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 |
| MC JC |
AM260479 |
3,376,159 |
(CGGTGGCGCTCG)2→1 |
coding (378‑389/1146 nt) |
phcR ← |
signal transduction histidine kinase containing a receiver domain (hybrid) |
|
| | | | seq id |
start |
end |
size |
←reads |
reads→ |
gene |
description |
|---|
| * |
* |
÷ |
AM260479 |
3376140 |
3376151 |
12 |
25 [0] |
[0] 25 |
phcR |
signal transduction histidine kinase containing a receiver domain (hybrid) |
|
| |
seq id |
position |
reads (cov) |
reads (cov) |
score |
skew |
freq |
annotation |
gene |
product |
| * |
? |
AM260479 |
3376152 = | 0 (0.000) | 22 (1.020) |
19/178 |
0.2 |
100% |
coding (396/1146 nt) |
phcR |
signal transduction histidine kinase containing a receiver domain (hybrid) |
| ? | AM260479 |
= 3376139 |
0 (0.000) | coding (409/1146 nt) |
phcR |
signal transduction histidine kinase containing a receiver domain (hybrid) |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ACTCGCCGGCGACACGTCCGCGGATGCCGTGGGCAAAGTTGGCGATGGCAGCCAGCGGGGTATTCAGCTCATGCGCCAGGAAGGCCAGGGTCTCGTCGATCGCCATCAGCCGGTGCTGGCGCAGGGTGCGCTCGCGGTGGCGCTC‑GCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTCAGCGGCTTTTCCAGGATGCGGAAGACTTCGCCGCTGTTGACCGTTTCCAGCAGCACATCCTTGTCGGCATAGGCGGTGACCAGGATGCGCACGATC > AM260479/3376013‑3376305
|
ACTCGCCGGCGACACGTCCGCGGATGCCGTGGGCAAAGTTGGCGATGGCAGCCAGCGGGGTATTCAGCTCATGCGCCAGGAAGGCCAGGGTCTCGTCGATCGCCATCAGCCGGTGCTGGCGCAGGGTGCGCTCGCGGTGGCGCTCGGCGG < GWNJ‑0478:712:GW2002102894th:2:1216:8669:30529/150‑1 (MQ=60)
ACGTCCGCGGATGCCGTGGGCAAAGTTGGCGATGGCAGCCAGCGGGGTATTCAGCTCATGCGCCAGGAAGGCCAGGGTCTCGTCGATCGCCATCAGCCGGTGCTGGCGCAGGGT‑‑‑‑‑‑‑‑‑‑‑‑GCGCTC‑GCGGTGGCGCTCGGCGGCGCCTGCCAGCAC < GWNJ‑0478:712:GW2002102894th:2:2213:5241:27285/150‑1 (MQ=60)
gtagctccgtctcgtgggctcggagatgtgtataagagacagGGGGTATTCAGCTCATGCGCCAGGAAGGCCAGGGTCTCGTCGATCGCCATCAGCCGGTGCTGGCGCAGGGT‑‑‑‑‑‑‑‑‑‑‑‑GCGCTC‑GCGGTGGCGCTCGGCGGCGCCTGCCAGCAC < GWNJ‑0478:712:GW2002102894th:2:1207:10553:79366/107‑1 (MQ=60)
agacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagGGCCAGGGTCTCGTCGATCGCCATCAGCCGGTGCTGGCGCAGGGT‑‑‑‑‑‑‑‑‑‑‑‑GCGCTC‑GCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGT < GWNJ‑0478:712:GW2002102894th:2:1101:11818:93752/92‑1 (MQ=60)
CAGCGGGGTATTCAGCTCATGCGCCAGGAAGGCCAGGGTCTCGTCGATCGCCATCAGCCGGTGCTGGCGCAGGGT‑‑‑‑‑‑‑‑‑‑‑‑GCGCTC‑GCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTCAGCGGCTTTTCCAGGAT > GWNJ‑0478:712:GW2002102894th:2:1215:18886:22285/1‑150 (MQ=60)
CCAGGAAGGCCAGGGTCTCGTCGATCGCCATCAGCCGGTGCTGGCGCAGGGT‑‑‑‑‑‑‑‑‑‑‑‑GCGCTC‑GCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTCAGCGGCTTTTCCAGGATGCGGAAGACTTCGCCGCTGTTG > GWNJ‑0478:712:GW2002102894th:2:2205:13185:83352/1‑149 (MQ=60)
GGTCTCGTCGATCGCCATCAGCCGGTGCTGGCGCAGGGT‑‑‑‑‑‑‑‑‑‑‑‑GCGCTC‑GCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTCAGCGGCTTTTCCAGGATGCGGAAGACTTCGCCGCTGTTGACCGTTTCCAGCAG < GWNJ‑0478:712:GW2002102894th:2:2109:14082:61167/150‑1 (MQ=60)
CGATCGCCATCAGCCGGTGCTGGCGCAGGGT‑‑‑‑‑‑‑‑‑‑‑‑GCGCTC‑GCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTCAGCGGCTTTTCCAGGATGCGGAAGACTTCGCCGCTGTTGACCGTTTCCAGCAGCACATCCT < GWNJ‑0478:712:GW2002102894th:2:1106:14291:14052/150‑1 (MQ=60)
ggcgcagggtGCGCTC‑GCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTCAGCGGCTTTTCCAGGATGCGGAAGACTTCGCCGCTGTTGACCGTTTCCAGCAGCACATCCTTGTCGGCATAGGCGGTGAC < GWNJ‑0478:712:GW2002102894th:2:1213:5633:30532/138‑1 (MQ=60)
gggtGCGCTC‑GCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTCAGCGGCTTTTCCAGGATGCGGAAGACTTCGCCGCTGTTGACCGTTTCCAGCctgtctcttatacacatctccgagcccacgagacgg > GWNJ‑0478:712:GW2002102894th:2:2108:11527:82541/5‑113 (MQ=60)
gggtGCGCTC‑GCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTCAGCGGCTTTTCCAGGATGCGGAAGACTTCGCCGCTGTTGACCGTTTCCAGCAGCACATCCTTGTCGGCATAGGCGGTGACCAGGATGC > GWNJ‑0478:712:GW2002102894th:2:2202:6921:101086/5‑150 (MQ=60)
C‑GCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTCAGCGGCTTTTCCAGGATGCGGAAGACTTCGCCGCTGTTGACCGTTTCCAGCAGCACATCCTTGTCGGCATAGGCGGTGACCAGGATGCGCACGATC < GWNJ‑0478:712:GW2002102894th:2:2215:6570:69118/149‑1 (MQ=60)
|
ACTCGCCGGCGACACGTCCGCGGATGCCGTGGGCAAAGTTGGCGATGGCAGCCAGCGGGGTATTCAGCTCATGCGCCAGGAAGGCCAGGGTCTCGTCGATCGCCATCAGCCGGTGCTGGCGCAGGGTGCGCTCGCGGTGGCGCTC‑GCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTCAGCGGCTTTTCCAGGATGCGGAAGACTTCGCCGCTGTTGACCGTTTCCAGCAGCACATCCTTGTCGGCATAGGCGGTGACCAGGATGCGCACGATC > AM260479/3376013‑3376305
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
