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
|
146 |
27.9 |
2327082 |
89.7% |
2087392 |
107.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AM260479 |
3,998,635 |
+C |
intergenic (‑221/+527) |
h16_A3705 ← / ← h16_A3706 |
transcriptional regulator, LysR‑family/conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 3,998,633 | 1 | . | C | 100.0%
| 110.2
/ NA
| 29 | intergenic (‑219/+529) | h16_A3705/h16_A3706 | transcriptional regulator, LysR‑family/conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (16/13); total (16/13) |
ATGCCTAATATCTAGCCATCGGATGCCGCAATGCAACATAGTCTTTCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACG‑CCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGGTAGCCAAGTTCGATCCGTACACCGACGGCGCCC > AM260479/3998521‑3998761
|
aTGCCTAATATCTAGCCATCGGATGCCGCAATGCAACATAGTCTTTCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCAccc > 2:65710/1‑134 (MQ=255)
aTCGGATGCCGCAATGCAACATAGTCTTTCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCg > 1:710066/1‑134 (MQ=255)
aTCGGATGCCGCAATGCAACATAGTCTTTCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCg > 1:395459/1‑134 (MQ=255)
gTCTTTCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCa < 2:506954/91‑1 (MQ=255)
gTCTTTCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCa > 1:506954/1‑91 (MQ=255)
gTCTTTCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGa < 2:719956/133‑1 (MQ=255)
tttCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACgg > 1:474620/1‑134 (MQ=255)
gtcgAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATAAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAg > 1:1158979/1‑134 (MQ=255)
gAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACGGCTACGCCCTGTCGGCTGTGGCCCCCCTCGCCGCCCCCCTGCCGCCCGACCCGGCCTTTCCCAAAAACGGCAAGTTc > 2:74971/1‑134 (MQ=255)
gAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGtt < 1:455099/133‑1 (MQ=255)
gAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTc < 1:807682/134‑1 (MQ=255)
cTCAGGCATCCATTCAATAGAGAAAGCCTGAATCATTAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCa < 1:74971/134‑1 (MQ=255)
cATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGgcgc < 1:930513/134‑1 (MQ=255)
agaAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGGTAGcc < 1:65710/134‑1 (MQ=255)
gaAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTcgccgc > 1:590350/1‑60 (MQ=255)
gaAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTcgccgc < 2:590350/60‑1 (MQ=255)
gaAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCa > 1:64196/1‑113 (MQ=255)
gaAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCa < 2:64196/113‑1 (MQ=255)
aaGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCa > 1:241499/1‑111 (MQ=255)
aaGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCa < 2:241499/111‑1 (MQ=255)
aaGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGGTAGCCAAg > 1:220473/1‑134 (MQ=255)
ccTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGGTAGCCAAGTTc > 1:128749/1‑134 (MQ=255)
gAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGGTAGCCAAGTTCGAt > 2:476961/1‑134 (MQ=255)
aTGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGtt < 1:997753/89‑1 (MQ=255)
aTGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGtt > 2:997753/1‑89 (MQ=255)
aTGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGGTAGCCAAGTTc > 2:341694/1‑126 (MQ=255)
aTGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGGTAGCCAAGTTc < 1:341694/126‑1 (MQ=255)
gCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGGTAGCCAAGTTCGATCCGTACACCGACGGCGcc < 1:476961/134‑1 (MQ=255)
cTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGGTAGCCAAGTTCGATCCGTACACCGACGGCGccc > 2:104208/1‑134 (MQ=255)
|
ATGCCTAATATCTAGCCATCGGATGCCGCAATGCAACATAGTCTTTCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACG‑CCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGGTAGCCAAGTTCGATCCGTACACCGACGGCGCCC > AM260479/3998521‑3998761
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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
ATTGTGGATCCTGATATTTATTGATATGAGGGAAATGCCTAATATCTAGCCATCGGATGCCGCAATGCAACATAGTCTTTCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACG‑CCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGGTAGCCAAGTTCGATCCGTACACCGACGGCGCCCGCACCGGCAAGTTC > AM260479/3998487‑3998775
|
gtgtctcgtgggctcggagatgtgtataagagacagGCCTAATATCTAGCCATCGGATGCCGCAATGCAACATAGTCTTTCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACG‑CCC < GWNJ‑0478:712:GW2002102894th:2:1115:1562:3776/114‑1 (MQ=60)
aagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacaGCCGCAATGCAACATAGTCTTTCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACG‑CCC < GWNJ‑0478:712:GW2002102894th:2:1212:12010:25331/92‑1 (MQ=60)
ATTGTGGATCCTGATATTTATTGATATGAGGGAAATGCCTAATATCTAGCCATCGGATGCCGCAATGCAACATAGTCTTTCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACG‑CCC < GWNJ‑0478:712:GW2002102894th:2:1103:20225:72774/150‑1 (MQ=60)
ATTGTGGATCCTGATATTTATTGATATGAGGGAAATGCCTAATATCTAGCCATCGGATGCCGCAATGCAACATAGTCTTTCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACG‑CCC < GWNJ‑0478:712:GW2002102894th:2:1213:12258:45689/150‑1 (MQ=60)
GCCTAATATCTAGCCATCGGATGCCGCAATGCAACATAGTCTTTCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGG > GWNJ‑0478:712:GW2002102894th:2:2108:12244:75089/1‑150 (MQ=60)
GCCTAATATCTAGCCATCGGATGCCGCAATGCAACATAGTCTTTCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGG > GWNJ‑0478:712:GW2002102894th:2:1206:8001:54381/1‑150 (MQ=60)
CCGCAATGCAACATAGTCTTTCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCctgtctcttatacacatctccgagcccac > GWNJ‑0478:712:GW2002102894th:2:1212:20597:36928/1‑121 (MQ=60)
CAATGCAACATAGTCTTTCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGC > GWNJ‑0478:712:GW2002102894th:2:1210:4675:77208/1‑150 (MQ=60)
GCAACATAGTCTTTCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATAAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGT > GWNJ‑0478:712:GW2002102894th:2:2216:10888:78779/1‑150 (MQ=60)
cgtgggctcggagatgtgtataagagacagGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGA < GWNJ‑0478:712:GW2002102894th:2:2207:2838:65760/119‑1 (MQ=60)
CGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGAC < GWNJ‑0478:712:GW2002102894th:2:2112:20319:92275/150‑1 (MQ=60)
CGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGA < GWNJ‑0478:712:GW2002102894th:2:1211:4697:76833/149‑1 (MQ=60)
GCTCAGGCATCCATTCAATAGAGAAAGCCTGAATCATTAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGG < GWNJ‑0478:712:GW2002102894th:2:1104:11055:65540/150‑1 (MQ=60)
CATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttc > GWNJ‑0478:712:GW2002102894th:2:2101:17366:47989/1‑90 (MQ=60)
CATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGGctgtctc > GWNJ‑0478:712:GW2002102894th:2:1102:12203:100652/1‑143 (MQ=60)
TCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGGctgtctctt > GWNJ‑0478:712:GW2002102894th:2:1115:16526:66448/1‑141 (MQ=60)
TCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGGTAGCCAAGT > GWNJ‑0478:712:GW2002102894th:2:1112:8814:62930/1‑150 (MQ=60)
CCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGGTAGCCAAGTT < GWNJ‑0478:712:GW2002102894th:2:2204:6957:78454/150‑1 (MQ=60)
ATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGGTAGCCAAGTTCG > GWNJ‑0478:712:GW2002102894th:2:1108:8787:75952/1‑150 (MQ=60)
GAGAAAGCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGGTAGCCAAGTTCGATCCGTAC < GWNJ‑0478:712:GW2002102894th:2:1104:19473:10134/150‑1 (MQ=60)
GCCTGAATCATGAAAACCAACCGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGGTAGCCAAGTTCGATCCGTACACCGAC < GWNJ‑0478:712:GW2002102894th:2:1205:10047:41352/150‑1 (MQ=60)
CGCTACGCCCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGGTAGCCAAGTTCGATCCGTACACCGACGGCGCCCGCACCGGCAAGTTC < GWNJ‑0478:712:GW2002102894th:2:1210:5696:89515/150‑1 (MQ=60)
|
ATTGTGGATCCTGATATTTATTGATATGAGGGAAATGCCTAATATCTAGCCATCGGATGCCGCAATGCAACATAGTCTTTCGTCGAAGTGACGGCTCAGGCATCCATGCAATAGAGAAAGCCTGAATCATGAAAACCAACCGCTACG‑CCTGATCGCTGTCGCCACCCTCGCCGCCGCCCTGTCGGCCGCACCGGCCTTTGCCAAGAACGGCAAGTTCGATGTGTTCACCGACGGCGCCAAGGTAGCCAAGTTCGATCCGTACACCGACGGCGCCCGCACCGGCAAGTTC > AM260479/3998487‑3998775
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
