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 I208 R1
|
222 |
13.1 |
731276 |
96.6% |
706412 |
85.9 |
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%
| 74.6
/ NA
| 21 | N169T (AAC→ACC) | BW25113_RS12740 | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (13/8); total (13/8) |
CTTCGCTGGTACTGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAAACACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCG > NZ_CP009273/2554035‑2554200
|
cTTCGCTGGTACTGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAAccac < 2:232381/90‑1 (MQ=255)
tGGTACTGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTaa > 1:152933/1‑90 (MQ=255)
tGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATg > 1:161660/1‑90 (MQ=255)
cacaGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTc < 2:231410/90‑1 (MQ=255)
cacaGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTc > 1:79275/1‑90 (MQ=255)
gATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAAcc < 2:89186/90‑1 (MQ=255)
gATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAAcc < 2:266839/90‑1 (MQ=255)
gggTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGGTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAAc > 2:28951/1‑90 (MQ=255)
ggTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACttgtt > 1:321609/1‑90 (MQ=255)
ggTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACttgtt > 2:199424/1‑90 (MQ=255)
ggTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACttgtt > 1:152994/1‑90 (MQ=255)
ggTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACttgtt > 2:306992/1‑90 (MQ=255)
ggTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACttgtt > 2:79076/1‑90 (MQ=255)
ggTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACttgtt > 1:118824/1‑90 (MQ=255)
aGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAg < 1:238125/90‑1 (MQ=255)
gAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTa > 2:152239/1‑90 (MQ=255)
aaTCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGa > 1:228668/1‑90 (MQ=255)
aTCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGaa < 1:199424/90‑1 (MQ=255)
cAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCta < 1:360135/90‑1 (MQ=255)
cAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCta < 2:228668/90‑1 (MQ=255)
gAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATAc > 2:166447/1‑90 (MQ=255)
cTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCg < 1:79076/90‑1 (MQ=255)
|
CTTCGCTGGTACTGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAAACACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCG > NZ_CP009273/2554035‑2554200
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ 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
GTGCTCTTTGTTACTTCGCTGGTACTGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAAACACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCGGCAGAAAGGGAG > NZ_CP009273/2554022‑2554212
|
GTGCTCTTTGTTACTTCGCTGGTACTGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAAC < SRR3722090.295315/100‑1 (MQ=60)
TGCTCTTTGTTACTTCGCTGGTACTGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACC < SRR3722090.238954/100‑1 (MQ=60)
GTTACTTCGCTGGTACTGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAA > SRR3722090.154493/1‑100 (MQ=60)
TCGCTGGTACTGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATG > SRR3722090.163290/1‑100 (MQ=60)
GGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTC > SRR3722090.80151/1‑100 (MQ=60)
GTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTT > SRR3722090.120087/1‑100 (MQ=60)
GTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTT > SRR3722090.154554/1‑100 (MQ=60)
GTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTT > SRR3722090.325783/1‑100 (MQ=60)
GTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGA > SRR3722090.231302/1‑100 (MQ=60)
AGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAG < SRR3722090.240956/100‑1 (MQ=60)
ATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATAC < SRR3722090.201620/100‑1 (MQ=60)
CAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGA < SRR3722090.364833/100‑1 (MQ=60)
CTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCGGCAGAAAGGG < SRR3722090.79948/100‑1 (MQ=60)
ATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCGGCAGAAAGGGAG > SRR3722090.329197/1‑100 (MQ=60)
|
GTGCTCTTTGTTACTTCGCTGGTACTGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAAACACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCGGCAGAAAGGGAG > NZ_CP009273/2554022‑2554212
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
