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 I210 R1
|
226 |
19.6 |
1130256 |
95.4% |
1078264 |
84.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,848,011 |
T→C |
T76A (ACT→GCT) |
ydjE ← |
MFS transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,848,011 | 0 | T | C | 100.0%
| 76.3
/ NA
| 24 | T76A (ACT→GCT) | ydjE | MFS transporter |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (12/12); total (12/12) |
GGCCCCTGTTGCAGCAATACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGTAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCAGCT > NZ_CP009273/1847925‑1848097
|
ggCCCCTGTTGCAGCAATACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAg > 2:544202/1‑90 (MQ=255)
gaTTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCg < 1:303445/90‑1 (MQ=255)
aTGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTa > 2:319751/1‑90 (MQ=255)
aTGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTa < 2:215659/90‑1 (MQ=255)
aaaCGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTa < 2:329108/74‑1 (MQ=255)
aaaCGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTa > 1:329108/1‑74 (MQ=255)
aaaCGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAggc < 2:118393/90‑1 (MQ=255)
ccgccCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGaa < 2:454391/90‑1 (MQ=255)
ccgccCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGaa < 2:559305/90‑1 (MQ=255)
gccCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAat > 1:315443/1‑90 (MQ=255)
agtCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGAcc < 2:108616/90‑1 (MQ=255)
gtCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCaa > 1:78467/1‑44 (MQ=255)
gtCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCaa < 2:78467/44‑1 (MQ=255)
gtCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAattat > 2:299104/1‑83 (MQ=255)
gtCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAattat < 1:299104/83‑1 (MQ=255)
gtCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGAcca > 2:362971/1‑90 (MQ=255)
cAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGAccatccat > 2:95955/1‑90 (MQ=255)
aaTAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCAtt < 2:487894/90‑1 (MQ=255)
caccaGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCg < 2:199071/42‑1 (MQ=255)
caccaGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCg > 1:199071/1‑42 (MQ=255)
caccaGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCa > 2:490857/1‑90 (MQ=255)
caccaGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCa > 2:533888/1‑90 (MQ=255)
caccaGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCa > 2:246133/1‑90 (MQ=255)
caGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCAGCt < 1:246133/90‑1 (MQ=255)
|
GGCCCCTGTTGCAGCAATACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGTAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCAGCT > NZ_CP009273/1847925‑1848097
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ 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
GATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGTAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCAGCTTTGCTAAGAC > NZ_CP009273/1847957‑1848107
|
GATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTctgtct > SRR3722092.334946/1‑94 (MQ=60)
GATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGC < SRR3722092.308788/100‑1 (MQ=60)
GCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCtgtctcttatacacatctgacgctgccgacgaccatcttagtgtagatct > SRR3722092.327766/1‑50 (MQ=60)
GCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAAT > SRR3722092.321023/1‑100 (MQ=60)
GCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCtgtctcttatacacatctgacgctgccgacgacca > SRR3722092.79810/1‑65 (MQ=60)
CAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCC < SRR3722092.304353/100‑1 (MQ=60)
CCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCctgtctcttatacacatctgacgctgccgacgaccatc > SRR3722092.202359/1‑62 (MQ=60)
CAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCAGCTTTGCTAAGAC < SRR3722092.250122/100‑1 (MQ=60)
|
GATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGTAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCAGCTTTGCTAAGAC > NZ_CP009273/1847957‑1848107
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
