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 |
AM260480 |
159,389 |
+G |
intergenic (‑21/‑334) |
h16_B0138 ← / → h16_B0139 |
transcriptional regulator, IclR‑family/conserved hypothetical transmembrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260480 | 159,388 | 1 | . | G | 100.0%
| 120.6
/ NA
| 40 | intergenic (‑20/‑335) | h16_B0138/h16_B0139 | transcriptional regulator, IclR‑family/conserved hypothetical transmembrane protein |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (20/20); total (20/20) |
AGCGCCGGTTGCACCACCTCGGCCGGCGAAAACGTCTTGCGCATCACTTGTCCCAGCTCGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTT‑GCGGCAAA‑GTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTGGCGGGCGGTGAAGTGGGTCAACAGCGCCAGGGCGCCGTCCAGGGTCTT > AM260480/159265‑159513
|
aGCGCCGGTTGCACCACCTCGGCCGGCGAAAACGTCTTGCGCATCACTTGTCCCAGCTCGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAg < 1:1141695/134‑1 (MQ=255)
caccacCTCGGCCGGCGAAAACGTCTTGCGCATCACTTGTCCCAGCTCGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGca > 2:679777/1‑134 (MQ=255)
cgcATCACTTGTCCCAGCTCGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGcac > 2:983920/1‑107 (MQ=37)
cgcATCACTTGTCCCAGCTCGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGcac < 1:983920/107‑1 (MQ=37)
cgcATCACTTGTCCCAGCTCGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAgc < 2:379759/133‑1 (MQ=255)
ttGTCCCAGCTCGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACg < 2:1121676/103‑1 (MQ=25)
ttGTCCCAGCTCGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACg > 1:1121676/1‑103 (MQ=25)
cGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAg > 2:574475/1‑76 (MQ=25)
cGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAg < 1:574475/76‑1 (MQ=25)
gAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGccc > 1:483881/1‑133 (MQ=255)
gAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGccc > 2:539040/1‑133 (MQ=255)
gcAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAgctgggc < 1:539040/134‑1 (MQ=255)
aGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTggcgggc > 2:303082/1‑134 (MQ=255)
gTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGcaccac > 1:499716/1‑69 (MQ=17)
gTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGcaccac < 1:379189/69‑1 (MQ=17)
gTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGcaccac < 2:499716/69‑1 (MQ=17)
gTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGcaccac > 2:379189/1‑69 (MQ=17)
ggCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAg > 1:834846/1‑49 (MQ=11)
ggCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAg < 2:834846/49‑1 (MQ=11)
ggCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGcaccac < 1:50262/64‑1 (MQ=14)
ggCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGcaccac > 2:50262/1‑64 (MQ=14)
ggCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTcg < 2:725287/98‑1 (MQ=17)
ggCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTcg > 1:725287/1‑98 (MQ=17)
ggCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCa < 2:758247/102‑1 (MQ=18)
ggCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCa > 1:758247/1‑102 (MQ=18)
gCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTGGCGGGCGGt > 1:1012555/1‑126 (MQ=255)
gCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTGGCGGGCGGt < 2:1012555/126‑1 (MQ=255)
gcgcGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAgctgggc < 1:812428/110‑1 (MQ=18)
gcgcGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAgctgggc > 2:812428/1‑110 (MQ=18)
gCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTGGCGGGCGGTGAAGTGGGTCAACAGCGCCAgg > 2:70459/1‑134 (MQ=255)
cACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTGGCGGGCGGTGAAGTGGGTCAACAGCGCCAggg > 2:307528/1‑134 (MQ=255)
cACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTGGCGGGCGGTGAAGTGGGTCAACAGCGCCAg < 2:857043/132‑1 (MQ=255)
cACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTGGCGGGCGGTGAAGTGGGTCAACAGCGCCAg < 2:907140/132‑1 (MQ=255)
ggAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTGGCGGGCGGTGAAGTGGGTCAACAGCGCCAGGGCGCCg < 1:332812/134‑1 (MQ=255)
tggCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTGGCGGGCGGTGAAGTGGGTCAACAGCGCCAGGGCGCCg > 1:493338/3‑125 (MQ=255)
tggCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTGGCGGGCGGTGAAGTGGGTCAACAGCGCCAGGGCGCCg < 2:493338/123‑1 (MQ=255)
tggCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTGGCGGGCGGTGAAGTGGGTCAACAGCGCCAGGGCGCCGTCCAGGGTc > 1:1017355/3‑134 (MQ=255)
ggCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCgtgg > 2:689561/2‑40 (MQ=14)
ggCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCgtgg < 1:689561/39‑1 (MQ=14)
gCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTGGCGGGCGGTGAAGTGGGTCAACAGCGCCAGGGCGCCGTCCAGGGTCtt < 2:1017355/134‑1 (MQ=255)
|
AGCGCCGGTTGCACCACCTCGGCCGGCGAAAACGTCTTGCGCATCACTTGTCCCAGCTCGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTT‑GCGGCAAA‑GTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTGGCGGGCGGTGAAGTGGGTCAACAGCGCCAGGGCGCCGTCCAGGGTCTT > AM260480/159265‑159513
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CAGCGCCGGTTGCACCACCTCGGCCGGCGAAAACGTCTTGCGCATCACTTGTCCCAGCTCGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTT‑GCGGCAAA‑GTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTGGCGGGCGGTGAAGTGGGTCAACAGCGCCAGGGCGCCGTCCAGGGTCTTGAGC > AM260480/159264‑159517
|
attagcgagtgtctcgtgggctcggagatgtgtataagagacagTCACTTGTCCCAGCTCGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCAC < GWNJ‑0478:712:GW2002102894th:2:1216:9064:100130/106‑1 (MQ=60)
CAGCGCCGGTTGCACCACCTCGGCCGGCGAAAACGTCTTGCGCATCACTTGTCCCAGCTCGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCAC < GWNJ‑0478:712:GW2002102894th:2:2215:1500:83307/150‑1 (MQ=60)
tttttttattgttgttggtcttttttttttttttcaagcagaagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacagGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCAC < GWNJ‑0478:712:GW2002102894th:2:2211:5028:63508/49‑1 (MQ=60)
gtataagagacagGGCGAAAACGTCTTGCGCATCACTTGTCCCAGCTCGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCAC < GWNJ‑0478:712:GW2002102894th:2:2206:13350:85774/137‑1 (MQ=60)
atacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacagGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCC < GWNJ‑0478:712:GW2002102894th:2:1207:9177:94417/99‑1 (MQ=60)
acggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacagACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCC < GWNJ‑0478:712:GW2002102894th:2:1102:8959:18892/94‑1 (MQ=59)
tttttttttttttcaagcagaagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacaGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAG < GWNJ‑0478:712:GW2002102894th:2:2106:13968:98748/71‑1 (MQ=60)
CGTCTTGCGCATCACTTGTCCCAGCTCGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACtgcgctgtctcttatacacat > GWNJ‑0478:712:GW2002102894th:2:2214:10728:95256/1‑129 (MQ=60)
CACTTGTCCCAGCTCGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCC > GWNJ‑0478:712:GW2002102894th:2:1213:6336:67704/1‑149 (MQ=60)
GCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtat > GWNJ‑0478:712:GW2002102894th:2:1212:13247:47529/1‑99 (MQ=60)
CGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTGGCGGGCGGTGAAG < GWNJ‑0478:712:GW2002102894th:2:1214:6071:32279/150‑1 (MQ=60)
aagagacagGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTGGCGGGCGGTGAAG < GWNJ‑0478:712:GW2002102894th:2:2115:7835:34496/140‑1 (MQ=60)
ACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaa > GWNJ‑0478:712:GW2002102894th:2:2114:2089:38033/1‑79 (MQ=51)
ACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGctgtctcttatacacatctccg > GWNJ‑0478:712:GW2002102894th:2:2109:6442:95318/1‑128 (MQ=60)
ACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTctgtctcttatacacatc > GWNJ‑0478:712:GW2002102894th:2:2110:18524:65136/1‑132 (MQ=60)
CCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTGGCGGGCGGTGAAGTGGGT > GWNJ‑0478:712:GW2002102894th:2:2208:5716:47322/1‑150 (MQ=60)
GCACCANGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTGGCGGGCGGTGAAGTGGGTCAACAGCGCCAGGGCGCCGTCCAGGGTCT > GWNJ‑0478:712:GW2002102894th:2:1212:21289:14082/1‑150 (MQ=60)
GCACCAGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTGGCGGGCGGTGAAGTGGGTCAACAGCGCCAGGGCGCCGTCCAGGGTCT > GWNJ‑0478:712:GW2002102894th:2:2208:6117:74675/1‑150 (MQ=60)
AGGAAGCCGTTGGCGGCAAAGGTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTGGCGGGCGGTGAAGTGGGTCAACAGCGCCAGGGCGCCGTCCAGGGTCTTGAGC < GWNJ‑0478:712:GW2002102894th:2:1205:15108:13826/150‑1 (MQ=60)
|
CAGCGCCGGTTGCACCACCTCGGCCGGCGAAAACGTCTTGCGCATCACTTGTCCCAGCTCGAACCAGCGCAACCCCAGGCCGTAGCGGCCAAGCGCGTCCTGCACCAGGAAGCCGTT‑GCGGCAAA‑GTCGCCAGCGCGCGGTGCACCACGGCGTGGTGCACGCCGCTGTAGCGCGCCAGTTCGCGCACGCCCCAGCTGGGCTGGCGGGCGGTGAAGTGGGTCAACAGCGCCAGGGCGCCGTCCAGGGTCTTGAGC > AM260480/159264‑159517
|
| 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: ‑ |
