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 I197 R1
|
189 |
12.7 |
697584 |
97.1% |
677354 |
86.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,554,121 |
A→C |
N169T (AAC→ACC) |
BW25113_RS12740 → |
hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,554,121 | 0 | A | C | 100.0%
| 70.4
/ NA
| 22 | N169T (AAC→ACC) | BW25113_RS12740 | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (14/8); total (14/8) |
CTTCGCTGGTACTGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAAACACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCA > NZ_CP009273/2554035‑2554194
|
cTTCGCTGGTACTGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAAccac > 2:189411/1‑90 (MQ=255)
tCGCTGGTACTGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACgg > 2:215211/1‑90 (MQ=255)
tGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATg > 1:310828/1‑90 (MQ=255)
ggCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTaaaaaa < 1:195677/87‑1 (MQ=255)
ggCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTaaaaaa > 2:195677/1‑87 (MQ=255)
ggCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGc < 2:193526/90‑1 (MQ=255)
cAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCt > 1:240544/1‑90 (MQ=255)
ggTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACt > 1:117599/1‑90 (MQ=255)
ggTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACt > 2:343854/1‑90 (MQ=255)
gTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACtt > 2:190336/1‑90 (MQ=255)
ggTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACttgtt > 1:174441/1‑90 (MQ=255)
ggTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACttgtt > 2:331403/1‑90 (MQ=255)
ggTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACttgtt > 2:23162/1‑90 (MQ=255)
ggTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACttgtt > 1:337739/1‑90 (MQ=255)
ggTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACttgtt > 1:182243/1‑90 (MQ=255)
aGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAg < 2:336597/90‑1 (MQ=255)
gggAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCg < 1:324959/90‑1 (MQ=255)
tCGACAAGCGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAg < 1:56576/90‑1 (MQ=255)
tCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAg < 2:72722/90‑1 (MQ=255)
cAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCta < 2:174441/90‑1 (MQ=255)
cAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCta > 2:41795/1‑90 (MQ=255)
aaaCGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCtat < 2:182243/90‑1 (MQ=255)
gCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCa > 1:211915/1‑90 (MQ=255)
|
CTTCGCTGGTACTGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAAACACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCA > NZ_CP009273/2554035‑2554194
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ 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
TCGCTGGTACTGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAAACACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCGGCAGAAAGGGAGTGCAACGA > NZ_CP009273/2554037‑2554220
|
TCGCTGGTACTGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATG > SRR3722076.315534/1‑100 (MQ=60)
CTGGTACTGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCT > SRR3722076.243933/1‑100 (MQ=60)
ACTGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATC < SRR3722076.198186/100‑1 (MQ=60)
CAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACT > SRR3722076.119005/1‑100 (MQ=60)
GTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTT > SRR3722076.176638/1‑100 (MQ=60)
GTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTT > SRR3722076.184569/1‑100 (MQ=60)
GTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTT > SRR3722076.342876/1‑100 (MQ=60)
GGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGC < SRR3722076.329906/100‑1 (MQ=60)
TCGACAAGCGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACC < SRR3722076.57277/100‑1 (MQ=60)
CGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCA > SRR3722076.214716/1‑100 (MQ=60)
CCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCGGCAGAAAGGGAGTGCAACGA < SRR3722076.237734/100‑1 (MQ=60)
|
TCGCTGGTACTGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAAACACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCGGCAGAAAGGGAGTGCAACGA > NZ_CP009273/2554037‑2554220
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
