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
|
154 |
26.6 |
2069536 |
90.2% |
1866721 |
108.9 |
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%
| 66.0
/ NA
| 18 | intergenic (‑53/‑222) | h16_A1136/grpE | conserved hypothetical protein/molecular chaperone GrpE |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base T (9/9); total (9/9) |
CCGGAAAGGCAGATAAAGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCA‑TTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGTCACGCCAGCGCCACTCTTGAAAAC > AM260479/1239924‑1240179
|
ccGGAAAGGCAGATAAAGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCA‑tttt < 1:548407/134‑1 (MQ=255)
aGGCAGATAAAGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCAt > 2:636866/1‑134 (MQ=255)
aTAAAGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTttat < 1:636866/134‑1 (MQ=255)
aaGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTttatta < 1:450766/133‑1 (MQ=255)
aaGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTAc > 1:23822/1‑134 (MQ=255)
tCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCAtt > 2:995645/1‑119 (MQ=255)
tCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCAtt < 1:995645/119‑1 (MQ=255)
tCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAgg < 2:23822/133‑1 (MQ=255)
cAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCAATTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCa > 1:246795/1‑134 (MQ=255)
gCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCA‑tttttg < 1:302686/69‑3 (MQ=255)
gCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCA‑tttttg > 2:302686/1‑67 (MQ=255)
cATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTg < 1:929263/133‑1 (MQ=255)
agagGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTttatta > 1:993558/1‑56 (MQ=255)
agagGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTttatta < 2:993558/56‑1 (MQ=255)
aaaGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAg < 1:684500/61‑1 (MQ=255)
aaaGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAg > 2:684500/1‑61 (MQ=255)
aaGATGAACCATCTCCACAACCCCCGGCATTTTTGTCAATTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGTCa < 2:246795/134‑1 (MQ=255)
ccATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGTCACGCCAgcg < 1:568566/134‑1 (MQ=255)
acaACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGTCACGCCAGCGCCACTCtt > 1:842071/1‑134 (MQ=255)
caACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGTCACGCCAGCGCCACTCtt > 2:736894/1‑133 (MQ=255)
cccGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGTCACGCCAGCGCCACTCTTGAAAAc > 1:151926/1‑134 (MQ=255)
|
CCGGAAAGGCAGATAAAGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCA‑TTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGTCACGCCAGCGCCACTCTTGAAAAC > AM260479/1239924‑1240179
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ 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‑TTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGTCACGCCAGCGCCACTCTTGAAAACCTGCGC > AM260479/1239923‑1240185
|
GCCGGAAAGGCAGATAAAGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTAC < GWNJ‑0478:712:GW2002102894th:2:2102:5882:10618/150‑1 (MQ=60)
CCGGAAAGGCAGATAAAGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACT > GWNJ‑0478:712:GW2002102894th:2:1103:7099:69119/1‑150 (MQ=60)
atacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTG < GWNJ‑0478:712:GW2002102894th:2:1205:7519:32688/99‑1 (MQ=60)
GGGCAGATAAAGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAAT < GWNJ‑0478:712:GW2002102894th:2:2214:18391:87409/150‑1 (MQ=60)
GATAAAGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAG < GWNJ‑0478:712:GW2002102894th:2:2109:6253:7849/150‑1 (MQ=60)
atttgtacttgtgtttttttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTG < GWNJ‑0478:712:GW2002102894th:2:2214:14573:24721/55‑1 (MQ=60)
AAAGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTG < GWNJ‑0478:712:GW2002102894th:2:1212:15362:30510/149‑1 (MQ=60)
aagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGC < GWNJ‑0478:712:GW2002102894th:2:2110:14947:91090/91‑1 (MQ=60)
ttttttttttttgttttttttttttttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGC < GWNJ‑0478:712:GW2002102894th:2:2212:9827:38858/48‑1 (MQ=60)
GAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCAATTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCAT > GWNJ‑0478:712:GW2002102894th:2:1116:9947:45028/1‑150 (MQ=60)
cggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCC < GWNJ‑0478:712:GW2002102894th:2:2110:11594:19922/95‑1 (MQ=60)
gatgtagctccgtctcgtgggctcggagatgtgtataagagacagCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCG < GWNJ‑0478:712:GW2002102894th:2:2115:21116:90445/105‑1 (MQ=60)
GCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTG < GWNJ‑0478:712:GW2002102894th:2:2210:19494:10611/149‑1 (MQ=60)
GGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgct > GWNJ‑0478:712:GW2002102894th:2:2214:18468:75233/1‑86 (MQ=60)
AAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCctgtctcttatacacatctccgagcccacgtgacggagctacatctcgtatgccgtcttctgcttgaaaaaaaaaaaaaccacaacaagtcaat > GWNJ‑0478:712:GW2002102894th:2:2215:8869:82689/1‑56 (MQ=60)
AGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGTCACGCCAGCGCCACTCTTG > GWNJ‑0478:712:GW2002102894th:2:2205:6416:68730/1‑150 (MQ=60)
ACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaaaaaaaaaaaaaaacacaaaaaaaataaaaagg > GWNJ‑0478:712:GW2002102894th:2:2105:18555:48886/1‑49 (MQ=60)
ACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGTCACGCCAGCGCCACTCTTGAAAACC < GWNJ‑0478:712:GW2002102894th:2:2105:21223:56575/150‑1 (MQ=60)
ACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGTCACGCCAGCGCCACTCTTGAAAACC > GWNJ‑0478:712:GW2002102894th:2:1111:10440:95273/1‑150 (MQ=60)
TCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCtgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaaaaaa > GWNJ‑0478:712:GW2002102894th:2:2206:10335:72669/1‑77 (MQ=60)
CTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGTCACGCCAGCGCCACTCTTGAAAACCTGCGC > GWNJ‑0478:712:GW2002102894th:2:2215:19846:18876/1‑150 (MQ=60)
CTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCATGGCCTTTGTAACCGTGTGTTTCCGCGTCACGCCAGCGCCACTCctgtctcttatac > GWNJ‑0478:712:GW2002102894th:2:1116:15903:32625/1‑136 (MQ=60)
|
GCCGGAAAGGCAGATAAAGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCA‑TTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGTCACGCCAGCGCCACTCTTGAAAACCTGCGC > AM260479/1239923‑1240185
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
