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 |
|
A2 F5 I178 R1
|
167 |
28.0 |
1137820 |
95.3% |
1084342 |
115.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
441,095 |
T→C |
Y343C (TAC→TGC) |
yajR ← |
MFS transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 441,095 | 0 | T | C | 100.0%
| 89.9
/ NA
| 24 | Y343C (TAC→TGC) | yajR | MFS transporter |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (12/12); total (12/12) |
GGTACTGGCGACTGTCAGCCACACTGCGGCCAGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGTAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAAAGCTGCACGCCGACCACCA > NZ_CP009273/440962‑441209
|
ggTACTGGCGACTGTCAGCCACACTGCGGCCAGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAaca > 1:60348/1‑139 (MQ=255)
cTGCCGACTCTCACCCACCCTCCGGCCATCATTGCGCCAGCGAAAAATACCCCCTGCCCGCCAACCATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACAccc < 2:382815/138‑1 (MQ=255)
gACTGTCAGCCACACTGCGGCCAGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGcc > 1:88278/1‑139 (MQ=255)
aCTTTCAGCCCCCCTGCGGCCAGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCg < 2:88278/139‑1 (MQ=255)
tGTCAGCCACACTGCGGCCAGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTa > 1:448201/1‑139 (MQ=255)
gCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACTCCAAGAAACTGGCTGGTGGAGCAAACACCCAt < 1:492577/101‑1 (MQ=255)
gCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCAt > 2:492577/1‑101 (MQ=255)
cTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCagg < 2:448201/139‑1 (MQ=255)
tCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCtt > 1:33442/1‑139 (MQ=255)
tCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCtt > 1:249/1‑139 (MQ=255)
tCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCtt > 1:276620/1‑139 (MQ=255)
gCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCaaa > 1:290529/1‑139 (MQ=255)
ccGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCaaa < 2:60348/138‑1 (MQ=255)
cGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGa < 1:271238/108‑1 (MQ=255)
cGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGa > 2:271238/1‑108 (MQ=255)
aTCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACg < 1:451765/139‑1 (MQ=255)
cacccgccCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCca < 2:26692/136‑1 (MQ=255)
gccgccCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCcac > 1:334327/1‑138 (MQ=255)
cGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCAt < 1:263707/46‑1 (MQ=255)
cGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCAt > 2:263707/1‑46 (MQ=255)
tCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAAAGCTGCACGCCGac < 2:276620/139‑1 (MQ=255)
acgccaAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAAAGCTGCACGCCGAccacca < 1:464812/139‑1 (MQ=255)
gctggTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTgg < 1:164658/45‑1 (MQ=255)
gctggTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTgg > 2:164658/1‑45 (MQ=255)
|
GGTACTGGCGACTGTCAGCCACACTGCGGCCAGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGTAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAAAGCTGCACGCCGACCACCA > NZ_CP009273/440962‑441209
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CGGCGGTTCTTTCATGGTACTGGCGACTGTCAGCCACACTGCGGCCAGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGTAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAAAGCTGCACGCCGACCACCAGTTGCCAGAAC > NZ_CP009273/440947‑441220
|
ccggtcgcgtgggctcggagatgtgtataagagacagACTGCGGCCAGCATTGCGCCAGCGAGAAATCCCCCCTGCCCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAA < SRR3722132.316355/114‑1 (MQ=60)
GGTTCTTTCATGGTACTGGCGACTGTCAGCCACACTGCGGCCAGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACAC > SRR3722132.61418/1‑151 (MQ=60)
ATGGTACTGGCGACTGTCAGCCACACTGCGGCCAGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCG > SRR3722132.89917/1‑151 (MQ=60)
GTACTGGCGACTGTCAGCCACACTGCGGCCAGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTAC > SRR3722132.456269/1‑151 (MQ=60)
ggggctcggagatgtgtataagagacagGCATTGCGCCAGCGAGAAATCCCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACTCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTT < SRR3722132.501324/123‑1 (MQ=60)
gtgttattttttttttcaagcagaagacggcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTT < SRR3722132.268743/68‑1 (MQ=60)
gattaaaggtgtgtttttcaagcagaagacggcatacgatatctagtacggtctcgtgggctcggagatgtgtataagagacaGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTAC < SRR3722132.167764/68‑1 (MQ=60)
ggaaatgtgtataagaggcagtTCAAAAATGCCGTTAATCCAGCCGCCCAGCGACCCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGC < SRR3722132.276411/129‑1 (MQ=60)
CCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTC > SRR3722132.255/1‑151 (MQ=60)
CCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTC > SRR3722132.281888/1‑151 (MQ=60)
CCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTC > SRR3722132.34027/1‑151 (MQ=60)
CCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAAT > SRR3722132.296048/1‑151 (MQ=60)
CCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACA > SRR3722132.340554/1‑150 (MQ=60)
AATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAA < SRR3722132.459886/151‑1 (MQ=60)
CACGCCAAGAAACTGGCTGGTGGAGCAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAAAGCTGCACGCCGACCACCAGTTGCCAGAAC < SRR3722132.473133/151‑1 (MQ=60)
|
CGGCGGTTCTTTCATGGTACTGGCGACTGTCAGCCACACTGCGGCCAGCATTGCGCCAGCGAGAAATACCCCCTGACCGTCAAACATGCCGTTAATCCAGCCGCCCAGCGAACCGCCAATCGCCACGCCAAGAAACTGGCTGGTGGAGTAAACACCCATCGCCGTACCTTTGTAACCTGCTGGCGACTCTTTACTGATAAGTGAGGGCAGGAGGGCTTCCATCAAATTAAACGCCACAAAGAAAAGCTGCACGCCGACCACCAGTTGCCAGAAC > NZ_CP009273/440947‑441220
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
