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 I228 R1
|
214 |
26.5 |
1448192 |
97.1% |
1406194 |
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%
| 50.1
/ NA
| 14 | 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 (2/12); total (2/12) |
GAATTCTTTTCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGATCATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTATTGTTGTGTTT > NZ_CP009273/2061262‑2061428
|
gAATTCTTTTCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAgtgg < 2:562408/90‑1 (MQ=255)
cTTTTCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTg < 1:6635/90‑1 (MQ=255)
ttCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAAt < 1:517235/90‑1 (MQ=255)
tcAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCgg < 1:211352/90‑1 (MQ=255)
gCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACt > 1:452152/1‑90 (MQ=255)
aCTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGtcatc < 2:528528/90‑1 (MQ=255)
tCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCAc < 2:296748/90‑1 (MQ=255)
ggTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTAtt < 2:500562/90‑1 (MQ=255)
aTGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTtata < 1:81105/90‑1 (MQ=255)
ggCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTtatata > 1:60414/1‑90 (MQ=255)
aTACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGaa < 1:77557/90‑1 (MQ=255)
gCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTAttgttg < 1:300600/90‑1 (MQ=255)
cAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTATTGTTgtgt < 2:60414/90‑1 (MQ=255)
ggAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTATTGTTGTGttt < 2:6226/90‑1 (MQ=255)
|
GAATTCTTTTCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGATCATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTATTGTTGTGTTT > NZ_CP009273/2061262‑2061428
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TCTCCAAGAAAGCGAATTCTTTTCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGATCATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTATTGTTGTGTTTTGTAC > NZ_CP009273/2061249‑2061433
|
TCTCCAAGAAAGCGAATTCTTTTCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAG < SRR3722112.634985/100‑1 (MQ=60)
CTTTTCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAA < SRR3722112.6718/100‑1 (MQ=60)
TTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGG < SRR3722112.524829/100‑1 (MQ=60)
CTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACT > SRR3722112.458494/1‑100 (MQ=60)
TCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTC < SRR3722112.213908/100‑1 (MQ=60)
nnnnnnnnnnnnnnnnnnnnTGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCAC < SRR3722112.522593/80‑1 (MQ=60)
acattgacattcgtcggcagcgtcagatgtgtataagagaCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACG < SRR3722112.424346/60‑1 (MQ=60)
CCATGGTAATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATA > SRR3722112.61143/1‑100 (MQ=60)
ATGGCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAG < SRR3722112.82099/100‑1 (MQ=60)
GCCCAAATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATctgtctcttatacacatctgacgctgccgacgaatgtcaatgtgtagatc > SRR3722112.585982/1‑50 (MQ=60)
ATACGAAGTTGCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTATTGTTG < SRR3722112.78497/100‑1 (MQ=60)
GCTCAGGAACATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTATTGTTGTGTTTTGTAC < SRR3722112.304067/100‑1 (MQ=60)
|
TCTCCAAGAAAGCGAATTCTTTTCTCAAATTCTGCATTCTCAGACACAGCTTTCTACTCCATGGTAATGGCCCAAATACGAAGTTGCTCAGGATCATTAGTGGTGCTGAGAAGTTAAATAACCATGCGGAGTACCACTCGTCATCACGTATTTATATATCATGAAGCTATTGTTGTGTTTTGTAC > NZ_CP009273/2061249‑2061433
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
