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 |
619,859 |
G→T |
H108N (CAC→AAC) |
acrA1 ← |
Cation/multidrug efflux system, mebrane‑fusion component |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 619,859 | 0 | G | T | 100.0%
| 115.0
/ NA
| 31 | H108N (CAC→AAC) | acrA1 | Cation/multidrug efflux system, mebrane‑fusion component |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base T (14/17); total (14/17) |
GGAACGGGCGCGGGTCGATCTCGGCCAGCACGTCGCCGGCCTTGACCATCTGGCCTTCCTTGAACAGCACCTTGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTGGCCCAGGCCGTTGAGCACCACATCCATATCGCGCTTGGCCACGGTGGCGACCACCACGGGCGAGCGCGGCATGCCGGGGCCGCCGGCGCCACCCCGCGCGCCCG > AM260479/619730‑619963
|
ggAACGGGCGCGGGTCGATCTCGGCCAGCACGTCGCCGGCCTTGACCATCTGGCCTTCCTTGAACAGCACCTTGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGcc > 2:1042425/1‑133 (MQ=255)
gAACGGGCGCGGGTCGATCTCGGCCAGCACGTCGCCGGCCTTGACCATCTGGCCTTCCTTGAACAGCACCTTGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGcc > 2:417715/1‑132 (MQ=255)
gAACGGGCGCGGGTCGATCTCGGCCAGCACGTCGCCGGCCTTGACCATCTGGCCTTCCTTGAACAGCACCTTGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGcc < 1:301546/132‑1 (MQ=255)
gAACGGGCGCGGGTCGATCTCGGCCAGCACGTCGCCGGCCTTGACCATCTGGCCTTCCTTGAACAGCACCTTGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGcc > 1:531974/1‑132 (MQ=255)
gcgcGGGTCGATCTCGGCCAGCACGTCGCCGGCCTTGACCATCTGGCCTTCCTTGAACAGCACCTTGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGCCCAGGCCGt < 2:527749/134‑1 (MQ=255)
cgGGTCGATCTCGGCCAGCACGTCGCCGGCCTTGACCATCTGGCCTTCCTTGAACAGCACCTTGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGCCCAGGCCGTTGa < 2:531974/134‑1 (MQ=255)
cgGGTCGATCTCGGCCAGCACGTCGCCGGCCTTGACCATCTGGCCTTCCTTGAACAGCACCTTGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGCCCAGGCCGTTGa < 2:1039846/134‑1 (MQ=255)
gggTCGATCTCGGCCAGCACGTCGCCGGCCTTGACCATCTGGCCTTCCTTGAACAGCACCTTGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGCCCAGGCCGTTGAg > 1:219098/1‑134 (MQ=255)
ggTCGATCTCGGCCAGCACGTCGCCGGCCTTGACCATCTGGCCTTCCTTGAACAGCACCTTGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGCCCAGGCCGTTGAGc < 1:36353/134‑1 (MQ=255)
gCACGTCGCCGGCCTTGACCATCTGGCCTTCCTTGAACAGCACCTTGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGcc > 1:468862/1‑106 (MQ=255)
gCACGTCGCCGGCCTTGACCATCTGGCCTTCCTTGAACAGCACCTTGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGcc < 2:468862/106‑1 (MQ=255)
tCGCCGGCCTTGACCATCTGGCCTTCCTTGAACAGCACCTTGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGCCCAGGCCGTTGAGCACCACATCCATATCGCGCtt > 2:365314/1‑134 (MQ=255)
ccGGCCTTGACCATCTGGCCTTCCTTGAACAGCACCTTGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGCCCAGGCCGTTGAGCACCACATCCATATCGCGCTTGGc < 2:615278/134‑1 (MQ=255)
gACCATCTGGCCTTCCTTGAACAGCACCTTGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGCCCAGGCCGTTGAGCACCACATCCATATCGCGCTTGGCCACGGTg < 1:365314/133‑1 (MQ=255)
aCCATCTGGCCTTCCTTGAACAGCACCTTGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGCCCAGGCCGTTGAGCACCACATCCATATCGCGCTTGGCCACGGTgg < 1:261940/133‑1 (MQ=255)
ccttGAACAGCACCTTGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGCCCAGGCCGTTGAGCACCACATCCATATCGCGCTTGGCCACGGTGGCGACCACCACggg < 2:219098/133‑1 (MQ=255)
ttGAGCAGTGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGcc > 1:989274/1‑62 (MQ=255)
ttGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGcc < 2:989274/62‑1 (MQ=255)
ttGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGcc > 2:760797/1‑62 (MQ=255)
ttGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGcc < 1:760797/62‑1 (MQ=255)
ttGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGCCCAGGCCGTTGa > 2:538399/1‑73 (MQ=255)
ttGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGCCCAGGCCGTTGa < 1:538399/73‑1 (MQ=255)
ttGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGCCCAGGCCGTTGAGCACCACATCCATATCGCGCTTGGc < 1:908770/98‑1 (MQ=255)
ttGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGCCCAGGCCGTTGAGCACCACATCCATATCGCGCTTGGc > 2:908770/1‑98 (MQ=255)
ttGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGCCCAGGCCGTTGAGCACCACATCCATATCGCGCTTGGCCACGGTGGCGACCACCACGGGCGAGCGCGGCATGcc > 1:1137426/1‑134 (MQ=255)
ccGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGCCCAGGCCGTTGa < 1:957509/61‑1 (MQ=255)
ccGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGCCCAGGCCGTTGa > 2:957509/1‑61 (MQ=255)
cacCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGCCCAGGCCGTTGa < 2:257760/56‑1 (MQ=255)
cacCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGCCCAGGCCGTTGa > 1:257760/1‑56 (MQ=255)
cACGGTGACGTTGGACACCGGGGTCACGTTGCCCAGGCCGTTGAGCACCACATCCATATCGCGCTTGGCCACGGTGGCGACCACCACGGGCGAGCGCGGCATGCCGGGGCCGCCGGCGCCACCCCGCGCGCCCg < 1:980072/134‑1 (MQ=255)
cACGGTGACGTTGGACACCGGGGTCACGTTGCCCAGGCCGTTGAGCACCACATCCATATCGCGCTTGGCCACGGTGGCGACCACCACGGGCGAGCGCGGCATGCCGGGGCCGCCGGCGCCACCCCGCGCGCCCg > 2:980072/1‑134 (MQ=255)
|
GGAACGGGCGCGGGTCGATCTCGGCCAGCACGTCGCCGGCCTTGACCATCTGGCCTTCCTTGAACAGCACCTTGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTGGCCCAGGCCGTTGAGCACCACATCCATATCGCGCTTGGCCACGGTGGCGACCACCACGGGCGAGCGCGGCATGCCGGGGCCGCCGGCGCCACCCCGCGCGCCCG > AM260479/619730‑619963
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ 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
TGGTCCAGCGCCGCCTGGAACGGGCGCGGGTCGATCTCGGCCAGCACGTCGCCGGCCTTGACCATCTGGCCTTCCTTGAACAGCACCTTGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTGGCCCAGGCCGTTGAGCACCACATCCATATCGCGCTTGGCCACGGTGGCGACCACCACGGGCGAGCGCGGCATGCCGGGGCCGCCGGCGCCACCCCGCGCGCCCGGGCCGCTGGCGCCCCGCTGCGCGCCTGCAGCCC > AM260479/619714‑619996
|
gagtgtctcgtgggctcggagatgtgtataagagacagGGCCAGCACGTCGCCGGCCTTGACCATCTGGCCTTCCTTGAACAGCACCTTGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGCCC < GWNJ‑0478:712:GW2002102894th:2:1102:12381:100600/112‑1 (MQ=60)
GTCCAGCGCCGCCTGGAACGGGCGCGGGTCGATCTCGGCCAGCACGTCGCCGGCCTTGACCATCTGGCCTTCCTTGAACAGCACCTTGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGCCC > GWNJ‑0478:712:GW2002102894th:2:1215:10487:57038/1‑148 (MQ=60)
GCCTGGAACGGGCGCGGGTCGATCTCGGCCAGCACGTCGCCGGCCTTGACCATCTGGCCTTCCTTGAACAGCACCTTGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGCCCAGGCCGTTGAGC > GWNJ‑0478:712:GW2002102894th:2:1112:3288:56011/1‑150 (MQ=60)
agacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacagTCCTTGAACAGCACCTTGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGCCCAGGCCGTTGAGCAC < GWNJ‑0478:712:GW2002102894th:2:2110:3070:49361/92‑1 (MQ=60)
GGAACGGGCGCGGGTCGATCTCGGCCAGCACGTCGCCGGCCTTGACCATCTGGCCTTCCTTGAACAGCACCTTGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGCCCAGGCCGTTGAGCAC < GWNJ‑0478:712:GW2002102894th:2:1201:19641:93711/148‑1 (MQ=60)
gagattagcgagtgtctcgtgggctcggagatgtgtataagagacagTCCTTGAACAGCACCTTGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGCCCAGGCCGTTGAGCACCACATCCATAT < GWNJ‑0478:712:GW2002102894th:2:1215:3299:86752/103‑1 (MQ=60)
aagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacagACCTTGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGCCCAGGCCGTTGAGCACCACATCCATAT < GWNJ‑0478:712:GW2002102894th:2:2209:20356:36690/91‑1 (MQ=60)
GGGTCGATCTCGGCCAGCACGTCGCCGGCCTTGACCATCTGGCCTTCCTTGAACAGCACCTTGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGCCCAGGCCGTTGAGCACCACATCCATATCG < GWNJ‑0478:712:GW2002102894th:2:1105:13045:29472/150‑1 (MQ=60)
GGTCGATCTCGGCCAGCACGTCGCCGGCCTTGACCATCTGGCCTTCCTTGAACAGCACCTTGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGCCCAGGCCGTTGAGCACCtgtctcttatac > GWNJ‑0478:712:GW2002102894th:2:1210:14295:47420/1‑137 (MQ=60)
cggagatgtgtataagagacagTCCTTGAACAGCACCTTGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGCCCAGGCCGTTGAGCACCACATCCATATCGCGCTTGGCCACGGTGGCGACCAC < GWNJ‑0478:712:GW2002102894th:2:2202:16058:46441/128‑1 (MQ=60)
tctctgttgctcttctttttttttttttcaagcagaagacggcatacgagcttagcgagtgtctcgtgggctcggagatgtgtataagagacaGGCCCAGGCCGTTGAGCACCACATCCATATCGCGCTTGGCCACGGTGGCGACCAC < GWNJ‑0478:712:GW2002102894th:2:2116:21039:40702/55‑1 (MQ=60)
TGACCATCTGGCCTTCCTTGAACAGCACCTTGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGCCCAGGCCGTTGAGCACCACATCCATATCGCGCTTGGCCACGGTGGCGACCACCACGGGC < GWNJ‑0478:712:GW2002102894th:2:1204:7064:82110/149‑1 (MQ=60)
GACCATCTGGCCTTCCTTGAACAGCACCTTGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGCCCAGGCCGTTGAGCACCACATCCATATCGCGCTTGGCCACGGTGGCGACCACCACGGGCG < GWNJ‑0478:712:GW2002102894th:2:1114:10967:69053/149‑1 (MQ=60)
TCCTTGAACAGCACCTTGAGCAGTGGGCCGGACACCTGCGCGTGCACGGTGACGTTGGACACCGGGGTCACGTTGCCCAGGCCGTTGAGCACCtgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtct > GWNJ‑0478:712:GW2002102894th:2:2207:11895:17503/1‑93 (MQ=60)
TCCTTGAACAGCACCTTGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGCCCAGGCCGTTGAGCACCACATCCATATCGCGCTTGGCCACGGTGGCGACCACCACGGGCGAGCGCGGCATGCCG > GWNJ‑0478:712:GW2002102894th:2:2215:9532:79127/1‑150 (MQ=60)
GAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTTGCCCAGGCCGTTGAGCACCACATCCATATCtgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgct > GWNJ‑0478:712:GW2002102894th:2:1114:6919:48372/1‑87 (MQ=60)
GCACGGTGACGTTGGACACCGGGGTCACGTTGCCCAGGCCGTTGAGCACCACATCCATATCGCGCTTGGCCACGGTGGCGACCACCACGGGCGAGCGCGGCATGCCGGGGCCGCCGGCGCCACCCCGCGCGCCCGtggtggtcgccaccg < GWNJ‑0478:712:GW2002102894th:2:2206:3334:63819/150‑16 (MQ=60)
GGGGTCACGTTGCCCAGGCCGTTGAGCACCACATCCActgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaaaaaaactatggcatgcactgggtccgccaggctccaggca > GWNJ‑0478:712:GW2002102894th:2:2210:19941:40150/1‑37 (MQ=60)
|
TGGTCCAGCGCCGCCTGGAACGGGCGCGGGTCGATCTCGGCCAGCACGTCGCCGGCCTTGACCATCTGGCCTTCCTTGAACAGCACCTTGAGCAGCGGGCCGGACACCTGCGCGCGCACGGTGACGTTGGACACCGGGGTCACGTGGCCCAGGCCGTTGAGCACCACATCCATATCGCGCTTGGCCACGGTGGCGACCACCACGGGCGAGCGCGGCATGCCGGGGCCGCCGGCGCCACCCCGCGCGCCCGGGCCGCTGGCGCCCCGCTGCGCGCCTGCAGCCC > AM260479/619714‑619996
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
