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 I227 R1
|
223 |
21.3 |
1167702 |
97.0% |
1132670 |
86.4 |
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%
| 85.8
/ NA
| 27 | N169T (AAC→ACC) | BW25113_RS12740 | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (12/15); total (12/15) |
TGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAAACACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCGGCA > NZ_CP009273/2554047‑2554203
|
tGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATg > 1:29666/1‑90 (MQ=255)
ggCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGc > 2:173765/1‑90 (MQ=255)
cacaGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTc < 1:173765/90‑1 (MQ=255)
cacaGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTc > 1:248133/1‑90 (MQ=255)
caGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTg > 2:121995/1‑90 (MQ=255)
ttGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAAccac > 2:395265/1‑62 (MQ=255)
ttGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAAccac < 1:395265/62‑1 (MQ=255)
gATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAAcc < 1:95147/90‑1 (MQ=255)
tGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATC‑AAAACCACGGTTAAAAAATGCCTCGATCGGCTGGTCAACCACTTCa > 1:275908/1‑90 (MQ=255)
ggTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACttgtt > 2:298905/1‑90 (MQ=255)
ggTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACttgtt > 1:420481/1‑90 (MQ=255)
ggTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACttgtt > 2:143188/1‑90 (MQ=255)
ggggAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGc < 1:143188/90‑1 (MQ=255)
gAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAAc > 2:79353/1‑68 (MQ=255)
gAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAAc < 1:79353/68‑1 (MQ=255)
aaCAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTAc < 2:29666/90‑1 (MQ=255)
cAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTg < 1:461241/90‑1 (MQ=255)
cAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTg > 1:365046/1‑90 (MQ=255)
tCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAg < 2:167909/90‑1 (MQ=255)
tCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAg < 1:400315/90‑1 (MQ=255)
tCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAg < 2:403979/90‑1 (MQ=255)
tCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAg < 2:483505/90‑1 (MQ=255)
tCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAg < 2:528372/90‑1 (MQ=255)
gACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGc > 1:173650/1‑90 (MQ=255)
cAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCta < 2:17693/90‑1 (MQ=255)
cTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCg < 1:45966/90‑1 (MQ=255)
cTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCg < 2:211886/90‑1 (MQ=255)
cTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCg < 1:281439/90‑1 (MQ=255)
tCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCGGCa > 2:275089/1‑90 (MQ=255)
|
TGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAAACACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCGGCA > NZ_CP009273/2554047‑2554203
|
| 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
GTGCTCTTTGTTACTTCGCTGGTACTGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAAACACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCGGCAGAAAGGG > NZ_CP009273/2554022‑2554210
|
GTGCTCTTTGTTACTTCGCTGGTACTGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAAC < SRR3722111.98169/100‑1 (MQ=60)
gatgtgtataagagacagAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAA < SRR3722111.400996/82‑1 (MQ=60)
TCGCTGGTACTGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATG > SRR3722111.30027/1‑100 (MQ=60)
GGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTC > SRR3722111.251054/1‑100 (MQ=60)
CACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCA < SRR3722111.175931/100‑1 (MQ=60)
GTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATC‑AAAACCACGGTTAAAAAATGCCTCGATCGGCTGGTCAACCACTTCA > SRR3722111.279342/1‑100 (MQ=60)
tataagagacaGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAAC < SRR3722111.80320/89‑1 (MQ=60)
GATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACT < SRR3722111.96326/100‑1 (MQ=60)
GTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTT > SRR3722111.426696/1‑100 (MQ=60)
GGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTG > SRR3722111.370164/1‑100 (MQ=60)
GGGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGG < SRR3722111.144990/100‑1 (MQ=60)
GGGAACAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGC > SRR3722111.175815/1‑100 (MQ=60)
CAATCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATAT < SRR3722111.468260/100‑1 (MQ=60)
TCGACAAACGAGCCAGGCTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACC < SRR3722111.406148/100‑1 (MQ=60)
CTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCGGCAGAAAGGG < SRR3722111.284981/100‑1 (MQ=60)
CTATCAAAAACCACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCGGCAGAAAGGG < SRR3722111.46533/100‑1 (MQ=60)
|
GTGCTCTTTGTTACTTCGCTGGTACTGGCAAAAACTCACAGTTGGGATGGTGCAGGGTTGGTAGGGGAACAATCGACAAACGAGCCAGGCTATCAAAAAACACGGTTAAAAAATGCCTCGATCGTCTGGTCAACCACTTCAAACTTGTTGAGCGTACTGAAGGCTATATACCAGGATCGGCAGAAAGGG > NZ_CP009273/2554022‑2554210
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
