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
|
155 |
25.8 |
2285122 |
88.0% |
2010907 |
104.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AM260479 |
1,076,517 |
C→T |
P273L (CCG→CTG) |
cpaF3 → |
flp pilus assembly ATPase CpaF |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 1,076,517 | 0 | C | T | 100.0%
| 126.1
/ NA
| 33 | P273L (CCG→CTG) | cpaF3 | flp pilus assembly ATPase CpaF |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (16/17); total (16/17) |
ATGCGAACTGGTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCCGGGTCCGCTCGAAGAGCCGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTGATCTTTACCGACGACCGCGCCGTGTTGGGCGCCATC > AM260479/1076386‑1076644
|
aTGCGAACTGGTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGc > 2:811231/1‑134 (MQ=255)
tGCGAACTGGTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAgctgct > 1:331685/1‑134 (MQ=255)
gAACTGGTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGa < 2:331685/134‑1 (MQ=255)
gTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGAt < 1:11019/132‑1 (MQ=255)
gTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGAt < 1:811231/132‑1 (MQ=255)
tCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAACTGCTGGACGATGAc > 1:55160/1‑134 (MQ=255)
gacATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCAt < 2:1111297/134‑1 (MQ=255)
acATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATg > 1:956521/1‑134 (MQ=255)
tCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTc < 2:956521/134‑1 (MQ=255)
gtgtTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGAc > 1:312130/1‑132 (MQ=255)
tgtTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGtc < 2:940702/104‑1 (MQ=255)
tgtTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGtc > 1:940702/1‑104 (MQ=255)
ttCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACg > 1:690155/1‑91 (MQ=255)
ttCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACg < 2:690155/91‑1 (MQ=255)
ttCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGAc > 1:471504/1‑129 (MQ=255)
ccGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGAc < 1:583155/94‑1 (MQ=255)
ccGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGAc > 2:583155/1‑94 (MQ=255)
ccAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCg < 2:471504/134‑1 (MQ=255)
tGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAAc > 2:327180/1‑98 (MQ=255)
tGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAAc < 1:327180/98‑1 (MQ=255)
tCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCg < 2:271235/62‑1 (MQ=255)
tCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCg > 1:271235/1‑62 (MQ=255)
tttGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTGATCtt > 1:173257/1‑134 (MQ=255)
tGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGt < 2:365195/93‑1 (MQ=255)
tGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGt > 1:365195/1‑93 (MQ=255)
aTCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCgg < 2:285032/43‑1 (MQ=37)
aTCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCgg > 1:285032/1‑43 (MQ=37)
cGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTGATCTTTACCGACGACCGCGCCGTGTTGGgc < 2:173257/134‑1 (MQ=255)
cGCTCGAAGAACTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTGATCTTTACCGACGACCGCGCCGTGTTGGgc < 2:55160/134‑1 (MQ=255)
cTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTc > 1:864342/1‑95 (MQ=255)
cTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTc < 2:864342/95‑1 (MQ=255)
aaGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGAcgc > 1:869200/1‑87 (MQ=255)
aaGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGAcgc < 2:869200/87‑1 (MQ=255)
aaGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTGATCTTTACCGACGACCGCGCCGTGTTGGGCGCCATc > 2:929215/1‑134 (MQ=255)
|
ATGCGAACTGGTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCCGGGTCCGCTCGAAGAGCCGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTGATCTTTACCGACGACCGCGCCGTGTTGGGCGCCATC > AM260479/1076386‑1076644
|
| 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
TGGCCGAGGACGAGCTATGCGAACTGGTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCCGGGTCCGCTCGAAGAGCCGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTGATCTTTACCGACGACCGCGCCGTGTTGGGCGCCATCGAGCGCATCGTCGCGCCGCTG > AM260479/1076370‑1076665
|
TGGCCGAGGACGAGCTATGCGAACTGGTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGC > GWNJ‑0478:712:GW2002102894th:2:1203:14489:74589/1‑150 (MQ=60)
GCCGAGGACGAGCTATGCGAACTGGTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTG > GWNJ‑0478:712:GW2002102894th:2:1205:2354:12781/1‑150 (MQ=60)
gagtgtctcgtgggctcggagatgtgtataagagacagCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACG < GWNJ‑0478:712:GW2002102894th:2:1112:1502:89269/112‑1 (MQ=60)
AGCTATGCGAACTGGTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAACTGCTGGACGATGACG > GWNJ‑0478:712:GW2002102894th:2:1102:5158:49951/1‑150 (MQ=60)
GGTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAA < GWNJ‑0478:712:GW2002102894th:2:1101:14730:72426/148‑1 (MQ=60)
GGTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAA < GWNJ‑0478:712:GW2002102894th:2:2115:4313:77566/148‑1 (MQ=60)
ggctcggagatgtgtataagagacagCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATC < GWNJ‑0478:712:GW2002102894th:2:2101:14662:61795/124‑1 (MQ=60)
GCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGG > GWNJ‑0478:712:GW2002102894th:2:2206:20260:22804/1‑150 (MQ=60)
ATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACG > GWNJ‑0478:712:GW2002102894th:2:1203:18108:88048/1‑148 (MQ=60)
TCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCctgtctcttatacac > GWNJ‑0478:712:GW2002102894th:2:2209:4495:34909/1‑134 (MQ=60)
CCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCCtgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatg > GWNJ‑0478:712:GW2002102894th:2:2109:11027:70229/1‑99 (MQ=60)
cggagatgtgtataagagacagGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATC < GWNJ‑0478:712:GW2002102894th:2:1202:5090:84578/128‑1 (MQ=60)
CTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGctgtctcttatacacatctccgagcccac > GWNJ‑0478:712:GW2002102894th:2:2108:2757:28937/1‑121 (MQ=60)
CTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACG > GWNJ‑0478:712:GW2002102894th:2:1210:13602:93073/1‑145 (MQ=60)
CGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtct > GWNJ‑0478:712:GW2002102894th:2:1116:18089:33549/1‑92 (MQ=60)
CTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTGATCTTT > GWNJ‑0478:712:GW2002102894th:2:1110:16145:30277/1‑150 (MQ=60)
CAAGCAGAGCGTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGctgtctcttatacacatctccgagccc > GWNJ‑0478:712:GW2002102894th:2:1207:8320:15682/1‑123 (MQ=60)
GTCTTTGACGAAGTGATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaaaaaaa > GWNJ‑0478:712:GW2002102894th:2:1201:18733:17256/1‑73 (MQ=60)
ATCGGGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTGATCTTTACCtgtctcttatacacatctccgagc > GWNJ‑0478:712:GW2002102894th:2:2201:20973:61757/1‑126 (MQ=60)
ataagagacagGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTGATCTTTACCGACGACCGCGCCGTGTTGGGCGCCAT < GWNJ‑0478:712:GW2002102894th:2:1101:6647:5044/138‑1 (MQ=60)
GGCTGGGTCCGCTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTGATCTctgtctcttatacacatctccgagcccacg > GWNJ‑0478:712:GW2002102894th:2:2201:16258:93159/1‑117 (MQ=60)
CTCGAAGAGCTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTGATCTTTACCGACGACCGCGCCGTGTTGGGCGCCATCGAGCGCATCGTC > GWNJ‑0478:712:GW2002102894th:2:1210:15066:3403/1‑150 (MQ=60)
CTGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTGATCTTTACCGACGACCGCGCCGTGTTGGGCGCCATCGAGCGCATCGTCGCGCCGCTG > GWNJ‑0478:712:GW2002102894th:2:2212:16462:27801/1‑150 (MQ=60)
|
TGGCCGAGGACGAGCTATGCGAACTGGTCGGCTCGCTGCTCGACGACATCCTCAAGGAGAGCGTGTTCCGCAGCCAGGAGATCCCGCTGGACGCGCTCAAGCAGAGCGTCTTTGACGAAGTGATCGGGCCGGGTCCGCTCGAAGAGCCGCTGGACGATGACGCGGTCTCGGAAATCATGGTCAACTGCCATGACGAGATCTTTGTCGAGCGCGCCGGCAGGCTGACGCGTTCGCCGGTGATCTTTACCGACGACCGCGCCGTGTTGGGCGCCATCGAGCGCATCGTCGCGCCGCTG > AM260479/1076370‑1076665
|
| 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: ‑ |
