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 |
3,840,691 |
T→G |
N432H (AAC→CAC) |
uhpC ← |
MFS transporter family glucose‑6‑phosphate receptor UhpC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,840,691 | 0 | T | G | 100.0%
| 70.9
/ NA
| 21 | N432H (AAC→CAC) | uhpC | MFS transporter family glucose‑6‑phosphate receptor UhpC |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (10/11); total (10/11) |
CCAGGCAAAACCTGGAAAATTTCTTAGTTTTGCCGGATATGAAGTGAAAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTTCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAGAGATAACCACAAAAAATCCGCTCCAGTGCCAGG > NZ_CP009273/3840604‑3840768
|
ccAGGCAAAACCTGGAAAATTTCTTAGTTTTGCCGGATATGAAGTGAAAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTGCa > 2:48476/1‑90 (MQ=255)
aaaCCTGGAAAATTTCTTAGTTTTGCCGGATATGAAGTGAAAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTGCAAAAAggg < 2:583553/90‑1 (MQ=255)
aCCTGGAAAATTTCTTAGTTTTGCCGGATATGAAGTGAAAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTGCAAAAAGGGCa < 2:345587/90‑1 (MQ=255)
tGGAAAATTTCTTAGTTTTGCCGGATATGAAGTGAAAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTa < 1:155358/90‑1 (MQ=255)
tttCTTAGTTTTGCCGGATATGAAGTGAAAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAAcagcag > 2:12381/1‑90 (MQ=255)
tGAAGTGAAAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGa < 1:223985/90‑1 (MQ=255)
aaGTGAAAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATa > 2:668416/1‑90 (MQ=255)
aGTGAAAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATag < 1:341974/90‑1 (MQ=255)
gAAAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTGCAAAAAggg > 1:593502/1‑52 (MQ=255)
gAAAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTGCAAAAAggg < 2:593502/52‑1 (MQ=255)
gAAAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAgaga > 1:702443/1‑90 (MQ=255)
gAAAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAgaga > 1:270813/1‑90 (MQ=255)
aaaGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAGAGATa < 1:401826/90‑1 (MQ=255)
aaGGTGAGATGCATAACGCTTCGCGCGGGGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCTCGGCGGTGATAGAGATac < 2:722731/90‑2 (MQ=255)
aTCACGCTTCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAGAGATAACCACAAAAAATc > 2:407582/1‑90 (MQ=255)
tCACGCTTCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAGAGATAACCACAAAAAATcc > 1:82573/1‑90 (MQ=255)
cTTCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAGAGATAACCACAAAAAATCCGCTcc < 2:82573/90‑1 (MQ=255)
tCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATag > 1:532085/1‑64 (MQ=255)
tCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATag < 2:532085/64‑1 (MQ=255)
tCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAGAGATAACCACAAAAAATCCGCTCCAg > 1:231947/1‑90 (MQ=255)
gtgtCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAGAGATAACCACAAAAAATCCGCTCCAGTGCCAgg < 2:270813/90‑1 (MQ=255)
|
CCAGGCAAAACCTGGAAAATTTCTTAGTTTTGCCGGATATGAAGTGAAAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTTCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAGAGATAACCACAAAAAATCCGCTCCAGTGCCAGG > NZ_CP009273/3840604‑3840768
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ 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
TGGAAAATTTCTTAGTTTTGCCGGATATGAAGTGAAAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTTCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAGAGATAACCACAAAAAATCCGCTCCAGTGCCAGGTATCGAGTACTT > NZ_CP009273/3840616‑3840780
|
TGGAAAATTTCTTAGTTTTGCCGGATATGAAGTGAAAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGC < SRR3722073.158510/100‑1 (MQ=60)
GATATGAAGTGAAAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCctgtctcttatacacatctgacgctgcc > SRR3722073.605893/1‑72 (MQ=60)
GATATGAAGTGAAAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAGAGA > SRR3722073.276541/1‑100 (MQ=60)
GATATGAAGTGAAAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAGAGA > SRR3722073.716684/1‑100 (MQ=60)
TGAAGTGAAAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAGAGATAAC < SRR3722073.228641/100‑1 (MQ=60)
AGTGAAAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAGAGATAACCAC < SRR3722073.349231/100‑1 (MQ=60)
AAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAGAGATAACCACAAAAA < SRR3722073.410389/100‑1 (MQ=60)
GTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAGAGATAACCACAAAAAATCC > SRR3722073.84438/1‑100 (MQ=60)
GCATCACGCTTCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAGAGATAACCACctgtctcttatacaca > SRR3722073.543195/1‑84 (MQ=60)
GCATCACGCTTCGCGCGGTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAGAGATAACCACAAAAAATCCGCTCCAG > SRR3722073.236794/1‑100 (MQ=60)
GTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAGAGATAACCACAAAAAATCCGCTCCAGTGCCAGGTATCGAGTAC > SRR3722073.523041/1‑100 (MQ=60)
GTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAGAGATAACCACAAAAAATCCGCTCCAGTGCCAGGTATCGAGTAC > SRR3722073.553824/1‑100 (MQ=60)
GTGTCTGGGCGTGCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAGAGATAACCACAAAAAATCCGCTCCAGTGCCAGGTATCGAGTAC < SRR3722073.726542/100‑1 (MQ=60)
GACTGGGCGTGCAAAAAGGGCAGGAACAGCAGTGCGGAAATCCCGGCGGCGATAGAAATAACCACAAAAAATCCGCTCCAGGGCCAGGTATCGAGTACTT > SRR3722073.435036/1‑100 (MQ=60)
|
TGGAAAATTTCTTAGTTTTGCCGGATATGAAGTGAAAAGGTGAGATGCATCACGCTTCGCGCGGTGTCTGGGCGTTCAAAAAGGGCAGTAACAGCAGTGCGGAAATCCCGGCGGCGATAGAGATAACCACAAAAAATCCGCTCCAGTGCCAGGTATCGAGTACTT > NZ_CP009273/3840616‑3840780
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
