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 |
1,240,057 |
+T |
intergenic (‑57/‑218) |
h16_A1136 ← / → grpE |
conserved hypothetical protein/molecular chaperone GrpE |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 1,240,053 | 1 | . | T | 100.0%
| 109.2
/ NA
| 29 | intergenic (‑53/‑222) | h16_A1136/grpE | conserved hypothetical protein/molecular chaperone GrpE |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base T (14/15); total (14/15) |
GCAGATAAAGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCA‑TTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGTCACGCCAGCGCCACTCTT > AM260479/1239932‑1240173
|
gCAGATAAAGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCAttt > 2:738696/1‑134 (MQ=255)
aGATAAAGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCAttttt < 1:1042850/134‑1 (MQ=255)
aaGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTttatta < 1:738696/133‑1 (MQ=255)
gACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTAc > 2:834680/1‑123 (MQ=255)
gACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTAc < 1:834680/123‑1 (MQ=255)
gACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCt > 2:554684/1‑132 (MQ=255)
gCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGa > 2:1015912/1‑134 (MQ=255)
gCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATgc < 1:343659/134‑1 (MQ=255)
aCTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATaa < 2:501445/126‑1 (MQ=255)
aCTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATaa > 1:501445/1‑126 (MQ=255)
aCTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCA‑tttt < 1:304936/74‑1 (MQ=255)
aCTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCA‑tttt > 2:304936/1‑74 (MQ=255)
cTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGAt < 1:1015912/134‑1 (MQ=255)
cTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATgc < 1:277566/105‑1 (MQ=255)
cTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATgc > 2:277566/1‑105 (MQ=255)
ttATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAAt < 2:610961/87‑1 (MQ=255)
ttATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAAt > 1:610961/1‑87 (MQ=255)
tGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGcc < 2:720529/133‑1 (MQ=255)
tGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGcc < 1:554684/133‑1 (MQ=255)
aCCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCata > 1:1136168/1‑119 (MQ=255)
aCCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCata < 2:1136168/119‑1 (MQ=255)
tCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCg > 1:664380/1‑134 (MQ=255)
gAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCg > 1:156904/1‑100 (MQ=255)
gAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCg < 2:156904/100‑1 (MQ=255)
aaGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCA‑ttt < 1:311078/42‑1 (MQ=255)
aaGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCA‑ttt > 2:311078/1‑42 (MQ=255)
tGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCttt < 1:285860/108‑1 (MQ=255)
tGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCttt > 2:285860/1‑108 (MQ=255)
caACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCg < 2:149598/72‑1 (MQ=255)
caACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCg > 1:149598/1‑72 (MQ=255)
caACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGTCACGCCAGCGCCACTCtt > 2:131459/1‑133 (MQ=255)
cccGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCg > 2:703363/1‑67 (MQ=255)
cccGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCg < 1:703363/67‑1 (MQ=255)
|
GCAGATAAAGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCA‑TTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGTCACGCCAGCGCCACTCTT > AM260479/1239932‑1240173
|
| 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
GCCGGAAAGGCAGATAAAGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCA‑TTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGTCACGCCAGCGCCACTCTTGAAAACCTGCGCCTTGCCACCACCT > AM260479/1239923‑1240198
|
tttttttttttcaagcagaagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacagTGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTA < GWNJ‑0478:712:GW2002102894th:2:1203:12337:81433/72‑1 (MQ=60)
agattagcgagtgtctcgtgggctcggagatgtgtataagagacagAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTAC < GWNJ‑0478:712:GW2002102894th:2:1203:9231:43354/104‑1 (MQ=60)
CAGATAAAGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTT < GWNJ‑0478:712:GW2002102894th:2:2212:21005:6085/150‑1 (MQ=60)
AAAGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGA < GWNJ‑0478:712:GW2002102894th:2:2114:19296:94398/150‑1 (MQ=60)
AAAGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTG < GWNJ‑0478:712:GW2002102894th:2:2111:3992:96555/149‑1 (MQ=60)
gtgtataagagacAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGG < GWNJ‑0478:712:GW2002102894th:2:1116:14549:69390/137‑1 (MQ=60)
GGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGG < GWNJ‑0478:712:GW2002102894th:2:1205:15948:84289/150‑1 (MQ=60)
AGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGAT > GWNJ‑0478:712:GW2002102894th:2:1212:3253:42556/1‑150 (MQ=60)
GTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATctgtctcttatacacatctccgagcccacg > GWNJ‑0478:712:GW2002102894th:2:2102:13079:44392/1‑117 (MQ=60)
gcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacagACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCC < GWNJ‑0478:712:GW2002102894th:2:2109:17550:4593/97‑1 (MQ=60)
caagcagaagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacagCCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCC < GWNJ‑0478:712:GW2002102894th:2:1112:3229:5407/84‑1 (MQ=60)
ACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCC < GWNJ‑0478:712:GW2002102894th:2:2211:3490:63352/150‑1 (MQ=60)
GCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAC > GWNJ‑0478:712:GW2002102894th:2:2216:8439:67980/1‑150 (MQ=60)
aagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacaggcatTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAAC < GWNJ‑0478:712:GW2002102894th:2:2114:2717:84522/87‑1 (MQ=60)
ATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGT > GWNJ‑0478:712:GW2002102894th:2:2107:8179:73641/1‑150 (MQ=60)
ATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCG < GWNJ‑0478:712:GW2002102894th:2:1214:2148:97982/149‑1 (MQ=60)
ATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCctgtctcttatacacatctc > GWNJ‑0478:712:GW2002102894th:2:1111:1721:42525/1‑130 (MQ=60)
ataagagacaGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTC < GWNJ‑0478:712:GW2002102894th:2:1201:15549:22650/139‑1 (MQ=60)
AAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaaaaaaaaaaaaaacatattaag > GWNJ‑0478:712:GW2002102894th:2:2210:10447:22514/1‑56 (MQ=60)
GATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCctgtctcttatacacatctccgagcccacgagacactcgctaatctcg > GWNJ‑0478:712:GW2002102894th:2:1111:2149:4687/1‑102 (MQ=60)
CCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCtgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaaaaaaaaaaaaacaaaaaa > GWNJ‑0478:712:GW2002102894th:2:2213:17984:86511/1‑61 (MQ=60)
CCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGTCACGCCctgtctcttatacacatctccgagcc > GWNJ‑0478:712:GW2002102894th:2:2216:16166:17366/1‑124 (MQ=60)
CCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGTCACGCCAGCGCCACTCTTGAAAACCTGCGCCTTGCCACC > GWNJ‑0478:712:GW2002102894th:2:2215:10917:7866/1‑150 (MQ=60)
GCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaaaaaaaaaaaacaaaaggaaataac > GWNJ‑0478:712:GW2002102894th:2:1105:14538:94860/1‑54 (MQ=60)
|
GCCGGAAAGGCAGATAAAGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCA‑TTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGTCACGCCAGCGCCACTCTTGAAAACCTGCGCCTTGCCACCACCT > AM260479/1239923‑1240198
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
