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 |
1,240,057 |
+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%
| 130.0
/ NA
| 34 | intergenic (‑53/‑222) | h16_A1136/grpE | conserved hypothetical protein/molecular chaperone GrpE |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base T (15/19); total (15/19) |
CCGGAAAGGCAGATAAAGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCA‑TTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGTCACGCCAGCGCCACTCTTGAAAACC > AM260479/1239924‑1240180
|
ccGGAAAGGCAGATAAAGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCA‑tttt < 1:107307/134‑1 (MQ=255)
aaaGGCAGATAAAGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAATGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCA‑tttttgt > 1:625928/1‑130 (MQ=255)
aaGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTttatta < 1:167821/133‑1 (MQ=255)
aaGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAATGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTttatta < 2:625928/133‑1 (MQ=255)
tCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAAt > 1:220649/1‑134 (MQ=255)
gCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGa > 1:1010963/1‑134 (MQ=255)
gCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGa > 2:856684/1‑134 (MQ=255)
gCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATgc < 2:220649/134‑1 (MQ=255)
gtCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTttatta > 2:982425/1‑94 (MQ=255)
gtCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTttatta < 1:982425/94‑1 (MQ=255)
tGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGAt < 1:144886/133‑1 (MQ=255)
tGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGAt > 2:144886/1‑133 (MQ=255)
cAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCA‑tttt > 2:475867/1‑69 (MQ=255)
cAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCA‑tttt < 1:475867/69‑1 (MQ=255)
cTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCatat > 2:871109/1‑134 (MQ=255)
aTGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATg < 1:856684/132‑1 (MQ=255)
aTGCATGGCCAACATTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATg < 1:1078561/132‑1 (MQ=255)
tGCAGGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGcc < 2:410415/133‑1 (MQ=255)
tGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGcc < 1:871109/134‑1 (MQ=255)
aCCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATg < 1:950207/121‑1 (MQ=255)
aCCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATg > 2:950207/1‑121 (MQ=255)
agagGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTttat < 1:677102/54‑1 (MQ=39)
agagGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTttat > 2:677102/1‑54 (MQ=39)
acaAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATgc > 1:922556/1‑75 (MQ=255)
acaAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATgc < 2:922556/75‑1 (MQ=255)
caAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGAt < 1:1061692/72‑1 (MQ=255)
caAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGAt > 2:809293/1‑72 (MQ=255)
caAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGAt > 2:1061692/1‑72 (MQ=255)
caAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGAt < 1:809293/72‑1 (MQ=255)
aaCCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGTCACGCCa < 2:523470/133‑1 (MQ=255)
cacaACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGc > 2:258107/1‑52 (MQ=39)
cacaACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGc > 2:647639/1‑52 (MQ=39)
cacaACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGc < 1:647639/52‑1 (MQ=39)
cacaACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGc < 1:258107/52‑1 (MQ=39)
cacaACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGTCACGCCAGCGCCActc < 2:1010963/133‑1 (MQ=255)
ccccGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGc > 2:201572/1‑87 (MQ=255)
ccccGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGc < 1:201572/87‑1 (MQ=255)
ccGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGTCACGCCAGCGCCACTCTTGAAAAcc > 2:34852/1‑134 (MQ=255)
|
CCGGAAAGGCAGATAAAGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCA‑TTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGTCACGCCAGCGCCACTCTTGAAAACC > AM260479/1239924‑1240180
|
| 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
GGGGTGAATGCGCCGGAAAGGCAGATAAAGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCA‑TTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGTCACGCCAGCGCCACTCTTGAAAACCTGCGCCTTGCCACCACCTG > AM260479/1239912‑1240199
|
GGGGTGAATGCGCCGGAAAGGCAGATAAAGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTC < GWNJ‑0478:712:GW2002102894th:2:1111:14486:17202/150‑1 (MQ=60)
GGGTGAATGCGCCGGAAAGGCAGATAAAGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAATGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTC > GWNJ‑0478:712:GW2002102894th:2:2105:6349:25774/1‑149 (MQ=60)
atacgagtttagcgagtgtctcgtgggctcggagatgtgtataagagacagGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTAC < GWNJ‑0478:712:GW2002102894th:2:1213:17406:28151/99‑1 (MQ=60)
GCCGGAAAGGCAGATAAAGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTAC < GWNJ‑0478:712:GW2002102894th:2:1106:17107:68444/150‑1 (MQ=60)
GGCAGATAAAGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATC > GWNJ‑0478:712:GW2002102894th:2:1112:13258:85858/1‑150 (MQ=60)
caagcagaagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacagGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAG < GWNJ‑0478:712:GW2002102894th:2:2106:18064:23174/84‑1 (MQ=60)
ggctcggagatgtgtataagagacaGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTG < GWNJ‑0478:712:GW2002102894th:2:2206:6927:77411/125‑1 (MQ=60)
AAAGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTG < GWNJ‑0478:712:GW2002102894th:2:1110:15697:5642/149‑1 (MQ=60)
GTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGAT > GWNJ‑0478:712:GW2002102894th:2:2208:14444:39081/1‑150 (MQ=60)
tcaagcagaagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacagAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAA < GWNJ‑0478:712:GW2002102894th:2:1114:5600:71422/82‑1 (MQ=60)
tcaagcagaagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacagAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAA < GWNJ‑0478:712:GW2002102894th:2:2104:6140:53436/82‑1 (MQ=60)
cgagattagcgagtgtctcgtgggctcggagatgtgtataagagacagCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAA < GWNJ‑0478:712:GW2002102894th:2:2212:12331:7829/102‑1 (MQ=60)
cgagattagcgagtgtctcgtgggctcggagatgtgtataagagacagCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAA < GWNJ‑0478:712:GW2002102894th:2:2115:3553:20557/102‑1 (MQ=60)
ACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCC < GWNJ‑0478:712:GW2002102894th:2:1109:2897:84452/150‑1 (MQ=60)
TATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAAC < GWNJ‑0478:712:GW2002102894th:2:2116:14818:40053/148‑1 (MQ=60)
TATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAAC < GWNJ‑0478:712:GW2002102894th:2:2205:6573:96860/148‑1 (MQ=60)
TATGCATGGCCAACATTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAAC < GWNJ‑0478:712:GW2002102894th:2:2212:1708:91488/148‑1 (MQ=60)
ATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGT < GWNJ‑0478:712:GW2002102894th:2:2201:9789:10817/150‑1 (MQ=60)
cgtgggctcggagatgtgtataagagacaGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTG < GWNJ‑0478:712:GW2002102894th:2:1113:10875:85088/118‑1 (MQ=60)
CCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCtgtctcttatacacatctccgagcccacgagacactcgctaatc > GWNJ‑0478:712:GW2002102894th:2:2204:9168:31453/1‑106 (MQ=60)
GAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaaaaaaacctgcaaagtgaccggc > GWNJ‑0478:712:GW2002102894th:2:2215:11112:65018/1‑57 (MQ=60)
CCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGctgtctcttatacacatctccgagcccacgagacactcgctaagctcgtatgccgtcttctgcttgaaaaaaaaaaat > GWNJ‑0478:712:GW2002102894th:2:1204:5810:6531/1‑72 (MQ=60)
CCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGTCACGCCAGCGCCACTCTTGAAAACCTGCGCCT > GWNJ‑0478:712:GW2002102894th:2:1106:13911:89474/1‑150 (MQ=60)
GCATTTTTGTCATTTTTATTACTGGGAATCTTAGctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaaaaaaaaaaaacaatataaaaactcataaacatattaatagtatat > GWNJ‑0478:712:GW2002102894th:2:2208:19019:54572/1‑34 (MQ=60)
|
GGGGTGAATGCGCCGGAAAGGCAGATAAAGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCA‑TTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGTCACGCCAGCGCCACTCTTGAAAACCTGCGCCTTGCCACCACCTG > AM260479/1239912‑1240199
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
