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 |
AM260479 |
1,231,226 |
2 bp→CA |
intergenic (+63/‑151) |
glnE → / → h16_A1128 |
glutamine synthetase adenylyltransferase/Membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 1,231,226 | 0 | A | C | 100.0%
| 34.2
/ NA
| 10 | intergenic (+63/‑152) | glnE/h16_A1128 | glutamine synthetase adenylyltransferase/Membrane protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (7/3); total (7/3) |
| * | AM260479 | 1,231,227 | 0 | C | A | 100.0%
| 33.2
/ NA
| 10 | intergenic (+64/‑151) | glnE/h16_A1128 | glutamine synthetase adenylyltransferase/Membrane protein |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base A (7/3); total (7/3) |
TGCAGTACCTGGTGCTGCTGCACAACCCGGGCGCACCCGCAGCTGACGCGCAACGCGGGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCACCGCTGGCACTGGCGGTGGGCGATGCCTACCGGCTGTTCCGCGCGCGCCAGCACCAGCTGCGGCTCGAGGGGCAGGCGCATGCGCGCGTCGCGCCCGAGTCGGTGGCGCAGCAGACCGGA > AM260479/1231118‑1231346
||
tGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCCACGCTGGCACTGGCGGTGGGCGATGcc > 1:619302/1‑134 (MQ=255)
aCGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCCACGCTGGCACTGGCGGTGGGCGATGCCTACCGGCTGTTCCGCGCGCGCCAGCACCAGCTGCGGCTCGAg < 2:619302/132‑1 (MQ=255)
cgcTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCCACGCTGGCACTGGCGGTGGGCGATGCCTACCGGCTGTTCCGCGCGCGCCAGCACCAGCTGCGGCTCGAGGGGCAGGCGCATGCGCGCGTcgcg > 2:265404/1‑134 (MQ=255)
gcgcAGCGGGCGAGCTGGGCCTGATCGACGCCACGCTGGCACTGGCGGTGGGCGATGCCTACCGGCTGTTCCGCGCGCGCCAGCACCAGCTGCGGCTCGAGGGGCAGGCGCATGCGCGCGTCGCGCCCGAGTCg > 1:196215/1‑134 (MQ=255)
cGAGCTGGGCCTGATCGACGCCACGCTGGCACTGGCGGTGGGCGATGCCTACCGGCTGTTCCGCGCGCGCCAGCACCAGCTGCGGCTCGAGGGGCAGGCGCATGCGCGCGTCGCGCCCGAGTCGGTGGCgcag > 2:467500/1‑133 (MQ=255)
gCTGGGCCTGATCGACGCCACGCTGGCACTGGCGGTGGGCGATGCCTACCGGCTGTTCCGCGCGCGCCAGCACCAGCTGCGGCTCGAg < 1:409526/88‑1 (MQ=255)
gCTGGGCCTGATCGACGCCACGCTGGCACTGGCGGTGGGCGATGCCTACCGGCTGTTCCGCGCGCGCCAGCACCAGCTGCGGCTCGAg > 2:409526/1‑88 (MQ=255)
gCCTGATCGACGCCACGCTGGCACTGGCGGTGGGCGATGCCTACCGGCTGTTCCGCGCGCGCCAGCACCAGCTGCGGCTCGAGGGGCAGGCGCATGCGCGCGTCGCGCCCGAGTCGGTGGCGCAGCAGACCGGa > 1:350307/1‑134 (MQ=255)
aTCGACGCCACGCTGGCACTGGCGGTGGGCGATGCCTACCGGCTGTTCCGCGCGCGCCAGCACCa > 1:926060/1‑65 (MQ=255)
aTCGACGCCACGCTGGCACTGGCGGTGGGCGATGCCTACCGGCTGTTCCGCGCGCGCCAGCACCa < 2:926060/65‑1 (MQ=255)
||
TGCAGTACCTGGTGCTGCTGCACAACCCGGGCGCACCCGCAGCTGACGCGCAACGCGGGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCACCGCTGGCACTGGCGGTGGGCGATGCCTACCGGCTGTTCCGCGCGCGCCAGCACCAGCTGCGGCTCGAGGGGCAGGCGCATGCGCGCGTCGCGCCCGAGTCGGTGGCGCAGCAGACCGGA > AM260479/1231118‑1231346
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 36 ≤ 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
ATGGTCGATATCGAATTCACGGGTGCAGTACCTGGTGCTGCTGCACAACCCGGGCGCACCCGCAGCTGACGCGCAACGCGGGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCACCGCTGGCACTGGCGGTGGGCGATGCCTACCGGCTGTTCCGCGCGCGCCAGCACCAGCTGCGGCTCGAGGGGCAGGCGCATGCGCGCGTCGCGCCCGAGTCGGTGGCGCAGCAGACCGGACAGGTGCGCGCGCTGTGGC > AM260479/1231095‑1231365
|
gtataagagacaGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCCACGCTGGCACTGGCGGTGGG < GWNJ‑0478:712:GW2002102894th:2:1113:4232:59011/137‑1 (MQ=60)
ATATCGAATTCAC‑GGTGCAGTACCTGGTGCTGCTGCAC‑AGCCGGGCGCACCCGCAGCTGACGCGCAACGC‑GGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCCACGCTGGCACTGGCGGTGGGCGATGCCT > GWNJ‑0478:712:GW2002102894th:2:2106:12577:95196/1‑150 (MQ=60)
cgtgggctcggagatgtgtataagagacagGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCCACGCTGGCACTGGCGGTGGGCGATGCCTACCGGCTGTTCCGCGCGCGCCAGCACCAGCTGCGGCTCGAGGGGCAGGCGCATGCG < GWNJ‑0478:712:GW2002102894th:2:1211:12126:95260/118‑1 (MQ=60)
ATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCCACGCTGGCACTGGCGGTGGGCGATGCCTACCGGCTGTTCCGCGCGCGCCAGCACCAGCTGCGGCTCGAGGGGCAGGCGCATGCGCGCGTCGCGCCCGAGTCGG > GWNJ‑0478:712:GW2002102894th:2:1112:13167:56483/1‑150 (MQ=60)
CAGCGGGCGAGCTGGGCCTGATCGACGCCACGCTGGCACTGGCGGTGGGCGATGCCTACCGGCTGTTCCGCGCGCGCCAGCACCAGCTGCGGCTCGAGGGGCAGGCGCATGCGCGCGTCGCGCCCGAGTCGGTGGCGCAGCAGACCGGAC > GWNJ‑0478:712:GW2002102894th:2:1206:6604:40246/1‑150 (MQ=60)
aagagacagGGGCCTGATCGACGCCACGCTGGCACTGGCGGTGGGCGATGCCTACCGGCTGTTCCGCGCGCGCCAGCACCAGCTGCGGCTCGAGGGGCAGGCGCATGCGCGCGTCGCGCCCGAGTCGGTGGCGCAGCAGACCGGACAGG < GWNJ‑0478:712:GW2002102894th:2:1102:8795:71142/140‑1 (MQ=60)
acaGAGCTGGGCCTGATCGACGCCACGCTGGCACTGGCGGTGGGCGATGCCTACCGGCTGTTCCGCGCGCGCCAGCACCAGCTGCGGCTCGAGGGGCAGGCGCATGCGCGCGTCGCGCCCGAGTCGGTGGCGCAGCAGACCGGACAGGTG < GWNJ‑0478:712:GW2002102894th:2:1108:20782:76720/147‑1 (MQ=60)
GGCGAGCTGGGCCTGATCGACGCCACGCTGGCACTGGCGGTGGGCGATGCCTACCGGCTGTTCCGCGCGCGCCAGCACCAGCTGCGGCTCGAGGGctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccg > GWNJ‑0478:712:GW2002102894th:2:2211:13444:91686/1‑95 (MQ=60)
AGCTGGGCCTGATCGACGCCACGCTGGCACTGGCGGTGGGCGATGCCTACCGGCTGTTCCGCGCGCGCCAGCACCAGCTGCGGCTCGAGGGGCAGGCGCATGCGCGCGTCGCGCCCGAGTCGGTGGCGCAGCAGACCGGACAGGctgtct > GWNJ‑0478:712:GW2002102894th:2:2214:19396:94329/1‑144 (MQ=60)
GGCCTGATCGACGCCACGCTGGCACTGGCGGTGGGCGATGCCTACCGGCTGTTCCGCGCGCGCCAGCACCAGCctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaaaaaaaaa > GWNJ‑0478:712:GW2002102894th:2:1111:6583:57567/1‑73 (MQ=60)
GATCGACGCCACGCTGGCACTGGCGGTGGGCGATGCCTACCGGCTGTTCCGCGCGCGCCAGCACCAGCTGCGGCTCGAGGGGCAGGCGCATGCGCGCGTCGCGCCCGAGTCGGTGGCGCAGCAGACCGGACAGGTGCGCGCGCTGTGGC > GWNJ‑0478:712:GW2002102894th:2:1110:11948:9382/1‑149 (MQ=60)
|
ATGGTCGATATCGAATTCACGGGTGCAGTACCTGGTGCTGCTGCACAACCCGGGCGCACCCGCAGCTGACGCGCAACGCGGGGCAATATCGCGCTGCTGCGCGCAGCGGGCGAGCTGGGCCTGATCGACGCACCGCTGGCACTGGCGGTGGGCGATGCCTACCGGCTGTTCCGCGCGCGCCAGCACCAGCTGCGGCTCGAGGGGCAGGCGCATGCGCGCGTCGCGCCCGAGTCGGTGGCGCAGCAGACCGGACAGGTGCGCGCGCTGTGGC > AM260479/1231095‑1231365
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
