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 F1 I1 R1
|
152 |
24.9 |
2083062 |
91.6% |
1908084 |
109.2 |
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%
| 96.1
/ NA
| 26 | P267L (CCG→CTG) | cpaF3 | flp pilus assembly ATPase CpaF |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (15/11); total (15/11) |
GAGCTATGCGAACTGGTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCCGGGTCCGCTCGAAGAGCCGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTGATCTTTACCGACGACCG > AM260479/1076381‑1076625
|
gAGCTATGCGAACTGGTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGaa > 1:357416/1‑132 (MQ=255)
aaCTGGTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGAc > 1:533844/1‑134 (MQ=255)
cATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATgg < 2:357416/134‑1 (MQ=255)
cATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATgg < 1:284149/134‑1 (MQ=255)
cATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATgg < 1:303323/134‑1 (MQ=255)
cAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTc > 2:669885/1‑88 (MQ=255)
cAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTc < 1:669885/88‑1 (MQ=255)
tgtTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGAc > 1:230052/1‑131 (MQ=255)
gtTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGAc > 1:2589/1‑130 (MQ=255)
gtTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGAc > 1:879907/1‑130 (MQ=255)
ttCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGAt < 1:741280/93‑1 (MQ=255)
ttCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGAt > 2:741280/1‑93 (MQ=255)
ccAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTc > 1:267261/1‑133 (MQ=255)
cccGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCg > 1:529394/1‑134 (MQ=255)
tGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATg < 2:208301/105‑1 (MQ=255)
tGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATg > 1:208301/1‑105 (MQ=255)
cTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATgg < 2:169327/85‑1 (MQ=255)
cTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATgg > 1:169327/1‑85 (MQ=255)
gagCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCgg < 2:2589/134‑1 (MQ=255)
gCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTg < 2:265560/134‑1 (MQ=255)
tCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTGATc > 2:459970/1‑134 (MQ=255)
tttGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTGATCtt > 2:612753/1‑134 (MQ=255)
tttGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTGATCtt > 2:721998/1‑134 (MQ=255)
tGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAAc > 1:147592/1‑73 (MQ=255)
tGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAAc < 2:147592/73‑1 (MQ=255)
aTCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTGATCTTTACCGACGACcg < 1:612753/134‑1 (MQ=255)
|
GAGCTATGCGAACTGGTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCCGGGTCCGCTCGAAGAGCCGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTGATCTTTACCGACGACCG > AM260479/1076381‑1076625
|
| 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
CCGCGTCAACGTCGCGCGCATGGCCGAGGACGAGCTATGCGAACTGGTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCCGGGTCCGCTCGAAGAGCCGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTGATCTTTACCGACGACCGCGCCGTGTTGGGCGCCATCG > AM260479/1076350‑1076645
|
cggagatgtgtataagagacaGGCCGAGGACGAGCTATGCGAACTGGTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCT < GWNJ‑0478:712:GW2002102894th:2:1213:5970:62811/129‑1 (MQ=60)
cgtggttgtgtgattccattttctcttttttttttttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacaGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGT < GWNJ‑0478:712:GW2002102894th:2:1108:7903:69647/40‑1 (MQ=60)
gtgtataagagacagTGGCCGAGGACGAGCTATGCGAACTGGTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTC < GWNJ‑0478:712:GW2002102894th:2:1205:14281:50849/135‑1 (MQ=60)
CGCATGGCCGAGGACGAGCTATGCGAACTGGTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAG > GWNJ‑0478:712:GW2002102894th:2:1206:16606:70538/1‑148 (MQ=60)
AGGACGAGCTATGCGAACTGGTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACG > GWNJ‑0478:712:GW2002102894th:2:2101:4060:77070/1‑150 (MQ=60)
cgtgggctcggagatgtgtataagagacagGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGAC < GWNJ‑0478:712:GW2002102894th:2:2111:16984:81938/118‑1 (MQ=60)
gggctcggagatgtgtataagagacagCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAA < GWNJ‑0478:712:GW2002102894th:2:2115:18750:90407/123‑1 (MQ=60)
ACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACG < GWNJ‑0478:712:GW2002102894th:2:1205:7969:20139/150‑1 (MQ=60)
ACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACG < GWNJ‑0478:712:GW2002102894th:2:1203:2500:88221/150‑1 (MQ=60)
TCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACG > GWNJ‑0478:712:GW2002102894th:2:1114:17356:37660/1‑147 (MQ=60)
CCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACG > GWNJ‑0478:712:GW2002102894th:2:1101:3609:20547/1‑146 (MQ=60)
CCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACG > GWNJ‑0478:712:GW2002102894th:2:2206:3089:81533/1‑146 (MQ=60)
GAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCG > GWNJ‑0478:712:GW2002102894th:2:1201:21143:66433/1‑149 (MQ=60)
CCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGG > GWNJ‑0478:712:GW2002102894th:2:2101:17398:44746/1‑150 (MQ=60)
GCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGctgtctcttatacac > GWNJ‑0478:712:GW2002102894th:2:1115:9792:19188/1‑135 (MQ=60)
ATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGctgtctcttatacacatctccgagcccacgagacg > GWNJ‑0478:712:GW2002102894th:2:1110:1601:98803/1‑115 (MQ=60)
CAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCctgtctcttatacacatctccgagcccacgagacggagctacatctc > GWNJ‑0478:712:GW2002102894th:2:1111:5395:70899/1‑103 (MQ=60)
GATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTGATCTTTACCGACGACCGCGCCGTGTTGGGCGC < GWNJ‑0478:712:GW2002102894th:2:2106:2388:24538/150‑1 (MQ=60)
GGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTGActgtctcttatacacatctccgagcccacgagacgg > GWNJ‑0478:712:GW2002102894th:2:1204:19327:16925/1‑114 (MQ=60)
GGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTGATCTTTACCGACGACCGCGCCGTGTTGGGCGCCATCG > GWNJ‑0478:712:GW2002102894th:2:1216:15617:17328/1‑150 (MQ=60)
|
CCGCGTCAACGTCGCGCGCATGGCCGAGGACGAGCTATGCGAACTGGTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCCGGGTCCGCTCGAAGAGCCGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTGATCTTTACCGACGACCGCGCCGTGTTGGGCGCCATCG > AM260479/1076350‑1076645
|
| 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: ‑ |
