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
|
149 |
26.7 |
2337422 |
87.5% |
2045244 |
105.0 |
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 |
20 [0] |
[0] 24 |
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) | 20 (0.930) |
15/170 |
0.3 |
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
ACGTCCGCGGATGCCGTGGGCAAAGTTGGCGATGGCAGCCAGCGGGGTATTCAGCTCATGCGCCAGGAAGGCCAGGGTCTCGTCGATCGCCATCAGCCGGTGCTGGCGCAGGGTGCGCTCGCGGTGGCGCTCGCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTCAGCGGCTTTTCCAGGATGCGGAAGACTTCGCCGCTGTTGACCGTTTCCAGCAGCACATCCTTGTCGGCATAGGCGGTGACCAGGATGC > AM260479/3376026‑3376297
|
attagcgagtgtctcgtgggctcggagatgtgtataagagacaGGGGTATTCAGCTCATGCGCCAGGAAGGCCAGGGTCTCGTCGATCGCCATCAGCCGGTGCTGGCGCAGGGT‑‑‑‑‑‑‑‑‑‑‑‑GCGCTCGCGGTGGCGCTCGGCGGCGCCTGCCAGCAC < GWNJ‑0478:712:GW2002102894th:2:1105:2283:24763/107‑1 (MQ=60)
ttcaagcagaagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacagGGCCAGGGTCTCGTCGATCGCCATCAGCCGGTGCTGGCGCAGGGT‑‑‑‑‑‑‑‑‑‑‑‑GCGCTCGCGGTGGCGCTCGGCGGCGCCTGCCAGCAC < GWNJ‑0478:712:GW2002102894th:2:2108:2482:78781/81‑1 (MQ=60)
GCCGTGGGCAAAGTTGGCGATGGCAGCCAGCGGGGTATTCAGCTCATGCGCCAGGAAGGCCAGGGTCTCGTCGATCGCCATCAGCCGGTGCTGGCGCAGGGT‑‑‑‑‑‑‑‑‑‑‑‑GCGCTCGCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGT < GWNJ‑0478:712:GW2002102894th:2:1209:16663:10787/149‑1 (MQ=60)
gtgggctcggagatgtgtataagagacaGGTATTCAGCTCATGCGCCAGGAAGGCCAGGGTCTCGTCGATCGCCATCAGCCGGTGCTGGCGCAGGGT‑‑‑‑‑‑‑‑‑‑‑‑GCGCTCGCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCA < GWNJ‑0478:712:GW2002102894th:2:2112:13442:93850/122‑1 (MQ=60)
GTTGGCGATGGCAGCCAGCGGGGTATTCAGCTCATGCGCCAGGAAGGCCAGGGTCTCGTCGATCGCCATCAGCCGGTGCTGGCGCAGGGT‑‑‑‑‑‑‑‑‑‑‑‑GCGCTCGCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTC > GWNJ‑0478:712:GW2002102894th:2:2206:20344:70055/1‑148 (MQ=60)
CCAGCGGGGTATTCAGCTCATGCGCCAGGAAGGCCAGGGTCTCGTCGATCGCCATCAGCCGGTGCTGGCGCAGGGT‑‑‑‑‑‑‑‑‑‑‑‑GCGCTCGCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTCAGCGGCTTTTCCAGGA < GWNJ‑0478:712:GW2002102894th:2:1210:8708:17673/150‑1 (MQ=60)
GGGTATTCAGCTCATGCGCCAGGAAGGCCAGGGTCTCGTCGATCGCCATCAGCCGGTGCTGGCGCAGGGT‑‑‑‑‑‑‑‑‑‑‑‑GCGCTCGCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTCAGCGGCctgtctcttatacac > GWNJ‑0478:712:GW2002102894th:2:1201:13829:74386/1‑134 (MQ=60)
aagcagaagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacaggtgctggcgcagggtGCGCTCGCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTCAGCGGCTTTTCC < GWNJ‑0478:712:GW2002102894th:2:1206:11822:74600/70‑1 (MQ=60)
CCAGGAAGGCCAGGGTCTCGTCGATCGCCATCAGCCGGTGCTGGCGCAGGGT‑‑‑‑‑‑‑‑‑‑‑‑GCGCTCGCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTCAGCGGCctgtctcttatacacatctccgagcccacgagac > GWNJ‑0478:712:GW2002102894th:2:1104:2813:80473/1‑116 (MQ=60)
CAGGAAGGCCAGGGTCTCGTCGATCGCCATCAGCCGGTGCTGGCGCAGGGT‑‑‑‑‑‑‑‑‑‑‑‑GCGCTCGCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTCAGCGGCTTTTCCAGGATGCGGAAGACTTCGCCGCTGTTGAC < GWNJ‑0478:712:GW2002102894th:2:2204:7301:55070/150‑1 (MQ=60)
GCCAGGGTCTCGTCGATCGCCATCAGCCGGTGCTGGCGCAGGGT‑‑‑‑‑‑‑‑‑‑‑‑GCGCTCGCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTCAGCGGCTTTTCCAGGATGCGGAAGACTTCGCCGCTGTTGACCGTTTCC > GWNJ‑0478:712:GW2002102894th:2:2211:18150:65098/1‑150 (MQ=60)
GTGCTGGCGCAGGGT‑‑‑‑‑‑‑‑‑‑‑‑GCGCTCGCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACtgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaaaaaaaaaaca > GWNJ‑0478:712:GW2002102894th:2:2111:18729:55416/1‑69 (MQ=60)
ggcgcagggtGCGCTCGCGGTGGCGCTCAGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTCAGCGGCTTTTCCAGGATGCGGAAGACTTCGCCGCTGTTGACCGTTTCCAGCAGCACATCCTTGTCGGCATAGGCGGTGACC > GWNJ‑0478:712:GW2002102894th:2:2211:19047:99117/11‑149 (MQ=60)
gggtGCGCTCGCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTCAGCGGCTTTTCCAGGATGCGGActgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttg > GWNJ‑0478:712:GW2002102894th:2:2106:17649:29429/5‑84 (MQ=60)
gggtGCGCTCGCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTCAGCGGCTTTTCCAGGATGCGGAAGACTTCGCCGCTGTTGACCGTTTCCAGCAGCACATCCTTGTCGGCATAGGCctgtctcttatac > GWNJ‑0478:712:GW2002102894th:2:2112:19524:69265/5‑136 (MQ=60)
GCGCTCGCGGTGGCGCTCGGCGGCGCCTGCCAGCACC < GWNJ‑0478:712:GW2002102894th:2:2116:10465:68776/37‑1 (MQ=9)
|
ACGTCCGCGGATGCCGTGGGCAAAGTTGGCGATGGCAGCCAGCGGGGTATTCAGCTCATGCGCCAGGAAGGCCAGGGTCTCGTCGATCGCCATCAGCCGGTGCTGGCGCAGGGTGCGCTCGCGGTGGCGCTCGCGGTGGCGCTCGGCGGCGCCTGCCAGCACCTCGCGCAGGTCGGCCACGCTCAGCGGCTTTTCCAGGATGCGGAAGACTTCGCCGCTGTTGACCGTTTCCAGCAGCACATCCTTGTCGGCATAGGCGGTGACCAGGATGC > AM260479/3376026‑3376297
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
