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 F2 I231 R1
|
218 |
12.8 |
703680 |
97.2% |
683976 |
86.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,778,934 |
(T)6→5 |
intergenic (‑564/+187) |
BW25113_RS25705 ← / ← BW25113_RS13825 |
DUF5507 domain‑containing protein/tRNA‑Ile |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,778,929 | 0 | T | . | 95.0%
| 77.0
/ ‑1.0
| 20 | intergenic (‑559/+192) | BW25113_RS25705/BW25113_RS13825 | DUF5507 domain‑containing protein/tRNA‑Ile |
| Reads supporting (aligned to +/- strand): ref base T (0/0); major base . (12/7); minor base G (0/1); total (12/8) |
| Fisher's exact test for biased strand distribution p-value = 4.00e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.14e-01 |
AGGGGTATAATAAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCATTTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAA > NZ_CP009273/2778841‑2778996
|
aGGGGTATAATAAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCAtt > 1:134476/1‑90 (MQ=255)
ataataAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCAtttttcca > 1:72499/1‑87 (MQ=255)
aTGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACtt > 1:245904/1‑90 (MQ=255)
gATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACtttt < 2:61428/90‑1 (MQ=255)
taataCTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGa > 2:97495/1‑90 (MQ=255)
ataCTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAAt > 2:100800/1‑90 (MQ=255)
tctGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGt > 2:135242/1‑90 (MQ=255)
ctGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTa > 2:136234/1‑90 (MQ=255)
tttATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGAt < 1:279873/90‑1 (MQ=255)
tttATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGAt < 2:245904/90‑1 (MQ=255)
tttATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGC‑GTTTTTCCAGGTACTTTTGAATGAGTACTGAt < 1:259527/90‑1 (MQ=255)
tATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATgg > 1:135416/1‑90 (MQ=255)
tATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATgg > 2:231881/1‑90 (MQ=255)
tATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATgg > 1:147335/1‑90 (MQ=255)
cGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATa < 2:134476/90‑1 (MQ=255)
ttAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATaaa > 1:335180/1‑90 (MQ=255)
aTTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATAc < 2:147335/90‑1 (MQ=255)
tAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGAt < 1:5336/62‑1 (MQ=255)
tAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGAt > 2:5336/1‑62 (MQ=255)
aTTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGTGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCa > 1:232739/1‑90 (MQ=255)
aTTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCa > 2:110193/1‑90 (MQ=255)
ttGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCaaa < 2:4923/90‑1 (MQ=255)
|
AGGGGTATAATAAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCATTTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAA > NZ_CP009273/2778841‑2778996
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ATGAAGGGGTATAATAAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCATTTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAAACACCAGCCCTCATTCGAAACCACCCACCGCACTTC > NZ_CP009273/2778837‑2779032
|
ATGAAGGGGTATAATAAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCA > SRR3722116.73409/1‑100 (MQ=60)
GGTATAATAAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTT > SRR3722116.249334/1‑100 (MQ=60)
ACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGG > SRR3722116.137000/1‑100 (MQ=60)
ACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGG > SRR3722116.149036/1‑100 (MQ=60)
GGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAA > SRR3722116.340179/1‑100 (MQ=60)
gatgtgtataagagacagATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATAC < SRR3722116.5404/82‑1 (MQ=60)
TTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATAC < SRR3722116.283931/100‑1 (MQ=60)
TTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGC‑GTTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATAC < SRR3722116.263231/100‑1 (MQ=60)
CATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGTGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCA > SRR3722116.235915/1‑100 (MQ=60)
TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAAACACCAGCCCTCATTCGAAACCACCCACCGCAC < SRR3722116.136821/100‑1 (MQ=60)
TTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAAACACCAGCCCTCATTCGAAACCACCCACCGCACTTC < SRR3722116.356110/100‑1 (MQ=60)
|
ATGAAGGGGTATAATAAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCATTTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAAACACCAGCCCTCATTCGAAACCACCCACCGCACTTC > NZ_CP009273/2778837‑2779032
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
