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 |
1,192,562 |
+C |
coding (163/594 nt) |
cccA → |
cytochrome c, mono‑or diheme variant |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260480 | 1,192,560 | 1 | . | C | 100.0%
| 106.4
/ NA
| 28 | V54A (GTC→GCC) | cccA | cytochrome c, mono‑or diheme variant |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (13/15); total (13/15) |
GTCCGGCTGGCTGGTATGGCTCTTGCGGAAACAGGGCAAACAACCAAGACCCGTCCACTGTAGGAGACATCCATGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGT‑CCTGACCGCCCTCCCGGCCGGCTCCGTGCTGGCCCATGGCGACGTCACGCCCCAGGCCGTCGATACCAAAGCGTTACCACAACTGGGCGACGAATGGCGCCCGGACAATCCCTACCGTAGCGGTGA > AM260480/1192443‑1192686
|
gTCCGGCTGGCTGGTATGGCTCTTGCGGAAACAGGGCAAACAACCAAGACCCGTCCACTGTAGGAGACATCCATGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGTCCCTGACCGCCCTcc < 1:428535/133‑1 (MQ=255)
cGGCTGGCTGGTATGGCTCTTGCGGAAACAGGGCAAACAACCAAGACCCGTCCACTGTAGGAGACATCCATGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGTCCCTGACCGCCCTCccggc > 2:1012289/1‑134 (MQ=255)
cGGCTGGCTGGTATGGCTCTTGCGGAAACAGGGCAAACAACCAAGACCCGTCCACTGTAGGAGACATCCATGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGAGCTTTGCGCGTCCCTGACCGCCCTCccggc > 1:516242/1‑134 (MQ=255)
gctggTATGGCTCTTGCGGAAACAGGGCAAACAACCAAGACCCGTCCACTGTAGGAGACATCCATGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGTCCCTGACCGCCCTCCCGGCCGGCTc > 1:931078/1‑134 (MQ=255)
tGCGGAAACAGGGCAAACAACCAAGACCCGTCCACTGTAGGAGACATCCATGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGt < 2:677203/95‑1 (MQ=255)
tGCGGAAACAGGGCAAACAACCAAGACCCGTCCACTGTAGGAGACATCCATGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGt > 1:677203/1‑95 (MQ=255)
gCGGAAACAGGGCAAACAACCAAGACCCGTCCACTGTAGGAGACATCCATGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGTCCCTGACCGCCCTCCCGGCCGGCTCCGTGCTGGCCCATgg > 1:978646/1‑134 (MQ=255)
gAAACAGGGCAAACAACCAAGACCCGTCCACTGTAGGAGACATCCATGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGTCCCTGACCGCCCTCCCGGCCGGCTCCGTGCTGGCCCATGGCGa < 2:978646/134‑1 (MQ=255)
cAAGACCCGTCCACTGTAGGAGACATCCATGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGTCCCTGACCGCCCTCCCGGCCGGCTCCGTGCTGGCCCATGGCGACGTCACGCCCCAGGCCg < 1:1012289/134‑1 (MQ=255)
cccGTCCACTGTAGGAGACATCCATGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGAGCTTTGCGCGTCCCTGACCGCCCTCCCGGCCGGCTCCGTGCTGGCCCATGGCGACGTCACGCCCCAGGCCGTCGAt < 2:516242/134‑1 (MQ=255)
tCCACTGTAGGAGACATCCATGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGTCCCTGACCGCCCTCCCGGCCGGCTCCGTGCTGGCCCATGGCGACGTCACGCCCCAGGCCGTCGATACCa < 2:802994/134‑1 (MQ=255)
cACTGTAGGAGACATCCATGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGTCCCTGACCGCCCTCCCGGCCGGCTCCGTGCTGGCCCATGGCGACGTCACGCCCCAGGCCGTCGATACCaaa < 1:328680/134‑1 (MQ=255)
cTGTAGGAGACATCCATGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGTCCCTGACCGCCCTCCCGGCCGGCTCCGTGCTGGCCCATGGCGACGTCACGCCCCAGGCCGTCGATACCAAAGc > 1:130555/1‑134 (MQ=255)
tGTAGGAGACATCCATGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGTCCCTGACCGCCCTcc < 1:405627/75‑1 (MQ=255)
tGTAGGAGACATCCATGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGTCCCTGACCGCCCTcc > 2:405627/1‑75 (MQ=255)
ggAGACATCCATGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGTCCCTGACCGCCCTcc < 1:235087/71‑1 (MQ=255)
ggAGACATCCATGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGTCCCTGACCGCCCTcc > 2:235087/1‑71 (MQ=255)
ggAGACATCCATGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGTCCCTGACCGCCCTCCCGGCCGGCTCCGTGCTGGCCCATGGCGACGTCACGCCCCAGGCCGTCGATACCAAAGCGTTAc > 1:70257/1‑134 (MQ=255)
aTGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGTCCCTGACCGCCCTCCCGGCCGGCTCCGTGCTGGCCCAt < 1:155725/84‑1 (MQ=255)
aTGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGTCCCTGACCGCCCTCCCGGCCGGCTCCGTGCTGGCCCAt > 2:155725/1‑84 (MQ=255)
aTGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGTCCCTGACCGCCCTCCCGGCCGGCTCCGTGCTGGCCCATGGCGACGTCACGCCCCAGGCCGTCGATACCAAAGCGTTACCACAACTggg > 2:598073/1‑134 (MQ=255)
aTGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGTCCCTGACCGCCCTCCCGGCCGGCTCCGTGCTGGCCCATGGCGACGTCACGCCCCAGGCCGTCGATACCAAAGCGTTACCACAACTggg > 2:442233/1‑134 (MQ=255)
aGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGTCCCTGACCGCCCTCCCGGCCGGCTCCGTGCTGGCCCATGGCGACGTCACGCCCCAGGCCGTCGATACCAAAGCGTTACCACAACTGGGCGACGAATgg < 1:598073/134‑1 (MQ=255)
gcgcCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGTCCCTGACCGCCCTCccggcc > 1:458861/1‑55 (MQ=255)
gcgcCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGTCCCTGACCGCCCTCccggcc < 2:458861/55‑1 (MQ=255)
cttgccttgcTCGCGCTTTGCGCGTCCCTGACCGCCCTCCCGGCCGGCTCCGTGCTGGCCCATGGCGACGTCACGCCCCAGGCCGTCGATACCAAAGCGTTACCACAACTGGGCGACGAATGGCGCCCGGACaa < 2:130555/134‑1 (MQ=255)
cgcTTTGCGCGTCCCTGACCGCCCTCCCGGCCGGCTCCGTGCTGGCCCATGGCGa > 2:221869/1‑55 (MQ=255)
cgcTTTGCGCGTCCCTGACCGCCCTCCCGGCCGGCTCCGTGCTGGCCCATGGCGa < 1:221869/55‑1 (MQ=255)
gcTTTGCGCGTCCCTGACCGCCCTCCCGGCCGGCTCCGTGCTGGCCCATGGCGACGTCACGCCCCAGGCCGTCGATACCAAAGCGTTACCACAACTGGGCGACGAATGGCGCCCGGACAATCCCTACCGTAGCg < 1:442233/134‑1 (MQ=255)
gcgcGTCCCTGACCGCCCTCCCGGCCGGCTCCGTGCTGGCCCATGGCGACGTCACGCCCCAGGCCGTCGATACCAAAGCGTTACCACAACTGGGCGACGAATGGCGCCCGGACAATCCCTACCGTAGCGGTGa < 2:70257/133‑1 (MQ=255)
|
GTCCGGCTGGCTGGTATGGCTCTTGCGGAAACAGGGCAAACAACCAAGACCCGTCCACTGTAGGAGACATCCATGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGT‑CCTGACCGCCCTCCCGGCCGGCTCCGTGCTGGCCCATGGCGACGTCACGCCCCAGGCCGTCGATACCAAAGCGTTACCACAACTGGGCGACGAATGGCGCCCGGACAATCCCTACCGTAGCGGTGA > AM260480/1192443‑1192686
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CCTCCGGGCCTGGTCCGGCTGGCTGGTATGGCTCTTGCGGAAACAGGGCAAACAACCAAGACCCGTCCACTGTAGGAGACATCCATGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGT‑CCTGACCGCCCTCCCGGCCGGCTCCGTGCTGGCCCATGGCGACGTCACGCCCCAGGCCGTCGATACCAAAGCGTTACCACAACTGGGCGACGAATGGCGCCCGGACAATCCCTACCGTAGCGGTGATGCGCACAAGGAG > AM260480/1192431‑1192699
|
CCTCCGGGCCTGGTCCGGCTGGCTGGTATGGCTCTTGCGGAAACAGGGCAAACAACCAAGACCCGTCCACTGTAGGAGACATCCATGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGAGCTTTGCGCGTCCCTGACCGCCCTCCCGGCC > GWNJ‑0478:712:GW2002102894th:2:1216:16546:84275/1‑150 (MQ=60)
GGCCTGGTCCGGCTGGCTGGTATGGCTCTTGCGGAAACAGGGCAAACAACCAAGACCCGTCCACTGTAGGAGACATCCATGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGTCCCTGACCGCCCTCCCGGCCGGCTCC > GWNJ‑0478:712:GW2002102894th:2:2210:1385:21790/1‑150 (MQ=60)
gatgtagctccgtctcgtgggctcggagatgtgtataagagacagCCAAGACCCGTCCACTGTAGGAGACATCCATGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGTCCCTGACCGCCCTCCCGGCCGGCTCCGTGC < GWNJ‑0478:712:GW2002102894th:2:1211:9624:73696/105‑1 (MQ=60)
acgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagGACCCGTCCACTGTAGGAGACATCCATGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGTCCCTGACCGCCCTCCCGGCCGGCTCCGTGC < GWNJ‑0478:712:GW2002102894th:2:1114:17856:77511/101‑1 (MQ=60)
GGTCCGGCTGGCTGGTATGGCTCTTGCGGAAACAGGGCAAACAACCAAGACCCGTCCACTGTAGGAGACATCCATGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGTCCCTGACCGCCCTCCCGGCCGGCTCCGTGC < GWNJ‑0478:712:GW2002102894th:2:1213:9386:6288/149‑1 (MQ=60)
GGCTGGTATGGCTCTTGCGGAAACAGGGCAAACAACCAAGACCCGTCCACTGTAGGAGACATCCATGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGTCCCTGACCGCCCTCCCtgtctcttatacacatctccgagc > GWNJ‑0478:712:GW2002102894th:2:2110:15464:48120/1‑126 (MQ=60)
GCTGGTATGGCTCTTGCGGAAACAGGGCAAACAACCAAGACCCGTCCACTGTAGGAGACATCCATGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGTCCCTGACCGCCCTCCCGGCCGGCTCCGTGCTGGCCCATGGC > GWNJ‑0478:712:GW2002102894th:2:2213:15779:92937/1‑150 (MQ=60)
ccgtctcgtgggctcggagatgtgtataagagacagCTGTAGGAGACATCCATGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGTCCCTGACCGCCCTCCCGGCCGGCTCCGTGCTGGCCCATGGCGACGTCACGCCC < GWNJ‑0478:712:GW2002102894th:2:1110:19938:18729/114‑1 (MQ=60)
aagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagTGCTTGCCTTGCTCGCGCTTTGCGCGTCCCTGACCGCCCTCCCGGCCGGCTCCGTGCTGGCCCATGGCGACGTCACGCCCCAGGC < GWNJ‑0478:712:GW2002102894th:2:1114:10207:2831/85‑1 (MQ=60)
ACCAAGACCCGTCCACTGTAGGAGACATCCATGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGTCCCTGACCGCCCTCCCGGCCGGCTCCGTGCTGGCCCATGGCGACGTCACGCCCCAGGCCGTCGATACCAAAGCG > GWNJ‑0478:712:GW2002102894th:2:1109:7537:69601/1‑150 (MQ=60)
CCAAGACCCGTCCACTGTAGGAGACATCCATGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGTCCCTGACCGCCCTCCCGGCCGGCTCCGTGCTGGCCCATGGCGACGTCACGCCCCAGGCCGTCGATACCAAAGCGT < GWNJ‑0478:712:GW2002102894th:2:2215:16531:77421/150‑1 (MQ=60)
GACCCGTCCACTGTAGGAGACATCCATGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGTCCCTGACCGCCCTCCCGGCCGGCTCCGTGCTGGCCCATGGCGACGTCACGCCCCAGGCCGTCGATACCAAAGCGTTACC > GWNJ‑0478:712:GW2002102894th:2:1104:16060:85781/1‑150 (MQ=60)
CCACTGTAGGAGACATCCATGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGTCCCTGACCGCCCTCCCGGCCGGCTCCGTGCTGGCCCATGGCGACGTCACGCCCCAGGCCGTCGATACCAAAGCGTTACCACAACTG < GWNJ‑0478:712:GW2002102894th:2:1207:4017:4888/150‑1 (MQ=60)
ATCCATGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGTCCCTGACCGCCCTCCCGGCCGGCTCCGTGCTGGCCCtgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgctt > GWNJ‑0478:712:GW2002102894th:2:1212:4966:75542/1‑86 (MQ=60)
CAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGTCCCTGACCGCCCTCCCGGCCGGCTCCGTGCTGGCCCATGGCGACGTCACGCCCCAGGCCGTCGATACCAAAGCGTTACCACAACTGGGCGACGAATGGCGCCCGGACAATCCC < GWNJ‑0478:712:GW2002102894th:2:2107:14999:55903/150‑1 (MQ=60)
CGCTTTGCGCGTCCCTGACCGCCCTCCCGGCCGGCTCCGTGCTGGCCCATGGCGACGTCACGCCCCAGGCCGTCGATACCAAAGCGTTACCACAACTGGGCGACGAATGGCGCCCGGACAATCCCTACCGTAGCGGTGATGCGCACAAGG < GWNJ‑0478:712:GW2002102894th:2:1213:15139:80908/150‑1 (MQ=60)
TTGCGCGTCCCTGACCGCCCTCCCGGCCGGCTCCGTGCTGGCCCATGGCGACGTCACGCCCCAGGCCGTCGATACCAAAGCGTTACCACAACTGGGCGACGAATGGCGCCCGGACAATCCCTACCGTAGCGGTGATGCGCACAAGGAG < GWNJ‑0478:712:GW2002102894th:2:1108:13660:90608/148‑1 (MQ=60)
|
CCTCCGGGCCTGGTCCGGCTGGCTGGTATGGCTCTTGCGGAAACAGGGCAAACAACCAAGACCCGTCCACTGTAGGAGACATCCATGAAAACGCAGCGCCGCCTGCTTGCCTTGCTCGCGCTTTGCGCGT‑CCTGACCGCCCTCCCGGCCGGCTCCGTGCTGGCCCATGGCGACGTCACGCCCCAGGCCGTCGATACCAAAGCGTTACCACAACTGGGCGACGAATGGCGCCCGGACAATCCCTACCGTAGCGGTGATGCGCACAAGGAG > AM260480/1192431‑1192699
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
