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 F4 I88 R1
|
217 |
30.5 |
1742422 |
95.9% |
1670982 |
87.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
678,913 |
A→G |
intergenic (‑64/+20) |
hscC ← / ← rihA |
molecular chaperone HscC/pyrimidine‑specific ribonucleoside hydrolase RihA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 678,913 | 0 | A | G | 100.0%
| 105.9
/ NA
| 28 | intergenic (‑64/+20) | hscC/rihA | molecular chaperone HscC/pyrimidine‑specific ribonucleoside hydrolase RihA |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (17/11); total (17/11) |
CAATGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGATCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGAC > NZ_CP009273/678825‑678995
|
cAATGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTc < 2:645493/91‑1 (MQ=255)
aaTGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCt < 2:87922/91‑1 (MQ=255)
aTGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCtt > 2:8496/1‑91 (MQ=255)
ttCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATg < 1:234709/91‑1 (MQ=255)
tGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACg < 1:684793/91‑1 (MQ=255)
aTCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGtt > 2:626204/1‑91 (MQ=255)
tttATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTaaaa > 2:642041/1‑91 (MQ=255)
ttGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGAc < 2:210927/91‑1 (MQ=255)
gaaagaaaAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGa > 2:650357/1‑91 (MQ=255)
aGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATcaacaa < 1:222403/91‑1 (MQ=255)
aGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATcaacaa < 1:668357/91‑1 (MQ=255)
aGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATcaacaa < 2:6347/91‑1 (MQ=255)
gATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACaaa > 1:766591/1‑91 (MQ=255)
gATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACaaa > 2:162706/1‑91 (MQ=255)
accaccCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGa < 1:164672/91‑1 (MQ=255)
accCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGa > 2:387984/1‑91 (MQ=255)
accCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGa > 2:459378/1‑91 (MQ=255)
accCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGa > 2:700272/1‑91 (MQ=255)
accCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGa > 2:816360/1‑91 (MQ=255)
accCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGa > 1:429324/1‑91 (MQ=255)
ggTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGCCGATCAAc > 1:574802/1‑91 (MQ=255)
aCGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCg > 2:32320/1‑91 (MQ=255)
aCGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCg > 1:844631/1‑91 (MQ=255)
gcgTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGt > 1:845215/1‑59 (MQ=255)
gcgTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGt < 2:845215/59‑1 (MQ=255)
gcgTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACAt > 2:143567/1‑87 (MQ=255)
gcgTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACAt < 1:143567/87‑1 (MQ=255)
gcgTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGAc > 2:237513/1‑91 (MQ=255)
|
CAATGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGATCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGAC > NZ_CP009273/678825‑678995
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ATACCAATGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGATCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATT > NZ_CP009273/678821‑679010
|
cagCCAATGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATC < SRR3722118.284620/98‑1 (MQ=60)
ATACCAATGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATAAAGACCACCCAGGTAACGCGTGGTGGTCTTAATC < SRR3722118.860736/101‑1 (MQ=60)
TTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTA < SRR3722118.239446/101‑1 (MQ=60)
TGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGC < SRR3722118.699675/101‑1 (MQ=60)
ATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAA > SRR3722118.227789/1‑101 (MQ=60)
GAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAA > SRR3722118.783419/1‑101 (MQ=60)
AGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACG < SRR3722118.226893/101‑1 (MQ=60)
AGATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACG < SRR3722118.682837/101‑1 (MQ=60)
GATTAAGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGA > SRR3722118.438379/1‑101 (MQ=60)
AGACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGCCGATCAAC > SRR3722118.586975/1‑101 (MQ=60)
ACCACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACAT < SRR3722118.167892/101‑1 (MQ=60)
CACCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCG > SRR3722118.863300/1‑101 (MQ=60)
CCCAGGTAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAActgtctcttatacacatctccg > SRR3722118.863893/1‑79 (MQ=60)
TAACGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTAC < SRR3722118.146316/101‑1 (MQ=60)
CGCGTGGTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGT > SRR3722118.21238/1‑101 (MQ=60)
GTGGTCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATT > SRR3722118.889950/1‑101 (MQ=60)
|
ATACCAATGGCGAGTTCTGCATTATCCATTGCATTTATATCTTGAAAGAAAAAGAGATAAACAGATTAAGACCACCCAGGTAACGCGTGGTGATCTTAATCAATGACGTGTGTTAAGCGTAAAATTTCAGACGATCAGCCAGTAAATCAACAAAGCCCTGACGATCAACATCGACCATTACGGTGGCATT > NZ_CP009273/678821‑679010
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
