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 |
|
A2 F13 I0 R1
|
203 |
85.6 |
3649704 |
98.8% |
3605907 |
146.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
4,798,322 |
A→G |
18.6% |
intergenic (‑177/+41) |
pvdH ← / ← PP_4224 |
diaminobutyrate‑2‑oxoglutarate transaminase/sensor histidine kinase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 4,798,322 | 0 | A | G | 18.6%
| 48.5
/ 5.0
| 32 | intergenic (‑177/+41) | pvdH/PP_4224 | diaminobutyrate‑2‑oxoglutarate transaminase/sensor histidine kinase |
| Reads supporting (aligned to +/- strand): ref base A (11/9); new base G (3/2); total (14/18) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01 |
CGGTGGACATGGGTAAATCCTCGCGAGCAAGCGGATGGGCGGTTATCGCTTTGGAAACGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAA‑CCC‑GCCCGTA‑GGAGCGGGTT‑CACCCGCGAAGAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTACGGCTGTCAAAGCGCAGGCTACCGGCACACCGCTGCACGATCGCCTGCAC > NC_002947_CJ‑RC/4798178‑4798464
|
cGGTGGACATGGGTAAATCCTCGCGAGCAAGCGGATGGGCGGTTATCGCTTTGGAAACGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAA‑CCC‑GCCCGTA‑GGAGCgg < 2:39149/149‑1 (MQ=255)
ggTGGACATGGGTAAATCCTCGCGAGCAAGCGGATGGGCGGTTATCGCTTTGGAAACGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTGAA‑CCC‑GCTCCTA‑cgggcggg < 3:290106/149‑1 (MQ=38)
ggTGGACATGGGTAAATCCTCGCGAGCAAGCGGATGGGCGGTTATCGCTTTGGAAACGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAA‑CCC‑GCCCGTA‑GGAGCggg < 6:404437/149‑1 (MQ=255)
ggTGGACATGGGTAAATCCTCGCGAGCAAGCGGATGGGCGGTTATCGCTTTGGAAACGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAA‑CCC‑GCCCGTA‑GGAGCggg < 3:43974/149‑1 (MQ=255)
ggTGGACATGGGTAAATCCTCGCGAGCAAGCGGATGGGCGGTTATCGCTTTGGAAACGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAA‑CCC‑GCCCGGA‑GGAGCggg > 8:96332/1‑149 (MQ=255)
gTGGACATGGGTAAATCCTCGCGAGCAAGCGGATGGGCGGTTATCGCTTTGGAAACGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGACCTCTTCGCGGGTTAA‑ACC‑GCCCGGT‑GGGGCgggg > 3:314419/1‑148 (MQ=255)
aCATGGGTAAATCCTCGCGAGCAAGCGGATGGGCGGTTATCGCTTTGGAAACGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTGAA‑CCC‑GCTCCTA‑CGGGCGGGTT‑TAc < 1:264360/149‑1 (MQ=38)
ggTAAATCCTCGCGAGCAAGCGGATGGGCGGTTATCGCTTTGGAAACGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAA‑CCC‑GCCCGTA‑GGAGCGGGTT‑CACCcgc < 2:453045/148‑1 (MQ=255)
tAAATCCTCGCGAGCAAGCGGATGGGCGGTTATCGCTTTGGAAACGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAA‑CCC‑GCCCGTA‑GGAGCGGGTT‑CACCCGCGaa < 8:427886/149‑1 (MQ=255)
aaaTCCTCGCGAGCAAGCGGATGGGCGGTTATCGCTTTGGAAACGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTGAA‑CCC‑GCTCCTA‑CGGGCGGGTT‑TACCCGCGaa < 8:169558/148‑1 (MQ=37)
cTCGCTAGCAAGCGGATGGGCGGTTATCGGTTTGTAAACGCTTTTGTGGGGGGAGGATTTAGCGGTTGTTACGCTATTTTATTTTTGTCGGTGCTGGCCTCTTCGCGGGTAAA‑CCC‑GCCCGTA‑GGAGCGGGTT‑CACCCGCGAAGAGGc < 6:179041/148‑1 (MQ=255)
aTGGGCGGTTCTCGCTTCGCAACCCCTTGCGTGGGGGCCGCATTTAGCGGTTGTCCCCCGATTTTATTTTTGTCTGTCCTGCCCCCTCCCCGGGTAAC‑CCC‑GCCCGTC‑GGCGCGGGTT‑CACCCGCGAAGAGGCCAGCACAGGCGATaaa < 4:307753/149‑1 (MQ=19)
ggCGGTTATCGCTTTGCAACCGCTTTTGGGGGGGTTGTTTTTTGGGGTTTTTCCCCTATTTTTTTTTTGTCTGTGGGGGCCTCTGCG‑GGGTAAACCCC‑GCCGGTC‑GGAGGGGTTT‑AACCCGCTAAGAGGCCAGCACAGGCGATAAACAt < 8:365124/149‑1 (MQ=255)
cGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAA‑CCC‑GCCCGTT‑GGGGCGGGTT‑GACCCGCGAAGAGGCCCGCCCCGGGGCTAAACCTCAAAGCCCAGGACGCGCCgg > 6:115585/1‑149 (MQ=37)
cgccttttttattttTGCTGGGGCGGGCCT‑TTGGGGGGTAAA‑CCC‑CCCGGGT‑GGCCGGGGTTACCCCGGCCATGAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTAc < 4:178695/143‑1 (MQ=255)
cattttttttttttGGCTGTGCGGCCCTCTCCGC‑GGTAAA‑CCC‑CCCCGTACGGCGGGGTTA‑AACCCGCTATGAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTACgg < 7:142428/145‑1 (MQ=255)
tttGTCTGTGATGGCCTTTGCGCGGGTAAA‑CCC‑TCCTTTT‑GTTGGGGTTT‑CACCCGCTATGAGGCCAGCACAGGCGATAAAAATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCAATACGGCTGTCAAAgc < 6:187173/148‑1 (MQ=255)
ttggTCTGTGCTGCCCTCTTCGC‑GGTAAA‑CCCGGCCCGTC‑GGTGCGGGTT‑CACCCGGTAAGAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTACGGCTGTCAAAgc < 6:193959/145‑1 (MQ=255)
ggcggcccTCTCCGCGGCAAAC‑CCC‑GCCGGCC‑GCCGCGGTTC‑CCCCCGCTAAGAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTACGGCTGTCAAAGCGCAGGCTAc < 2:326231/143‑1 (MQ=255)
ctctTCGCGGGTAAA‑CCC‑GCCCGTA‑GGAGCGGGTT‑CACCCGCGAAGAGGCCAGCACAGGCGATAAACATAAATGCCCAGGACGCCCCCGTACCAGCAACAAAACCCCCAAGCCCTCACTACGGCTGTCAAAGCGCAGGCTACCCGcaca > 2:380244/1‑149 (MQ=38)
ctctTCGCGGGTAAA‑CCC‑GCCCGTA‑GGAGCGGGTT‑CAACCGCGAAGAGGCCAGCACAGGCGATAAACATCAATGCCCAGGCCGCCCCCGGACCGGCAACAAAACCCGCCAGCCGTCACTACGGCTGTCAAAGCGCCGGCTACCGGcaca > 6:230329/1‑149 (MQ=38)
cgGGTAAA‑CCC‑GCCCGTA‑GGAGCGGGTT‑CACCCGCGAAGAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAATAAAACCCGCAAGCCGTCACTACGGCTGTc > 5:444627/1‑121 (MQ=255)
cgGGTAAA‑CCC‑GCCCGTA‑GGAGCGGGTT‑CACCCGCGAAGAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAATAAAACCCGCAAGCCGTCACTACGGCTGTc < 6:444627/121‑1 (MQ=255)
gtgaa‑CCC‑GCTCCTA‑CGGGCGGGTT‑TACCCGCGAAGAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTACGGCTGTCAAAGCGCAGGCTACCGGCACACCGCTGCAc > 5:189373/4‑148 (MQ=38)
gTAAA‑CCC‑GCCCTTA‑GGAGCGGGTT‑CACCCGCGAAGAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTACGGCTCTCAAAGCGCACGCTACCGGCACACCGCTGCAc > 2:128903/1‑148 (MQ=255)
gTAAA‑CCC‑GCCCGTA‑GGAGCGGGTT‑CACCCGCGAAGAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTACGGCTGTCAAAGCGCAGGCTACCGGCACACCGCTGCAc > 3:412446/1‑148 (MQ=255)
aa‑CCC‑GCCCGTA‑GGTGCGGTTA‑CACCGGCTAAGAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTACGGCTGTCAAAGCGCAGGCTACCGGCACACCGCTGCACGATc < 8:20665/149‑1 (MQ=255)
aa‑CCC‑GCCCGTA‑GGAGCGGGTT‑CACCCGCGAAGAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTACGGCTGTCAAAGCGCAGGCTACCGGCACACCGCTGCACGATc > 1:48487/1‑149 (MQ=255)
ccc‑gcccgTA‑GGAGCGGGTT‑CACCCGCGAAGAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTACGGCTGTCAAAGCGCAGGCTACCGGCACACCGCTGCACGATCGc > 7:276869/1‑149 (MQ=255)
cc‑gcccgTA‑GGAGCGGGTT‑CACCCGCGAAGAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTACGGCTGTCAAAGCGCAGGCTACCGGCACACCGCTGCACGATCGcc > 3:208976/1‑149 (MQ=255)
c‑gcccgTA‑GGAGCTGTTT‑CACCCGCGAAGAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTACGGCTGTCAAAGCGCAGGCTACCGGCACACCGCTGCACGATCGCCt < 6:258641/149‑1 (MQ=255)
gcccgTA‑GGAGCGGGTT‑CACCCGCGAAGAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTACGGCTGTCAAAGCGCAGGCTACCGGCACACCGCTGCACGATCGCCTg > 8:419779/1‑149 (MQ=255)
gTA‑GGAGCGGGTT‑CACCCGCGAAGAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTACGGCTGTCAAAGCGCAGGCTACCGGCACACCGCTGCACGATCGCCTGcac > 6:253179/1‑148 (MQ=255)
|
CGGTGGACATGGGTAAATCCTCGCGAGCAAGCGGATGGGCGGTTATCGCTTTGGAAACGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAA‑CCC‑GCCCGTA‑GGAGCGGGTT‑CACCCGCGAAGAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTACGGCTGTCAAAGCGCAGGCTACCGGCACACCGCTGCACGATCGCCTGCAC > NC_002947_CJ‑RC/4798178‑4798464
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
