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 I229 R1
|
214 |
17.4 |
943020 |
97.5% |
919444 |
87.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,834,360 |
G→C |
A247G (GCG→GGG) |
nepI ← |
purine ribonucleoside efflux pump NepI |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,834,360 | 0 | G | C | 100.0%
| 56.1
/ NA
| 19 | A247G (GCG→GGG) | nepI | purine ribonucleoside efflux pump NepI |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base C (7/12); total (7/12) |
AGAATGAACGACGAAAGCGACGTACCAATAAAGCTGGCGATACCAAAACTCAACAGCACCAGCGTTAAGCCATCCACGCCGAATCCCGCCAGGTTCATATACACCGGGCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGCCATC > NZ_CP009273/3834273‑3834446
|
aGAATGAACAACGAAAGCGACGTACCAATAAAGCTGGCGACACCAAAACTCAACAGCACCAGCGTTAAGCCATCCACGCCGAATcccccc < 2:210459/90‑1 (MQ=255)
tGAACGACGAAAGCGACGTACCAATAAAGCTGGCGATACCAAAACTCAACAGCACCAGCGTTAAGCCATCCACGCCGAATCCCCCCAGGt < 1:358066/90‑1 (MQ=255)
tGAACGACGAAAGCGACGTACCAATAAAGCTGGCGATACCAAAACTCAACAGCACCAGCGTTAAGCCATCCACGCCGAATCCCCCCAGGt < 1:398002/90‑1 (MQ=255)
tGAACGACGAAAGCGACGTACCAATAAAGCTGGCGATACCAAAACTCAACAGCACCAGCGTTAAGCCATCCACGCCGAATCCCCCCAGGt < 1:417612/90‑1 (MQ=255)
tGAACGACGAAAGCGACGTACCAATAAAGCTGGCGATACCAAAACTCAACAGCACCAGCGTTAAGCCATCCACGCCGAATCCCCCCAGGt < 2:206052/90‑1 (MQ=255)
tGAACGACGAAAGCGACGTACCAATAAAGCTGGCGATACCAAAACTCAACAGCACCAGCGTTAAGCCATCCACGCCGAATCCCCCCAGGt < 2:124572/90‑1 (MQ=255)
acgaAAGCGACGTACCAATAAAGCTGGCGATACCAAAACTCAACAGCACCAGCGTTAAGCCATCCACGCCGAATCCCCCCAGGTTCatat < 1:265120/90‑1 (MQ=255)
aGCGACGTACCAATAAAGCTGGCGATACCAAAACTCAACAGCACCAGCGTTAAGCCATCCACGCCGAATCCCCCCAGGTTCATATACAcc < 2:254383/90‑1 (MQ=255)
gACGTACCAATAAAGCTGGCGATACCAAAACTCAACAGCACCAGCGTTAAGCCATCCACGCCGAATCCCCCCAGGTTCATATACACCggg < 1:169832/90‑1 (MQ=255)
tGGCGATACCAAAACTCAACAGCACCAGCGTTAAGCCATCCACGCCGAATCCCCCCAGGTTCATATACACCGGGCGAATATACGTgaaga > 1:116664/1‑90 (MQ=255)
gCGATACCAAAACTCAACAGCACCAGCGTTAAGCCATCCACGCCGAATCCCCCCAGGTTCATATACACCGGGCGAATATACGTGAAGaaa > 2:52452/1‑90 (MQ=255)
cAGCACCAGCGTTAAGCCATCCACGCCGAATCCCCCCAGGTTCATATACACCGGGCGAATATACGTGAAGAAAGCAAACTGCCCGGCGaa < 2:81587/90‑1 (MQ=255)
gCACCAGCGTTAAGCCATCCACGCCGAATCCCCCCAGGTTCATATACACCGGGCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAg > 2:205669/1‑90 (MQ=255)
gCACCAGCGTTAAGCCATCCACGCCGAATCCCCCCAGGTTCATATACACCGGGCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAg > 1:284391/1‑90 (MQ=255)
cATCCACGCCGAATCCCCCCAGGTTCATATACACCGGGCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGa > 2:404645/1‑90 (MQ=255)
aTCCACGCCGAATCCCCCCAGGTTCATATACACCGGGCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCggt > 1:56967/1‑88 (MQ=255)
aCGCCGAATCCCCCCAGGTTCATATACACCGGGCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGatcatc < 1:404645/90‑1 (MQ=255)
cGAATCCCCCCAGGTTCATATACACCGGGCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTg < 2:94803/90‑1 (MQ=255)
cGAATCCCCCCAGGTTCATATACACCGGGCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTg < 1:5160/90‑1 (MQ=255)
aaTCCCCCCAGGTTCATATACACCGGGCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGcc > 1:468678/1‑90 (MQ=255)
ccccccAGGTTCATATACACCGGGCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGCCATc < 1:23632/90‑1 (MQ=255)
|
AGAATGAACGACGAAAGCGACGTACCAATAAAGCTGGCGATACCAAAACTCAACAGCACCAGCGTTAAGCCATCCACGCCGAATCCCGCCAGGTTCATATACACCGGGCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGCCATC > NZ_CP009273/3834273‑3834446
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 30 ≤ 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
GTTTAAGAATGAACGACGAAAGCGACGTACCAATAAAGCTGGCGATACCAAAACTCAACAGCACCAGCGTTAAGCCATCCACGCCGAATCCCGCCAGGTTCATATACACCGGGCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGCCATCACACCCGGACG > NZ_CP009273/3834268‑3834457
|
GTTTAAGAATGAACGACGAAAGCGACGTACCAATAAAGCTGGCGATACCAAAACTCAACAGCACCAGCGTTAAGCCATCCACGCCGAATCCCCCCAGGTT < SRR3722113.467804/100‑1 (MQ=60)
TGAACGACGAAAGCGACGTACCAATAAAGCTGGCGATACCAAAACTCAACAGCACCAGCGTTAAGCCATCCACGCCGAATCCCCCCAGGTTCATATACAC < SRR3722113.361736/100‑1 (MQ=60)
TGAACGACGAAAGCGACGTACCAATAAAGCTGGCGATACCAAAACTCAACAGCACCAGCGTTAAGCCATCCACGCCGAATCCCCCCAGGTTCATATACAC < SRR3722113.402169/100‑1 (MQ=60)
TGAACGACGAAAGCGACGTACCAATAAAGCTGGCGATACCAAAACTCAACAGCACCAGCGTTAAGCCATCCACGCCGAATCCCCCCAGGTTCATATACAC < SRR3722113.422023/100‑1 (MQ=60)
ACGAAAGCGACGTACCAATAAAGCTGGCGATACCAAAACTCAACAGCACCAGCGTTAAGCCATCCACGCCGAATCCCCCCAGGTTCATATACACCGGGCG < SRR3722113.267457/100‑1 (MQ=60)
GACGTACCAATAAAGCTGGCGATACCAAAACTCAACAGCACCAGCGTTAAGCCATCCACGCCGAATCCCCCCAGGTTCATATACACCGGGCGAATATACG < SRR3722113.171203/100‑1 (MQ=60)
CCAATAAAGCTGGCGATACCAAAACTCAACAGCACCAGCGTTAAGCCATCCACGCCGAATCCCCCCAGGTTCATATACACCGGGCGAATATACGTGAAGA > SRR3722113.117669/1‑100 (MQ=60)
AAACTCAACAGCACCAGCGTTAAGCCATCCACGCCGAATCCCCCCAGGTTCATATACACCGGGCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAG > SRR3722113.286957/1‑100 (MQ=60)
GCGTTAAGCCATCCACGCCGAATCCCCCCAGGTTCATATACACCGGGCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGGT > SRR3722113.57457/1‑100 (MQ=60)
ATCCACGCCGAATCCCCCCAGGTTCATATACACCGGGCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGCC > SRR3722113.473644/1‑100 (MQ=60)
ACGCCGAATCCCCCCAGGTTCATATACACCGGGCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGCCATCA < SRR3722113.408886/100‑1 (MQ=60)
CGAATCCCCCCAGGTTCATATACACCGGGCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGCCATCACACC < SRR3722113.5219/100‑1 (MQ=60)
CCCCCCAGGTTCATATACACCGGGCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGCCATCACACCCGGAC < SRR3722113.23833/100‑1 (MQ=60)
CCCCCAGGTTCATATACACCGGGCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGCCATCACACCCGGACG > SRR3722113.262605/1‑100 (MQ=60)
|
GTTTAAGAATGAACGACGAAAGCGACGTACCAATAAAGCTGGCGATACCAAAACTCAACAGCACCAGCGTTAAGCCATCCACGCCGAATCCCGCCAGGTTCATATACACCGGGCGAATATACGTGAAGAAAGCAAACTGCCCGGCGAAAGACATGAAGATGGCGATCATCCCTGCCATCACACCCGGACG > NZ_CP009273/3834268‑3834457
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
