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 F49 I1 R1
|
57 |
62.9 |
2678826 |
98.4% |
2635964 |
146.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
4,741,367 |
2 bp→GC |
intergenic (+497/+255) |
gltA → / ← yeiW |
citrate synthase/putative oxidoreductase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 4,741,367 | 0 | C | G | 97.2%
| 118.5
/ ‑4.3
| 37 | intergenic (+497/+256) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| Reads supporting (aligned to +/- strand): ref base C (0/1); major base G (16/19); minor base A (1/0); total (17/20) |
| Fisher's exact test for biased strand distribution p-value = 4.72e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.79e-01 |
| * | NC_002947_CJ‑RC | 4,741,368 | 0 | A | C | 97.3%
| 126.3
/ ‑3.4
| 37 | intergenic (+498/+255) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); major base C (17/19); minor base . (0/1); total (17/20) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CGCCTCCTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGAACCT‑CCGCCAACTGCAATTCGTGA‑ACCAAGCAAAAGGCCCCGAAAAGGCCCTCC‑GCAGCCCCCCCAACCTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCG > NC_002947_CJ‑RC/4741231‑4741497
||
cGCCTCCTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCg < 6:195799/148‑1 (MQ=255)
gCCTCCTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCgga < 8:61597/149‑3 (MQ=255)
tcctTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCggacac > 5:277569/1‑144 (MQ=255)
ctTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCggacacg < 1:263340/148‑7 (MQ=255)
gTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGtcctcct < 3:181231/148‑2 (MQ=255)
tgCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGcgcctc > 7:345830/1‑147 (MQ=255)
gcaCGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGcgcctcgacc > 8:239597/1‑143 (MQ=255)
gcaCGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGcgcctcgacc > 4:168140/1‑143 (MQ=255)
aCGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAgcg > 7:19869/1‑149 (MQ=255)
aCGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAgc < 3:138378/148‑1 (MQ=255)
ggcgTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGACACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGgcgc > 3:165605/1‑149 (MQ=255)
gcgTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGcc < 6:147342/149‑1 (MQ=255)
aCCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGAt > 6:277885/1‑149 (MQ=255)
ccGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATc < 3:168140/149‑1 (MQ=255)
gCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACg > 4:198166/1‑149 (MQ=255)
ccATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTTCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACgg < 6:259936/149‑1 (MQ=255)
tGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTca < 7:212715/149‑1 (MQ=255)
gTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTAAGCAGCTACTACGAATTGCAA‑TCGAGA‑ATCCAGGCAAAGGCCCCGGACACGTCCTCCAGCAGCGCCACGACCTTGGCCAGCGGCGCCAAGATCACGGTCACAcc > 2:302778/1‑149 (MQ=255)
tATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGtcctcctgcag < 1:246287/106‑6 (MQ=255)
tATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGtcctcctgcag > 2:246287/1‑101 (MQ=255)
ttGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACcgc > 8:163889/1‑148 (MQ=255)
cTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAgg > 2:219136/1‑149 (MQ=255)
tGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGc > 3:72719/1‑149 (MQ=255)
ggTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCACGGACACGTCCTCCTGCAGCGCCTCGCCCTTGGCCAGCGGCGCCTTGATAACGGTCACACCGCGATAGGCCt > 5:195089/1‑149 (MQ=255)
tataGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGATTCCATGC‑ACAGGCACCGGAGACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGTTAGGCCtt < 1:302778/148‑1 (MQ=255)
tataGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTg < 6:277569/149‑1 (MQ=255)
taGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGt < 4:21339/148‑1 (MQ=255)
aGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTa < 8:345830/148‑1 (MQ=255)
gTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACtt < 7:239597/149‑1 (MQ=255)
tCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACTCGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTg < 6:33984/149‑1 (MQ=255)
cAGCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGa > 6:44618/1‑149 (MQ=255)
gCTCTGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCGGACACGTCCTCCT‑GCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGAccc < 2:58298/149‑1 (MQ=255)
ctctGGTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGAccc < 8:241477/149‑1 (MQ=255)
gTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGTCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCa > 7:51080/1‑149 (MQ=255)
gTCACCTTCGTGCTTGAGCAGCT‑TCTGCGACTTGCATTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCa < 7:163889/149‑1 (MQ=255)
ttgcaTTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGGGGGACACCTTGATCCcgtcctc > 8:201821/5‑149 (MQ=255)
gcaTTCGTGA‑ATCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCcgtcctcg < 3:316388/146‑1 (MQ=255)
||
CGCCTCCTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGAACCT‑CCGCCAACTGCAATTCGTGA‑ACCAAGCAAAAGGCCCCGAAAAGGCCCTCC‑GCAGCCCCCCCAACCTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCG > NC_002947_CJ‑RC/4741231‑4741497
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
