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 F5 I102 R1
|
278 |
39.1 |
2251254 |
95.8% |
2156701 |
87.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
923,801 |
A→G |
V284A (GTC→GCC) |
cydC ← |
cysteine/glutathione ABC transporter ATP‑binding protein/permease CydC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 923,801 | 0 | A | G | 100.0%
| 167.0
/ NA
| 46 | V284A (GTC→GCC) | cydC | cysteine/glutathione ABC transporter ATP‑binding protein/permease CydC |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (23/23); total (23/23) |
CGTACGGCAGAGGCAATGACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGACAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCCACAGCATCAGGATCACCGCTAACGC > NZ_CP009273/923714‑923886
|
cgtacgGCAGAGGCAATGACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCaa > 1:712109/1‑91 (MQ=255)
cgtacgGCAGAGGCAATGACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCaa > 1:274973/1‑91 (MQ=255)
cgGCAGAGGCAATGACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAg > 2:264532/1‑91 (MQ=255)
ggCAGAGGCAATGACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAgg < 2:495934/91‑1 (MQ=255)
agagGCAATGACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCa < 2:903428/91‑1 (MQ=255)
gagGCAATGACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAAc > 2:827517/1‑84 (MQ=255)
gagGCAATGACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAAc < 1:827517/84‑1 (MQ=255)
gagGCAATGACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCaa > 1:146896/1‑91 (MQ=255)
gagGCAATGACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCaa > 2:369639/1‑91 (MQ=255)
gagGCAATGACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCaa > 2:312433/1‑91 (MQ=255)
cAATGACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTaa < 2:456240/91‑1 (MQ=255)
aaTGACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAAc < 2:548646/91‑1 (MQ=255)
aaTGACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAAc > 1:923434/1‑91 (MQ=255)
aCTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACgcgc < 2:146896/91‑1 (MQ=255)
ttGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCg < 1:441039/91‑1 (MQ=255)
ttGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCg > 1:917088/1‑91 (MQ=255)
tGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCgg > 2:138826/1‑91 (MQ=255)
ccccAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGt < 2:218303/91‑1 (MQ=255)
ccccAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGt < 1:600199/91‑1 (MQ=255)
ccccAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGt < 2:385909/91‑1 (MQ=255)
ccccAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGt > 1:313101/1‑91 (MQ=255)
aGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAg > 1:107826/1‑91 (MQ=255)
cTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTg < 1:205603/91‑1 (MQ=255)
tGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTgc > 1:204339/1‑91 (MQ=255)
tGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCa < 2:125728/91‑1 (MQ=255)
gCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCaa > 2:221520/1‑91 (MQ=255)
aCCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAAcg > 1:741606/1‑91 (MQ=255)
cccGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAAcgc < 1:828143/91‑1 (MQ=255)
cGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAAcgccg > 2:1043220/1‑91 (MQ=255)
ttACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACgccgcc > 2:488963/1‑91 (MQ=255)
cTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGa < 2:783139/91‑1 (MQ=255)
gCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCa > 2:1053704/1‑91 (MQ=255)
gCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCa < 1:322585/91‑1 (MQ=255)
ccAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCAt < 2:712109/91‑1 (MQ=255)
gTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCg > 1:864441/1‑53 (MQ=255)
gTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCg < 2:864441/53‑1 (MQ=255)
gTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCca > 2:956947/1‑91 (MQ=255)
tGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCcac < 2:489472/91‑1 (MQ=255)
tGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCcac < 1:216314/91‑1 (MQ=255)
tGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCcac < 2:714297/91‑1 (MQ=255)
tGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCcac < 1:1043220/91‑1 (MQ=255)
ttCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCCACAGc > 2:761073/1‑91 (MQ=255)
tCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGc > 1:826042/1‑80 (MQ=255)
tCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGc < 2:826042/80‑1 (MQ=255)
cgcgGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCCACAGCATCAgg > 2:333755/1‑91 (MQ=255)
ggCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCCACAGCATCAGGATc < 2:329966/91‑1 (MQ=255)
agaaggCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCCACAGCATCAGGATCACCGCTAAcgc < 1:364888/91‑1 (MQ=255)
|
CGTACGGCAGAGGCAATGACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGACAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCCACAGCATCAGGATCACCGCTAACGC > NZ_CP009273/923714‑923886
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 31 ≤ 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
GTCAGAGATACGTACGGCAGAGGCAATGACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGACAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCCACAGCATCAGGATCACCGCTAACGCGCCAATGAGCA > NZ_CP009273/923704‑923897
|
GTCAGAGATACGTACGGCAGAGGCAATGACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAA > SRR3722125.727465/1‑101 (MQ=60)
GTCAGAGATACGTACGGCAGAGGCAATGACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAA > SRR3722125.280534/1‑101 (MQ=60)
ACGTACGGCAGAGGCAATGACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAA > SRR3722125.149696/1‑101 (MQ=60)
TACGGCAGAGGCAATGACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTA < SRR3722125.845689/101‑1 (MQ=60)
CGCCAGAGGCAATGACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAAC > SRR3722125.943936/1‑101 (MQ=60)
AGGCAATGACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCG > SRR3722125.937435/1‑101 (MQ=60)
CAATGACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGT > SRR3722125.319541/1‑101 (MQ=60)
GACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAG > SRR3722125.109865/1‑101 (MQ=60)
TTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCAT < SRR3722125.450341/101‑1 (MQ=60)
CCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGC < SRR3722125.613119/101‑1 (MQ=60)
CCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGC > SRR3722125.208371/1‑101 (MQ=60)
GCGGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACG > SRR3722125.757597/1‑101 (MQ=60)
CTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGC < SRR3722125.209656/101‑1 (MQ=60)
CCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGC < SRR3722125.846328/101‑1 (MQ=60)
ACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATctgtctcttatacacatctccgagccca > SRR3722125.883514/1‑73 (MQ=60)
TGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCCACAGCC > SRR3722125.844173/1‑101 (MQ=60)
GCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCCACAGCAT < SRR3722125.329205/101‑1 (MQ=60)
TGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCCACAGCATCAGGA < SRR3722125.220581/101‑1 (MQ=60)
TGCTTCAAACGCGGCTAACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCCACAGCATCAGGA < SRR3722125.1066630/101‑1 (MQ=60)
ACGCGCAGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCCACActgtctcttatacacatctccgagcc > SRR3722125.614093/1‑75 (MQ=60)
AGAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCCACAGCATCAGGATCACCGCTAACGCGCCAATGAGC < SRR3722125.372551/101‑1 (MQ=60)
GAAGGCAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCCACAGCATCAGGATCACCGCTAACGCGCCAATGAGCA > SRR3722125.511641/1‑101 (MQ=60)
|
GTCAGAGATACGTACGGCAGAGGCAATGACTTGCCCCAGATGCTGAAATGCACCCGTTACTGGTGCCAGTGCTTCAAACGCGGCTAACGCGCAGAAGACAAACAGGGCAATTAACGCGCCGGGTTGAGCATTGCCGCCAACGCCGCCAGACGCCATCCACAGCATCAGGATCACCGCTAACGCGCCAATGAGCA > NZ_CP009273/923704‑923897
|
| 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: ‑ |
