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 |
|
A24 F15 I2 R1
|
9 |
48.1 |
1671394 |
94.4% |
1577795 |
141.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913_3_bme_pgi |
3,560,455 |
+G |
intergenic (‑2/+1) |
glpR ← / ← glpR |
pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913_3_bme_pgi | 3,560,455 | 1 | . | G | 96.8%
| 92.9
/ ‑3.8
| 31 | intergenic (‑2/+1) | glpR/glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base G (9/21); total (9/22) |
| 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 |
GCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGC‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGAC > NC_000913_3_bme_pgi/3560307‑3560589
|
gacGATATGGATAAAGTGGTGCGAGCCATTGGGGTTTTGCGCAGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCGGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGc < 2:316945/147‑1 (MQ=255)
gaaatCCATAACCAGCGTCCAGCCATTGGGGATTTGCTCCGCCACGTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGcgca < 2:580381/146‑4 (MQ=255)
aCAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAGGttt < 1:600203/149‑1 (MQ=255)
gAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTACCCGACCTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCTCCGc < 2:559439/149‑1 (MQ=255)
gCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGAGGCTCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCTCCGCCa < 1:349608/149‑1 (MQ=255)
ccATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCTCCGCCAg > 1:701188/1‑149 (MQ=255)
cATTGGGGATTTGCTCCGCCAGTTTGCGGGCGATGCGCTCGTTTCCTTCGGCCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCT‑ATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGc < 2:664050/149‑1 (MQ=255)
ggggTTTGGTCCGGCGCTTTGGGGGCGATGCGCTTTTTTTGTTCGGTCTGGCTGGCCTTTCGATCGCGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGTTGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCAtt < 2:141509/149‑1 (MQ=255)
gggATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCAtt > 1:384207/1‑149 (MQ=255)
gATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAg < 2:380470/126‑1 (MQ=255)
gATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAg > 1:380470/1‑126 (MQ=255)
ccGCCACCTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCgcgg < 1:728240/149‑1 (MQ=255)
cGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCgcggc < 1:678596/149‑1 (MQ=255)
cTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATa < 1:718303/149‑1 (MQ=255)
tGCGGGCGATGGGCTCTTTTTCATCGGTCTGGGTGGCTTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTc < 2:193495/149‑1 (MQ=255)
gggCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCTCCGCCCGCTCATTGAGGTCGCGGCGAATAGTCTGc > 1:219433/1‑149 (MQ=255)
tttttCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGgaga > 1:713662/1‑149 (MQ=255)
tttCTTCGGTCTGGGTTGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGaaa < 1:612662/149‑1 (MQ=255)
tttCTTCGGGCTGGTGGGCCTTGCGATTGTGCCACGGGATGTTAACCGAACTGAAAGGCAGCGCCGCACCGCC‑ATGATGCCGCAGCATCAGGTTTTCCGCCGCCAGCTCATCGAGGTCGCGCCGAATATTCTGCGGGCTGACGGAGaaa < 2:526046/149‑1 (MQ=255)
tgttgggTCTGGGTGGCCTGGCGATCGGGGCACGGGGTGTTGGCCGAGCTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGGTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATg < 2:335783/144‑1 (MQ=255)
cttcGGGCTGGGTGGCTTTGCGATCGTGGCACGGCGTGTGAACCGAACTGGAAGGCAGGGCCGCACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGc < 2:644854/149‑1 (MQ=255)
ggTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTa < 2:701188/149‑1 (MQ=255)
tCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTAcc > 1:425098/1‑149 (MQ=255)
cTGGGGGGCCTTGCGAGCGAGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGCATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCa < 1:398884/149‑1 (MQ=255)
gggCGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCTATCTTCAGGCTGCGGGCTGACGGAGAAATGCTCTACCAGc < 1:825570/149‑1 (MQ=255)
cggtCGGGCCTCGGGGTGGTAACCGGACTGGAGGTCAGCGCCGCACCGCC‑ATGATGGCGCAGGACCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACt < 2:671897/146‑1 (MQ=255)
cGTGTTAACCGAATGGGAAGGCAGCGTCGCACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATGGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCctgct < 2:318921/149‑1 (MQ=255)
ggtAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGAGGGCGCAGGATCAGGTTTTGCGCCGCCAGCTCATTGAGGTCGCGGCGAATATGCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGtt < 2:388620/147‑1 (MQ=255)
ttAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGttt > 1:404938/1‑149 (MQ=255)
tAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATa > 2:464933/1‑86 (MQ=255)
tAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATa < 1:464933/86‑1 (MQ=255)
cGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCGCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCCCTTCGGTACTGACATAACCCTGCTGTTTAACCa > 2:708325/1‑149 (MQ=255)
gccGCCAATGAGGGG‑CAGGGTCAGGTTTTGCTCCGCCAGCTCATTTAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGAc < 2:292055/148‑1 (MQ=255)
|
GCCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCC‑ATGATGGC‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGAC > NC_000913_3_bme_pgi/3560307‑3560589
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
