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 I227 R1
|
223 |
21.3 |
1167702 |
97.0% |
1132670 |
86.4 |
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%
| 74.9
/ NA
| 20 | 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 (4/16); total (4/16) |
GCGAATTCTTTTCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGATCATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTATTGTTG > NZ_CP009273/2061260‑2061423
|
gCGAATTCTTTTCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAgt > 2:61756/1‑90 (MQ=255)
gCGAATTCTTTTCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAgt < 1:413603/90‑1 (MQ=255)
cTTTTCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTg < 1:226511/90‑1 (MQ=255)
tctcAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGaa < 2:445446/90‑1 (MQ=255)
gCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAAcc > 2:434177/1‑90 (MQ=255)
tctcAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGc < 1:61756/90‑1 (MQ=255)
tcAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCgg < 1:36648/90‑1 (MQ=255)
cAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGa < 2:510349/90‑1 (MQ=255)
cAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGa < 1:434221/90‑1 (MQ=255)
acaGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACa < 1:508094/51‑1 (MQ=255)
aCTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGtcatc < 2:279616/90‑1 (MQ=255)
cTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGtcatca > 1:241100/1‑90 (MQ=255)
tCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCAc < 1:497562/90‑1 (MQ=255)
cATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGt < 2:205855/90‑1 (MQ=255)
cATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGt < 2:48469/90‑1 (MQ=255)
cATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGt < 1:399462/90‑1 (MQ=255)
cATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGt < 2:510880/90‑1 (MQ=255)
gTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTAttt < 1:242526/90‑1 (MQ=255)
ggCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTtatata > 1:462135/1‑90 (MQ=255)
gCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTAttgttg < 1:541929/90‑1 (MQ=255)
|
GCGAATTCTTTTCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGATCATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTATTGTTG > NZ_CP009273/2061260‑2061423
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ 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
CCAAGAAAGCGAATTCTTTTCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGATCATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTATTGTTGTGTTTTGTAC > NZ_CP009273/2061252‑2061433
|
CCAAGAAAGCGAATTCTTTTCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGG < SRR3722111.110428/100‑1 (MQ=60)
CCAAGAAAGCGAATTCTTTTCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGG < SRR3722111.76819/100‑1 (MQ=60)
cggcagcgtcagatgtgtataagagacagATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGctg < SRR3722111.515960/71‑4 (MQ=60)
GCGAATTCTTTTCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGA < SRR3722111.419689/100‑1 (MQ=60)
CTTTTCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAA < SRR3722111.229243/100‑1 (MQ=60)
TCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCAC < SRR3722111.62499/100‑1 (MQ=60)
TCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTC < SRR3722111.37076/100‑1 (MQ=60)
CAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCG < SRR3722111.440712/100‑1 (MQ=60)
CAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCA > SRR3722111.243971/1‑100 (MQ=60)
TTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGctgtctcttatacacatctgacgctgccgacgaatgtcaatgtgtag > SRR3722111.519221/1‑53 (MQ=60)
TCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATAT < SRR3722111.505215/100‑1 (MQ=60)
CCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATA > SRR3722111.469169/1‑100 (MQ=60)
CATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATAT < SRR3722111.405281/100‑1 (MQ=60)
GTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATG < SRR3722111.245404/100‑1 (MQ=60)
GCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTATTGTTGTGTTTTGTAC < SRR3722111.550448/100‑1 (MQ=60)
|
CCAAGAAAGCGAATTCTTTTCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGATCATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTATTGTTGTGTTTTGTAC > NZ_CP009273/2061252‑2061433
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
