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 I195 R1
|
222 |
27.1 |
1551108 |
96.0% |
1489063 |
86.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,061,342 |
T→A |
intergenic (‑576/‑774) |
BW25113_RS10415 ← / → BW25113_RS24005 |
IS5‑like element IS5 family transposase/TonB‑dependent receptor plug domain‑containing protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,061,342 | 0 | T | A | 100.0%
| 157.1
/ NA
| 42 | intergenic (‑576/‑774) | BW25113_RS10415/BW25113_RS24005 | IS5‑like element IS5 family transposase/TonB‑dependent receptor plug domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base A (9/33); total (9/33) |
GCGAATTCTTTTCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGATCATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTATTGTTGTGT > NZ_CP009273/2061260‑2061426
|
gCGAATTCTTTTCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAgt < 1:63945/90‑1 (MQ=255)
gCGAATTCTTTTCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAgt < 2:437581/90‑1 (MQ=255)
gCGAATTCTTATCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAgt < 2:491325/90‑1 (MQ=255)
cTTTTCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTg < 2:355575/90‑1 (MQ=255)
tctcAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGaa < 1:705840/90‑1 (MQ=255)
ttCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAAt < 1:666384/90‑1 (MQ=255)
cATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCa < 1:366493/90‑1 (MQ=255)
cATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCa < 2:525184/90‑1 (MQ=255)
tcAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCgg < 1:701023/90‑1 (MQ=255)
tcAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCgg < 1:377167/90‑1 (MQ=255)
acaGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTAcc < 1:488328/90‑1 (MQ=255)
caGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTgag > 1:449058/1‑64 (MQ=255)
caGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTgag < 2:449058/64‑1 (MQ=255)
gCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACt < 2:673963/90‑1 (MQ=255)
ccATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACg > 2:713885/1‑90 (MQ=255)
cATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGt < 2:103757/90‑1 (MQ=255)
aTGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGa < 1:518323/70‑1 (MQ=255)
aTGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGa > 2:518323/1‑70 (MQ=255)
aTGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTa > 1:337285/1‑90 (MQ=255)
tGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTAt < 2:337285/90‑1 (MQ=255)
ggTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGGGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTAtt < 2:337540/90‑1 (MQ=255)
tGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTtatat < 2:262867/90‑1 (MQ=255)
tGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTtatat < 2:308045/90‑1 (MQ=255)
tGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTtatat < 1:536649/90‑1 (MQ=255)
tGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTtatat < 1:500868/90‑1 (MQ=255)
ggCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGt < 1:561611/81‑1 (MQ=255)
ggCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGt > 2:561611/1‑81 (MQ=255)
aaaTACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATg > 1:322712/1‑90 (MQ=255)
acaCGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGCAGTCCCACTCGTCATCACGTATTTATATATCATGaa < 1:216455/88‑1 (MQ=255)
aTACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGaa < 2:312968/90‑1 (MQ=255)
aTACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGaa < 1:379703/90‑1 (MQ=255)
aCGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGc < 2:542131/90‑1 (MQ=255)
aaGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTAt < 1:105975/90‑1 (MQ=255)
aGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTtatata > 1:531909/1‑77 (MQ=255)
aGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTtatata < 2:531909/77‑1 (MQ=255)
ttGCTCAGGAATATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCGCTCGTCATCACGTATTTATATATCATGAAGCTAttgt < 2:410938/90‑1 (MQ=255)
tGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGaa > 2:486333/1‑81 (MQ=255)
tGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGaa < 1:486333/81‑1 (MQ=255)
tGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTAttgt > 1:425417/1‑89 (MQ=255)
tGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTAttgt < 2:425417/89‑1 (MQ=255)
gCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTAttgttg < 2:594140/90‑1 (MQ=255)
cAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTATTGTTgtgt < 2:713389/90‑1 (MQ=255)
|
GCGAATTCTTTTCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGATCATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTATTGTTGTGT > NZ_CP009273/2061260‑2061426
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CTCTCCAAGAAAGCGAATTCTTTTCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGATCATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTATTGTTGTGTTTTGTACATCAGTAG > NZ_CP009273/2061248‑2061441
|
CTCTCCAAGAAAGCGAATTCTTTTCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTA < SRR3722073.320305/100‑1 (MQ=60)
GCGAATTCTTTTCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGA < SRR3722073.65445/100‑1 (MQ=60)
TCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAAC < SRR3722073.720120/100‑1 (MQ=60)
TTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGG < SRR3722073.680038/100‑1 (MQ=60)
CATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTAC < SRR3722073.374269/100‑1 (MQ=60)
TTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATActgtctcttatacaca > SRR3722073.458645/1‑84 (MQ=60)
TCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTC < SRR3722073.385198/100‑1 (MQ=60)
TCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTC < SRR3722073.715236/100‑1 (MQ=60)
taagagacagTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCG < SRR3722073.529227/90‑1 (MQ=60)
ACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATC < SRR3722073.498699/100‑1 (MQ=60)
TTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTA > SRR3722073.344450/1‑100 (MQ=60)
CATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATAT < SRR3722073.573333/100‑1 (MQ=60)
GTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATG > SRR3722073.329563/1‑100 (MQ=60)
TGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGC < SRR3722073.511465/100‑1 (MQ=60)
TGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGC < SRR3722073.547852/100‑1 (MQ=60)
CCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTctg > SRR3722073.543014/1‑97 (MQ=60)
AATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTATTGTT > SRR3722073.434518/1‑100 (MQ=60)
ATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTATTGTTG < SRR3722073.387777/100‑1 (MQ=60)
ATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTATTGTTG < SRR3722073.496675/100‑1 (MQ=60)
ACACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGCAGTCCCACTCGTCATCACGTATTTATATATCATGAAGCTATTGTTG < SRR3722073.220915/100‑1 (MQ=60)
AAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTATTGTTGTGTTT < SRR3722073.108267/100‑1 (MQ=60)
GCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTATTGTTGTGTTTTGTAC > SRR3722073.771840/1‑100 (MQ=60)
ACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTATTGTTGTGTTTTGTACATCAGTAG < SRR3722073.402210/100‑1 (MQ=60)
|
CTCTCCAAGAAAGCGAATTCTTTTCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGATCATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTATTGTTGTGTTTTGTACATCAGTAG > NZ_CP009273/2061248‑2061441
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
