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 I184 R1
|
278 |
29.6 |
1166432 |
97.3% |
1134938 |
124.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
834,220 |
A→G |
D148D (GAT→GAC) |
ybiX ← |
PKHD‑type hydroxylase YbiX |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 834,220 | 0 | A | G | 100.0%
| 90.3
/ NA
| 27 | D148D (GAT→GAC) | ybiX | PKHD‑type hydroxylase YbiX |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (16/11); total (16/11) |
ATGGCGCGCTTTTTATCATCGCGGATCATCGACTGGATCCACATAAATGATGCCACTCGTACGCCGCGGGTTACGGGTGTCACGCAATGCAGGCTGCTGGAGGGATACAACACGAGATCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGGTGTCATTAACGACCAGTTCGCCGCCGTCGTAGCTTTGTGGATCGCTTAAAAACAGCGTGGCAGAAAGGTCAGTACGCATCCAGCCGTTTTGTGGA > NZ_CP009273/834104‑834352
|
aTGGCGCGCTTTTTATCATCGCGGATCATCGACTGGATCCACATAAATGATGCCACTCGTACGCCGCGGGTTACGGGTGTCACGCAATGCAGGCTGCTGGAGGGATACAACACGAGGTCGCCTGCCGGGAGTTTTAccc > 1:355017/1‑139 (MQ=255)
tttttATCATCGCGGATCATCGACTGGATCCACATAAATGATGCCACTCGTACGCCGCGGGTTACGGGTGTCACGCAATGCAGGCTGCTGGAGGGATACAACACGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTc > 1:167482/1‑139 (MQ=255)
ttATCATCGCGGATCATCGACTGGATCCACATAAATGATGCCACTCGTACGCCGCGGGTTACGGGTGTCACGCAATGCAGGCTGCTGGAGGGATACAACACGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTCCg < 2:483019/138‑1 (MQ=255)
cgcgGATCATCGACTGGATCCACATAAATGATGCCACTCGTACGCCGCGGGTTACGGGTGTCACGCAATGCAGGCTGCTGGAGGGATACAACACGAGGTCGCCTGCCGGGAGTTTTAc > 2:424380/1‑118 (MQ=255)
cgcgGATCATCGACTGGATCCACATAAATGATGCCACTCGTACGCCGCGGGTTACGGGTGTCACGCAATGCAGGCTGCTGGAGGGATACAACACGAGGTCGCCTGCCGGGAGTTTTAc < 1:424380/118‑1 (MQ=255)
cgcgGATCATCGACTGGATCCACATAAATGATGCCACTCGTACGCCGCGGGTTACGGGTGTCACGCAATGCAGGCTGCTGGAGGGATACAACACGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGgtgt > 2:117568/1‑138 (MQ=255)
atgatgCCACTCGTACGCCGCGGGTTACGGGTGTCACGCAATGCAGGCTGCTGGAGGGATACAACACGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGGTGTCATTAACGACCAGTTCGCCGCcgtcg > 1:374534/1‑137 (MQ=255)
atgatgCCACTCGTACGCCGCGGGTTACGGGTGTCACGCAATGCAGGCTGCTGGAGGGATACAACACGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGGTGTCATTAACGACCAGTTCGCCGCCGTCGTa < 1:516493/139‑1 (MQ=255)
tgCCACTCGTACGCCGCGGGTTACGGGTGTCACGCAATGCAGGCTGCTGGAGGGATACAACACGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGGTGTCATTAACGACCAGTTCGCCGCCGTCGTAGCtt > 2:334200/1‑139 (MQ=255)
gCCACTCGTACGCCGCGGGTTACGGGTGTCACGCAATGCAGGCTGCTGGAGGGATACAACACGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGGTGTCATTAACGACCAGTTCGCCGCCGTCGTAGCttt > 2:355517/1‑139 (MQ=255)
ccACTCGTACGCCGCGGGTTACGGGTGTCACGCAATGCAGGCTGCTGGAGGGATACAACACGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGGTGTCATTAACGACCAGTTCGCCGCCGTCGTAGCTTtg > 1:59572/1‑139 (MQ=255)
cTCGTACGCCGCGGGTTACGGGTGTCACGCAATGCAGGCTGCTGGAGGGATACAACACGAGGTCGCCTGCCGGGAGTTTTACCCGAtg > 1:286104/1‑88 (MQ=255)
cTCGTACGCCGCGGGTTACGGGTGTCACGCAATGCAGGCTGCTGGAGGGATACAACACGAGGTCGCCTGCCGGGAGTTTTACCCGAtg < 2:286104/88‑1 (MQ=255)
gTACGCCGCGGGTTACGGGTGTCACGCAATGCAGGCTGCTGGAGGGATACAACACGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGGTGTCATTAACGACCAGTTCGCCGCCGTCGTAGCTTTGTGGAt < 1:334200/138‑1 (MQ=255)
gccgcGGGTTACGGGTGTCACGCAATGCAGGCTGCTGGAGGGATACAACACGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGGTGTCATTAACGACCAGTTCGCCGCCGTCGTAGCTTTGTGGATCGCtt < 2:167482/139‑1 (MQ=255)
cgGGTTACGGGTGTCACGCAATGCAGGCTGCTGGAGGGATACAACACGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGGTGTCATTAACGACCAGTTCGCCGCcgtcg > 2:94626/1‑117 (MQ=255)
cgGGTTACGGGTGTCACGCAATGCAGGCTGCTGGAGGGATACAACACGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGGTGTCATTAACGACCAGTTCGCCGCCGTCGTAGCTTTGTGGATCGCTTaaa > 2:190315/1‑138 (MQ=255)
cgGGTCACGGGTGTCACGCAATGCAGGCTGCTGGAGGGATACAACACGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGGTGTCATTAACGACCAGTTCGCCGCcgtcg < 1:94626/117‑1 (MQ=255)
tCACGCAATGCAGGCTGCTGGAGGGATACAACACGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGGTGTCATTAACGACCAGTTCGCCGCCGTCGTAGCTTTGTGGATCGCTTAAAAACAGCGTGGCAGa < 1:117568/139‑1 (MQ=255)
aTGCAGGCTGCTGGAGGGATACAACACGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGGTGTCATTAACGACCAGTTCGCCGCCGTCGTAGCTTTGTGGATCGCTTAAAAACAGCGAGGCAGAAAGGt > 2:101971/1‑137 (MQ=255)
tgGAGGGATACAACACGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGGTGTCATTAACGACCAGTTCGCCGCCGTCGTa < 2:410410/88‑1 (MQ=255)
tgGAGGGATACAACACGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGGTGTCATTAACGACCAGTTCGCCGCCGTCGTa > 1:410410/1‑88 (MQ=255)
tgGAGGGATACAACACGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGGTGTCATTAACGACCAGTTCGCCGCCGTCGTAGCTTTGTGGATCGCTTAAAAACAGCGTGGCAGAAAGGTCAGTACGCATc > 2:141085/1‑137 (MQ=255)
aTACAACACGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGGTGTCATTAACGACCAGTTCGCCGCCGTCGTAGCTTTGTGGATCGCTTAAAAACAGCGTGGCAGAAAGGTCAGTACGCATCCAGcc > 2:209675/1‑135 (MQ=255)
aTACAACACGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGGTGTCATTAACGACCAGTTCGCCGCCGTCGTAGCTTTGTGGATCGCTTAAAAACAGCGTGGCAGAAAGGTCAGTACGCATCCAGcc < 1:209675/135‑1 (MQ=255)
aTACAACACGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGGTGTCATTAACGACCAGTTCGCCGCCGTCGTAGCTTTGTGGATCGCTTAAAAACAGCGTGGCAGAAAGGTCAGTACGCATCCAGCCGttt > 1:5784/1‑139 (MQ=255)
cacGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGGTGTCATTAACGACCAGTTCGCCGCCGTCGTAGCTTTGTGGATCGCTTAAAAACAGCGTGGCAGAAAGGTCAGTACGCATCCAGCCGTTTTGTGGa < 1:538442/139‑1 (MQ=255)
|
ATGGCGCGCTTTTTATCATCGCGGATCATCGACTGGATCCACATAAATGATGCCACTCGTACGCCGCGGGTTACGGGTGTCACGCAATGCAGGCTGCTGGAGGGATACAACACGAGATCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGGTGTCATTAACGACCAGTTCGCCGCCGTCGTAGCTTTGTGGATCGCTTAAAAACAGCGTGGCAGAAAGGTCAGTACGCATCCAGCCGTTTTGTGGA > NZ_CP009273/834104‑834352
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 34 ≤ 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
AGCGACTGAATATTGTTGTCCAGTTCAAACAGCATGGCGCGCTTTTTATCATCGCGGATCATCGACTGGATCCACATAAATGATGCCACTCGTACGCCGCGGGTTACGGGTGTCACGCAATGCAGGCTGCTGGAGGGATACAACACGAGATCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGGTGTCATTAACGACCAGTTCGCCGCCGTCGTAGCTTTGTGGATCGCTTAAAAACAGCGTGGCAGAAAGGTCAGTACGCATCCAGCCGTTTTGTGGATGGCTGCGTAC > NZ_CP009273/834071‑834363
|
AGCGACTGAATATTGTTGTCCAGTTCAAACAGCATGGCGCGCTTTTTATCATCGCGGATCATCGACTGGATCCACATAAATGATGCCACTCGTACGCCGCGGGTTACGGGTGTCACGCAATGCAGGCTGCTGGAGGGATACAACACGAGGT < SRR3722139.300688/151‑1 (MQ=60)
GTTCAAACAGCATGGCGCGCTTTTTATCATCGCGGATCATCGACTGGATCCACATAAATGATGCCACTCGTACGCCGCGGGTTACGGGTGTCACGCAATGCAGGCTGCTGGAGGGATACAACACGAGGTCGCCTGCCGGGAGTTTTACCCG > SRR3722139.359308/1‑151 (MQ=60)
ataagagacaGCTTTTTATCATCGCGGATCATCGACTGGATCCACATAAATGATGCCACTCGTACGCCGCGGGTTACGGGTGTCACGCAATGCAGGCTGCTGGAGGGATACAACACGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTC < SRR3722139.429380/141‑1 (MQ=60)
GCATGGCGCGCTTTTTATCATCGCGGATCATCGACTGGATCCACATAAATGATGCCACTCGTACGCCGCGGGTTACGGGTGTCACGCAATGCAGGCTGCTGGAGGGATACAACACGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTCC > SRR3722139.169584/1‑151 (MQ=60)
GATCCACATAAATGATGCCACTCGTACGCCGCGGGTTACGGGTGTCACGCAATGCAGGCTGCTGGAGGGATACAACACGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGGTGTCATTAACGACCAGTTCGCCGCCGTCGT > SRR3722139.379019/1‑149 (MQ=60)
CATAAATGATGCCACTCGTACGCCGCGGGTTACGGGTGTCACGCAATGCAGGCTGCTGGAGGGATACAACACGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGGTGTCATTAACGACCAGTTCGCCGCCGTCGTAGCTTTGT > SRR3722139.60250/1‑151 (MQ=60)
ataagagacagCTCGTACGCCGCGGGTCACGGGTGTCACGCAATGCAGGCTGCTGGAGGGATACAACACGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGGTGTCATTAACGACCAGTTCGCCGCCGTCGTAGCTTTGTGG < SRR3722139.95748/139‑1 (MQ=60)
AAATGATGCCACTCGTACGCCGCGGGTTACGGGTGTCACGCAATGCAGGCTGCTGGAGGGATACAACACGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGGctgtctcttatacacatctccgagcccacgagaccgtact > SRR3722139.289698/1‑110 (MQ=60)
AATGATGCCACTCGTACGCCGCGGGTTACGGGTGTCACGCAATGCAGGCTGCTGGAGGGATACAACACGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGGTGTCATTAACGACCAGTTCGCCGCCGTCGTAGCTTTGTGGAT < SRR3722139.522426/151‑1 (MQ=60)
CGGACGCCGCGGGTTACGGGTGTCACGCAATGCAGGCTGCTGGAGGGATACAACACGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGGTGTCATTAACGACCAGTTCGCCGCCGTCGTAGCTTTGTGGATCGCTTAAAAAC < SRR3722139.338288/150‑1 (MQ=60)
GTCACGCAATGCAGGCTGCTGGAGGGATACAACACGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGGTGTCATTAACGACCAGTTCGCCGCCGTCGTAGCTTTGTGGATCGCTTAAAAACAGCGTGGCAGAAAGGTCAGTAC < SRR3722139.118989/151‑1 (MQ=60)
ATGCAGGCTGCTGGAGGGATACAACACGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGGTGTCATTAACGACCAGTTCGCCGCCGTCGTAGCTTTGTGGATCtgtctcttatacacatctccgagcccacgagaccgtact > SRR3722139.415258/1‑111 (MQ=60)
CTGCTGGAGGGATACAACACGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGGTGTCATTAACGACCAGTTCGCCGCCGTCGTAGCTTTGTGGATCGCTTAAAAACAGCGTGGCAGAAAGGTCAGTACGCATCCAGCCGTTTT > SRR3722139.5839/1‑151 (MQ=60)
GAGGGATACAACACGAGGGCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGGTGTCATTAACGACCAGTTCGCCGCCGTCGTAGCTTTGTGGATCGCTTAAAAACAGCGTGGCAGAAAGGTCAGTACGCATCCAGCCGTTTTGTGGAT < SRR3722139.212280/151‑1 (MQ=60)
GATACAACACGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGATGGTGTCATTAACGACCAGTTCGCCGCCGTCGTAGCTGTGTGGATCGCTTAAAAACAGCGTGGCAGAAAGGTCAGTACGCATCCAGCCGTTTTGTGGAgggcg > SRR3722139.187977/1‑146 (MQ=60)
CAACACGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGGTGTCATTAACGACCAGTTCGCCGCCGTCGTAGCTTTGTGGATCGCTTAAAAACctgtctcttatacacatctccgagcccacgagaccgtactagatctcgtat > SRR3722139.220185/1‑100 (MQ=60)
ACACGAGGTCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGGTGTCATTAACGACCAGTTCGCCGCCGTCGTAGCTTTGTGGATCGCTTAAAAACAGCGTGGCAGAAAGGTCAGTACGCATCCAGCCGTTTTGTGGATGGCTGCGTAC < SRR3722139.544618/151‑1 (MQ=60)
|
AGCGACTGAATATTGTTGTCCAGTTCAAACAGCATGGCGCGCTTTTTATCATCGCGGATCATCGACTGGATCCACATAAATGATGCCACTCGTACGCCGCGGGTTACGGGTGTCACGCAATGCAGGCTGCTGGAGGGATACAACACGAGATCGCCTGCCGGGAGTTTTACCCGATGTTGTCCGAAGGTGTCATTAACGACCAGTTCGCCGCCGTCGTAGCTTTGTGGATCGCTTAAAAACAGCGTGGCAGAAAGGTCAGTACGCATCCAGCCGTTTTGTGGATGGCTGCGTAC > NZ_CP009273/834071‑834363
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
