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 |
AM260480 |
2,256,779 |
G→A |
P94S (CCG→TCG) |
h16_B1998 ← |
transcriptional regulator, XRE‑family |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260480 | 2,256,779 | 0 | G | A | 100.0%
| 95.7
/ NA
| 26 | P94S (CCG→TCG) | h16_B1998 | transcriptional regulator, XRE‑family |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (13/13); total (13/13) |
CAGCGTGAACGGCGGCACCATGACGAAGGGCTGCATCGCCTTGTCCACGCGCTCCGTGGCAATGGCTTCGTAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGGAACCCGGTCCGCGGCCTTGACCAGCAGGATCTCATTGCCGCGCTGCGGCTTGGCGATCAGCTGGTCGACGGTCACGTCGAGGGCCTCGGCCAGCT > AM260480/2256672‑2256874
|
cAGCGTGAACGGCGGCACCATGACGAAGGGCTGCATCGCCTTGTCCACGCGCTCCGTGGCAATGGCTTCGTAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCGGTCCGCGGcc > 1:751071/1‑124 (MQ=255)
cAGCGTGAACGGCGGCACCATGACGAAGGGCTGCATCGCCTTGTCCACGCGCTCCGTGGCAATGGCTTCGTAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCGGTCCGCGGcc < 2:751071/124‑1 (MQ=255)
gAACGGCGGCACCATGACGAAGGGCTGCATCGCCTTGTCCACGCGCTCCGTGGCAATGGCTTCGTAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCGGTCCGCGGCCTTGACCAGCAGGAtct > 2:930171/1‑134 (MQ=255)
aCGGCGGCACCATGACGAAGGGCTGCATCGCCTTGTCCACGCGCTCCGTGGCAATGGCTTCGTAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCGGTCCGCGGCCTTGACCAGCAGGATCTCa < 1:1008697/134‑1 (MQ=255)
tCGCCTTGTCCACGCGCTCCGTGGCAATGGCTTCGTAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCgg > 1:740605/1‑80 (MQ=255)
tCGCCTTGTCCACGCGCTCCGTGGCAATGGCTTCGTAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCgg < 2:740605/80‑1 (MQ=255)
gTCCACGCGCTCCGTGGCAATGGCTTCGTAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCGGTCcgc < 1:48657/78‑1 (MQ=255)
gTCCACGCGCTCCGTGGCAATGGCTTCGTAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCGGTCcgc > 2:48657/1‑78 (MQ=255)
gTCCACGCGCTCCGTGGCAATGGCTTCGTAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCGGTCCGCGGCCTTGACCAGCAGGATCTCATTGCCGCGCTGCGGCTTGGCGATCAGCTGGTCGa > 1:237813/1‑134 (MQ=255)
tCCGTGGCAATGGCTTCGTAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCGGTCCGCGGCCTTGACCAGCAGGATCTCATTGCCGCGCTGCGGCTTGGCGATCAGCt < 1:37738/118‑1 (MQ=255)
tCCGTGGCAATGGCTTCGTAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCGGTCCGCGGCCTTGACCAGCAGGATCTCATTGCCGCGCTGCGGCTTGGCGATCAGCt > 2:37738/1‑118 (MQ=255)
ggCAATGGCTTCGTAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCGGTCCGCGGCCTTGACCAGCAGGATCTCATTGCCGCGCTGCGGCTTGGCGATCAGCTGGTCGACGGTCACGTCGAggg > 1:223948/1‑134 (MQ=255)
ttCGTAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCgg > 1:706042/1‑49 (MQ=255)
ttCGTAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCgg < 2:706042/49‑1 (MQ=255)
ttCGTAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCGGTCCGCGGCCTTGACcagc < 2:79972/67‑1 (MQ=255)
ttCGTAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCGGTCCGCGGCCTTGACcagc > 1:79972/1‑67 (MQ=255)
gTAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCGGTCCGCGGCCTTGACCAGCAGGATCTCATTGCCGCGCTGCGGCTTGGCGATCAGCTGGTCGACGGTCACGTCGAGGGCCTCGGCCAGCt < 2:237813/134‑1 (MQ=255)
gTAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCGGTCCGCGGCCTTGACCAGCAGGATCTCATTGCCGCACTGCGGCTTGGCGATCAGCTGGTCGACGGTCACGTCGAGGGCCTCGGCCAGCt < 1:930171/134‑1 (MQ=255)
tataGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCGGTCCGCGGCCTTGACCAGCAGGATCTCATTGCCGCGCTGc < 1:909567/80‑1 (MQ=255)
tataGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCGGTCCGCGGCCTTGACCAGCAGGATCTCATTGCCGCGCTGc > 2:909567/1‑80 (MQ=255)
ggCGCTCGGCGGACGGGCTGAACGAAACCCGGTCCGCGGCCTTGACCAGCAGGATCTCATTGCCGCGCTGCGGCTTGGCGATCAGCTGGTCGACGGTCACGTCGAGGGCCTc > 2:74672/1‑112 (MQ=255)
ggCGCTCGGCGGACGGGCTGAACGAAACCCGGTCCGCGGCCTTGACCAGCAGGATCTCATTGCCGCGCTGCGGCTTGGCGATCAGCTGGTCGACGGTCACGTCGAGGGCCTc < 1:74672/112‑1 (MQ=255)
cTCGGCGGACGGGCTGAACGAAACCCGGTCCGCGGCCTTGACca < 2:189273/44‑1 (MQ=255)
cTCGGCGGACGGGCTGAACGAAACCCGGTCCGCGGCCTTGACca > 1:189273/1‑44 (MQ=255)
tCGGCGGACGGGCTGAACGAAACCCGGTCCGCGGCCTTGACCAGCAGGATCTCATTGCCGCGCTGCGGCtt > 2:241650/1‑71 (MQ=255)
tCGGCGGACGGGCTGAACGAAACCCGGTCCGCGGCCTTGACCAGCAGGATCTCATTGCCGCGCTGCGGCtt < 1:241650/71‑1 (MQ=255)
|
CAGCGTGAACGGCGGCACCATGACGAAGGGCTGCATCGCCTTGTCCACGCGCTCCGTGGCAATGGCTTCGTAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGGAACCCGGTCCGCGGCCTTGACCAGCAGGATCTCATTGCCGCGCTGCGGCTTGGCGATCAGCTGGTCGACGGTCACGTCGAGGGCCTCGGCCAGCT > AM260480/2256672‑2256874
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GCCGGCATGGCTGGCCATTGGCTGGTCTTGTGCCAGCGTGAACGGCGGCACCATGACGAAGGGCTGCATCGCCTTGTCCACGCGCTCCGTGGCAATGGCTTCGTAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGGAACCCGGTCCGCGGCCTTGACCAGCAGGATCTCATTGCCGCGCTGCGGCTTGGCGATCAGCTGGTCGACGGTCACGTCGAGGGCCTCGGCCAGCTTGAGCACCGTACCGATGGTCGGCGACGACAGGCCGCGCTCCAGCTTGGAC > AM260480/2256639‑2256924
|
catcgtctttttttttttccttcttttttttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCGGTC < GWNJ‑0478:712:GW2002102894th:2:2210:8203:54321/45‑1 (MQ=60)
agacagGGCCATTGGCTGGTCTTGTGCCAGCGTGAACGGCGGCACCATGACGAAGGGCTGCATCGCCTTGTCCACGCGCTCCGTGGCAATGGCTTCGTAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCGGTCCGCGGC < GWNJ‑0478:712:GW2002102894th:2:2201:14818:23008/144‑1 (MQ=60)
gtagctccgtctcgtgggctcggagatgtgtataagagacagGGGCTGCATCGCCTTGTCCACGCGCTCCGTGGCAATGGCTTCGTAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCGGTCCGCGGCCTTGACCAGCAG < GWNJ‑0478:712:GW2002102894th:2:1102:19545:37015/108‑1 (MQ=60)
TGGCTGGTCTTGTGCCAGCGTGAACGGCGGCACCATGACGAAGGGCTGCATCGCCTTGTCCACGCGCTCCGTGGCAATGGCTTCGTAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCGGTCCGCGGCCTTGACCAGC > GWNJ‑0478:712:GW2002102894th:2:2114:11400:71725/1‑148 (MQ=60)
AACGGCGGCACCATGACGAAGGGCTGCATCGCCTTGTCCACGCGCTCCGTGGCAATGGCTTCGTAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCGGTCCGCGGCCTTGACCAGCAGGATCTCATTGCCGCGCTGCGGC < GWNJ‑0478:712:GW2002102894th:2:2215:12083:57602/150‑1 (MQ=60)
agctccgtctcgtgggctcggagatgtgtataagagacaGCAATGGCTTCGTAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCGGTCCGCGGCCTTGACCAGCAGGATCTCATTGCCGCGCTGCGGCTTGGCGATCAGC < GWNJ‑0478:712:GW2002102894th:2:2208:7457:93274/111‑1 (MQ=60)
TGACGAAGGGCTGCCTCGCCTTGTCCACGCGCTCCGTGGCAATGGCTTCGTAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCGGTCCGCGGCCTTGACCctgtctcttatacacatctccgagcccacgagacggagct > GWNJ‑0478:712:GW2002102894th:2:2114:14224:12645/1‑110 (MQ=60)
acgagatgtagctccgtctcgtgggctcggagatgtgtataagagacAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCGGTCCGCGGCCTTGACCAGCAGGATCTCATTGCCGCGCTGCGGCTTGGCGATCAGCTGGTC < GWNJ‑0478:712:GW2002102894th:2:1116:16577:15160/103‑1 (MQ=60)
GGGCTGCATCGCCTTGTCCACGCGCTCCGTGGCAATGGCTTCGTAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCGGTCCGCGGCCTTGACCAGCAGGATCTCATTGCCGCGCTGCGGCTTGGCGATCAGCTGGTCGAC > GWNJ‑0478:712:GW2002102894th:2:1114:7904:93155/1‑150 (MQ=60)
agGCCTTGTCCACGCGCTCCGTGGCAATGGCTTCGTAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCGGTCCGCGGCCTTGACCAGCAGGATCTCATTGCCGCGCTGCGGCTTGGCGATCAGCTGGTCGACGGTCACGT < GWNJ‑0478:712:GW2002102894th:2:1105:14681:61523/148‑1 (MQ=60)
GTCCACGCGCTCCGTGGCAATGGCTTCGTAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCGGTCCGCGGCCTTGACCAGCAGGATCTCATTGCCGCGCTGCGGCTTGGCGATCAGCTGGTCGACGGTCACGTCGAGGGC > GWNJ‑0478:712:GW2002102894th:2:1114:10213:14665/1‑150 (MQ=60)
CTCCGTGGCAATGGCTTCGTAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCGGTCCGCGGCCTTGACCctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaaa > GWNJ‑0478:712:GW2002102894th:2:2112:12411:16637/1‑79 (MQ=60)
CTCCGTGGCAATGGCTTCGTAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCGGTCCGCGGCCTTGACCAGCAGGATCTCATTGCCGCtgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgc > GWNJ‑0478:712:GW2002102894th:2:1107:10624:47923/1‑98 (MQ=60)
agagacagCGTAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCGGTCCGCGGCCTTGACCAGCAGGATCTCATTGCCGCGCTGCGGCTTGGCGATCAGCTGGTCGACGGTCACGTCGAGGGCCTCGGCCAGCTTGAGCAC < GWNJ‑0478:712:GW2002102894th:2:1107:6219:14311/142‑1 (MQ=60)
CGTAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCGGTCCGCGGCCTTGACCAGCAGGATCTCATTGCCGCACTGCGGCTTGGCGATCAGCTGGTCGACGGTCACGTCGAGGGCCTCGGCCAGCTTGAGCACCGTACCGA < GWNJ‑0478:712:GW2002102894th:2:2210:20687:16246/150‑1 (MQ=60)
GGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGAAACCCGGTCCGCGGCCTTGACCAGCAGGATCTCATTGCCtgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcctgaaaaaaaaa > GWNJ‑0478:712:GW2002102894th:2:1112:2381:16897/1‑75 (MQ=60)
GGCTGAACGAAACCCGGTCCGCGGCCTTGACCAGCAGGATCTCATTGCCGCGCTGCGGCTTGGCGATCAGCTGGTCGACGGTCACGTCGAGGGCCTCGGCCAGCTTGAGCACCGTACCGATGGTCGGCGACGACAGGCCGCGCTCCAGCT > GWNJ‑0478:712:GW2002102894th:2:2204:12832:79185/1‑150 (MQ=60)
GAACGAAACCCGGTCCGCGGCCTTGACCAGCAGGATCTCctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaaaaaaaaaaaaaaaaaaaaaaaaagcagaagacaatgtcgt > GWNJ‑0478:712:GW2002102894th:2:1102:9207:58793/1‑39 (MQ=60)
GAACGAAACCCGGTCCGCGGCCTTGACCAGCAGGATCTCATTGCCGCGCTGCGGCTTGGCGATCAGCTGGTCGACGGTCACGTCGAGGGCCTCGGCCAGCTTGAGCACCGTACCGATGGTCGGCGACGACAGGCCGCGCTCCAGCTTGG > GWNJ‑0478:712:GW2002102894th:2:1113:20715:89238/1‑149 (MQ=60)
GAACGAAACCCGGTCCGCGGCCTTGACCAGCAGGATCTCATTGCCGCGCTGCGGCTTGGCGATCAGCTGGTCGACGGTCACGTCGAGGGCCTCGGCCAGCTTGAGCACCGTACCGATGGTCGGCGACGACAGGCCGCGCTCCAGCTTGG > GWNJ‑0478:712:GW2002102894th:2:1111:20999:37626/1‑149 (MQ=60)
AACGAAACCCGGTCCGCGGCCTTGACCAGCAGGATCTCATTGCCGCGCTGCGGCTTGGCGATCAGCTGGTCGACGGTCACGTCGAGGGCCTCGGCCAGCTTGAGCACCGTACCGATGGTCGGCGACGACAGGCCGCGCTCCAGCTTGGAC > GWNJ‑0478:712:GW2002102894th:2:2113:18820:98439/1‑150 (MQ=60)
|
GCCGGCATGGCTGGCCATTGGCTGGTCTTGTGCCAGCGTGAACGGCGGCACCATGACGAAGGGCTGCATCGCCTTGTCCACGCGCTCCGTGGCAATGGCTTCGTAGGTATAGCCCTGGCGCTCGGCGGACGGGCTGAACGGAACCCGGTCCGCGGCCTTGACCAGCAGGATCTCATTGCCGCGCTGCGGCTTGGCGATCAGCTGGTCGACGGTCACGTCGAGGGCCTCGGCCAGCTTGAGCACCGTACCGATGGTCGGCGACGACAGGCCGCGCTCCAGCTTGGAC > AM260480/2256639‑2256924
|
| 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: ‑ |
