCTATGCGAACTGGTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCCGGGTCCGCTCGAAGAGCCGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTGATCTTTACCGACGACCGCGC > AM260479/1076376‑1076628
|
aGGACGAGCTATGCGAACTGGTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTc < 2:457481/134‑1 (MQ=255)
tGCGAACTGGTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAgctgct > 1:597679/1‑134 (MQ=255)
tGCGAACTGGTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAgctgct > 2:751392/1‑134 (MQ=255)
cTGGTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGa > 1:312581/1‑134 (MQ=255)
gTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGAt < 2:859658/132‑1 (MQ=255)
gTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGAt < 2:697022/132‑1 (MQ=255)
gTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGa < 2:9132/134‑1 (MQ=255)
ggCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGAcgc > 2:1144770/1‑134 (MQ=255)
ggCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGAcg < 2:996121/133‑1 (MQ=255)
ggCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGAcg < 2:597679/133‑1 (MQ=255)
gctgctCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGt < 1:809967/132‑1 (MQ=255)
cAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGctgc < 1:330259/98‑4 (MQ=255)
cAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGctgc > 2:330259/1‑95 (MQ=255)
tgtTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGAc > 2:73005/1‑131 (MQ=255)
tgtTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGAc > 2:1031213/1‑131 (MQ=255)
tgtTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGAc > 1:7076/1‑131 (MQ=255)
gtTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGAc > 2:594429/1‑130 (MQ=255)
ttCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGAc > 2:974546/1‑129 (MQ=255)
gCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCttt > 1:103915/1‑134 (MQ=255)
gCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCttt > 2:42003/1‑134 (MQ=255)
gaTCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAgcgcg < 1:73005/134‑1 (MQ=255)
gaTCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAgcgcg < 1:1031213/134‑1 (MQ=255)
aTCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAgcgcgc < 1:594429/134‑1 (MQ=255)
ccGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCgg < 2:312581/134‑1 (MQ=255)
cTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGAt < 1:881681/63‑1 (MQ=255)
cTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGAt > 2:881681/1‑63 (MQ=255)
aaGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTc < 1:974546/134‑1 (MQ=255)
gCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTg < 2:103915/134‑1 (MQ=255)
tCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGAcg < 2:393027/54‑1 (MQ=38)
tCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGAcg > 1:393027/1‑54 (MQ=38)
aTCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTGATCTTTACCGACGACcg > 2:120645/1‑134 (MQ=255)
gggCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTGATCTTTACCGACGACCgcgc < 1:1144770/134‑1 (MQ=255)
|
AGGACGAGCTATGCGAACTGGTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCCGGGTCCGCTCGAAGAGCCGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTGATCTTTACCGACGACCGCGC > AM260479/1076376‑1076628
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CAACGTCGCGCGCATGGCCGAGGACGAGCTATGCGAACTGGTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCCGGGTCCGCTCGAAGAGCCGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTGATCTTTACCGACGACCGCGCCGTGTTGGGCGCCAT > AM260479/1076356‑1076643
|
CAACGTCGCGCGCATGGCCGAGGACGAGCTATGCGAACTGGTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTC < GWNJ‑0478:712:GW2002102894th:2:2212:1802:40318/149‑1 (MQ=60)
GCCGAGGACGAGCTATGCGAACTGGTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTG > GWNJ‑0478:712:GW2002102894th:2:2103:15084:47613/1‑150 (MQ=60)
GACGAGCTATGCGAACTGGTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGAT > GWNJ‑0478:712:GW2002102894th:2:1203:10371:81246/1‑150 (MQ=60)
cggagatgtgtataagagacagGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGG < GWNJ‑0478:712:GW2002102894th:2:1202:2578:97444/128‑1 (MQ=60)
gacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAA < GWNJ‑0478:712:GW2002102894th:2:2201:13638:79035/95‑1 (MQ=60)
CGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGT < GWNJ‑0478:712:GW2002102894th:2:2115:8852:23520/148‑1 (MQ=60)
TCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACG > GWNJ‑0478:712:GW2002102894th:2:1101:3663:47470/1‑147 (MQ=60)
AGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTG > GWNJ‑0478:712:GW2002102894th:2:1106:10434:48046/1‑150 (MQ=60)
AGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGC < GWNJ‑0478:712:GW2002102894th:2:1104:8753:65129/150‑1 (MQ=60)
AGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGC < GWNJ‑0478:712:GW2002102894th:2:2211:15025:49829/150‑1 (MQ=60)
GATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCG < GWNJ‑0478:712:GW2002102894th:2:2103:19279:27324/150‑1 (MQ=60)
CGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCActgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttg > GWNJ‑0478:712:GW2002102894th:2:1206:9241:77828/1‑84 (MQ=60)
CAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTGATCTTTAC < GWNJ‑0478:712:GW2002102894th:2:2206:3368:31012/150‑1 (MQ=60)
TTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTGATCTTTctgtctcttatacac > GWNJ‑0478:712:GW2002102894th:2:2216:12944:4871/1‑134 (MQ=60)
CGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTGATCTTTACCGACGACCGCGCCGTGTTGGGCGCCAT < GWNJ‑0478:712:GW2002102894th:2:2215:14953:96407/150‑1 (MQ=60)
|
CAACGTCGCGCGCATGGCCGAGGACGAGCTATGCGAACTGGTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCCGGGTCCGCTCGAAGAGCCGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTGATCTTTACCGACGACCGCGCCGTGTTGGGCGCCAT > AM260479/1076356‑1076643
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
