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
|
146 |
27.9 |
2327082 |
89.7% |
2087392 |
107.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AM260480 |
635,877 |
T→C |
E259E (GAA→GAG) |
fliM ← |
flagellar motor switch protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260480 | 635,877 | 0 | T | C | 100.0%
| 137.8
/ NA
| 36 | E259E (GAA→GAG) | fliM | flagellar motor switch protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (19/17); total (19/17) |
GGGCACGCCGTCCACCTTGCCGAACACCTTCTCCGGCAGCTCGATCGGCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACTTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCGTCCTGCAGCGGATTCATCAGCAGGTCCTTGAGCGGCTCGATCATCGCGTACGG > AM260480/635751‑635990
|
gggCACGCCGTCCACCTTGCCGAACACCTTCTCCGGCAGCTCGATCGGCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCcg < 1:1159233/134‑1 (MQ=255)
gCCGTCCACCTTGCCGAACACCTTCTCCGGCAGCTCGATCGGCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCcgcgcg > 1:346395/1‑132 (MQ=255)
ccGTCCACCTTGCCGAACACCTTCTCCGGCAGCTCGATCGGCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAg < 1:1102893/134‑1 (MQ=255)
cGTCCACCTTGCCGAACACCTTCTCCGGCAGCTCGATCGGCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCcgcg < 2:155292/128‑1 (MQ=255)
cGTCCACCTTGCCGAACACCTTCTCCGGCAGCTCGATCGGCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCcgcg > 1:155292/1‑128 (MQ=255)
ttGCCGAACACCTTCTCCGGCAGCTCGATCGGCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGa > 2:85925/1‑134 (MQ=255)
ccTTCTCCGGCAGCTCGATCGGCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGt > 1:425642/1‑133 (MQ=255)
tctcCGGCAGCTCGATCGGCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGAcc > 1:57785/1‑134 (MQ=255)
tcCGGCAGCTCGATCGGCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGAcc > 2:986046/1‑132 (MQ=255)
gCTCGATCGGCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTg < 2:478961/134‑1 (MQ=255)
ggCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGActtc < 1:85925/134‑1 (MQ=255)
cGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCg > 1:359965/1‑134 (MQ=255)
cGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCg > 2:1144136/1‑134 (MQ=255)
gCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCGTCCTGCAGCGGATtcat < 2:346395/134‑1 (MQ=255)
cAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCGTCCTGCAGCGGATtcatca < 1:1144136/134‑1 (MQ=255)
cGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCGTCCTGCAGCGGATTCATCAGCAGGTCCTTGAGc < 1:550438/134‑1 (MQ=255)
ggTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCGTCCTGCAGCGGATTCATCAGCAGGTCCTTGAGCg < 2:359965/134‑1 (MQ=255)
gCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAg < 1:595693/46‑1 (MQ=255)
gCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAg > 2:595693/1‑46 (MQ=255)
aGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTtct > 1:661701/1‑88 (MQ=255)
aGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTtct < 2:661701/88‑1 (MQ=255)
tGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCGTCCTGCAGCGGATTCATCAGCAGGTACTTGAGCGGCTCGATCATcgc < 2:425642/134‑1 (MQ=255)
gcgAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCg < 1:597648/43‑1 (MQ=255)
gcgAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCg > 2:597648/1‑43 (MQ=255)
gcgAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGt < 2:1039689/51‑1 (MQ=255)
gcgAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGt > 1:1039689/1‑51 (MQ=255)
gcgAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGccc > 2:754440/1‑66 (MQ=255)
gcgAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGccc < 1:754440/66‑1 (MQ=255)
gcgAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCt < 2:988938/67‑1 (MQ=255)
gcgAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCt > 1:988938/1‑67 (MQ=255)
gcgAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCGTCCTGCAGCGGATTCATCAGCAGGTCCTTGAGCGGCTCGATCATCGCGTa > 1:536014/1‑134 (MQ=255)
gAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGAc < 2:1139974/57‑1 (MQ=255)
gAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGAc > 1:1139974/1‑57 (MQ=255)
gAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCGTCCTGCAGTGGATTCATCAGCAGGTCCTTGAGCGGCTCGATCATCGCGTACg > 1:781037/1‑134 (MQ=255)
gAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCGTCCTGCAGCGGATTCATCAGCAGGTCCTTGAGCGGCTCGATCATCGCGTACg > 1:676093/1‑134 (MQ=255)
aaCTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCGTCCTGCAGCGGATTCATCAGCAGGTCCTTGAGCGGCTCGATCATCGCGTACgg > 1:670083/1‑134 (MQ=255)
|
GGGCACGCCGTCCACCTTGCCGAACACCTTCTCCGGCAGCTCGATCGGCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACTTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCGTCCTGCAGCGGATTCATCAGCAGGTCCTTGAGCGGCTCGATCATCGCGTACGG > AM260480/635751‑635990
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ 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
TTGCATGACGGGCACGCCGTCCACCTTGCCGAACACCTTCTCCGGCAGCTCGATCGGCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACTTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCGTCCTGCAGCGGATTCATCAGCAGGTCCTTGAGCGGCTCGATCATCGCGTACGGCAGGCACACGTGGAGCTGCCCGCCGACG > AM260480/635742‑636018
|
TTGCATGACGGGCACGCCGTCCACCTTGCCGAACACCTTCTCCGGCAGCTCGATCGGCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGC > GWNJ‑0478:712:GW2002102894th:2:1205:5546:68982/1‑148 (MQ=60)
GCATGACGGGCACGCCGTCCACCTTGCCGAACACCTTCTCCGGCAGCTCGATCGGCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCT > GWNJ‑0478:712:GW2002102894th:2:1111:12850:21786/1‑150 (MQ=60)
CGGGCACGCCGTCCACCTTGCCGAACACCTTCTCCGGCAGCTCGATCGGCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGG < GWNJ‑0478:712:GW2002102894th:2:2216:2689:80413/150‑1 (MQ=60)
GCCGTCCACCTTGCCGAACACCTTCTCCGGCAGCTCGATCGGCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTG < GWNJ‑0478:712:GW2002102894th:2:2214:19813:14095/150‑1 (MQ=60)
tttttttcaagcagaagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacagCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTG < GWNJ‑0478:712:GW2002102894th:2:2101:5906:82378/76‑1 (MQ=60)
CCACCTTGCCGAACACCTTCTCCGGCAGCTCGATCGGCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTG > GWNJ‑0478:712:GW2002102894th:2:1209:19092:21754/1‑149 (MQ=60)
tttttgttttcaagcagaagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagggacaGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGA < GWNJ‑0478:712:GW2002102894th:2:2101:14715:94532/74‑1 (MQ=60)
CCTTGCCGAACACCTTCTCCGGCAGCTCGATCGGCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCC > GWNJ‑0478:712:GW2002102894th:2:1102:13880:61041/1‑150 (MQ=60)
ggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacaGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTC < GWNJ‑0478:712:GW2002102894th:2:2110:4258:15889/97‑1 (MQ=60)
GCTCGATCGGCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCGT > GWNJ‑0478:712:GW2002102894th:2:1204:12625:50465/1‑150 (MQ=60)
CGGCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCGTCCTGCAG < GWNJ‑0478:712:GW2002102894th:2:1107:3988:30927/150‑1 (MQ=60)
CCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCGTCCTGCAGCGGATTCATCAGCAGGTCCTTGAGCG < GWNJ‑0478:712:GW2002102894th:2:2216:2533:10081/150‑1 (MQ=60)
GCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCGTCCTGCAGCGGATctgtctcttatacacatctccgagcccacg > GWNJ‑0478:712:GW2002102894th:2:2104:16232:92820/1‑118 (MQ=60)
ACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCGTCCTGCAGCGGATTCATCAGCAGGTCCTTGAGCGGCTCGATCATCGCG < GWNJ‑0478:712:GW2002102894th:2:1214:13521:42547/150‑1 (MQ=60)
GTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaa > GWNJ‑0478:712:GW2002102894th:2:2211:3822:91697/1‑81 (MQ=60)
GTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCtgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgc > GWNJ‑0478:712:GW2002102894th:2:2207:4285:15979/1‑98 (MQ=60)
GTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCGTCCTGCAGCGGATTCATCAGCAGGTCCTTGAGCGGCTCGATCATCGCGTAC > GWNJ‑0478:712:GW2002102894th:2:1215:6228:75578/1‑150 (MQ=60)
GCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgc > GWNJ‑0478:712:GW2002102894th:2:2215:5657:90638/1‑87 (MQ=60)
GCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCGTCCTGCAGTGGATTCATCAGCAGGTCCTTGAGCGGCTCGATCATCGCGTACGG > GWNJ‑0478:712:GW2002102894th:2:2113:16195:54519/1‑150 (MQ=60)
GCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCGTCCTGCAGCGGATTCATCAGCAGGTCCTTGAGCGGCTCGATCATCGCGTACGG > GWNJ‑0478:712:GW2002102894th:2:2107:10222:77907/1‑150 (MQ=60)
CTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCGTCCTGCAGCGGATTCATCAGCAGGTCCTTGAGCGGCTCGATCATCGCGTACGGC > GWNJ‑0478:712:GW2002102894th:2:2107:3654:42963/1‑150 (MQ=60)
GCTCCACCTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCGTCCTGCAGCGGATTCATCAGCAGGTCCTTGAGCGGCTCGATCATCGCGTACGGCAGGCACtgtctcttatacacatctccg > GWNJ‑0478:712:GW2002102894th:2:1116:1358:19421/1‑128 (MQ=60)
|
TTGCATGACGGGCACGCCGTCCACCTTGCCGAACACCTTCTCCGGCAGCTCGATCGGCAGCACGTCGCCGGCGCGCATCGCCAGCACTTCGGCCACGGTGCTCTGCAGGTGCGCGAACTCGGCCACCAGCTCCACTTCGGCCGCGCGCAGCTGCGTGGACAGTTGCGTGACCCAGCCCTTGTCGACTTCCTTCTCGTCCTGCAGCGGATTCATCAGCAGGTCCTTGAGCGGCTCGATCATCGCGTACGGCAGGCACACGTGGAGCTGCCCGCCGACG > AM260480/635742‑636018
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
