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 I179 R1
|
182 |
40.3 |
1547118 |
96.8% |
1497610 |
120.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,060,660 |
T→C |
L390P (CTC→CCC) |
yccE → |
YccE family protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,060,660 | 0 | T | C | 100.0%
| 62.2
/ NA
| 19 | L390P (CTC→CCC) | yccE | YccE family protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (12/7); total (12/7) |
CTCATTATTTATTGTTAATAGTAATGTGGCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCTCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCGTTATGCAATTTAATGGCAAAGGCATATGCTAAAAACCATTGTTATTAGTCTCACACTT > NZ_CP009273/1060538‑1060793
|
cTCATTATTTATTGTTAATAGTAATGTGGCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACttttt > 1:485651/1‑139 (MQ=255)
ttatttatTGTTAATAGTAATGTGGCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTc < 2:470881/139‑1 (MQ=255)
atttattGTTAATAGTAATGTGGCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGTAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAg > 2:611679/1‑139 (MQ=255)
attGTTAATAGTAATGTGGCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTAccccc < 2:590390/115‑1 (MQ=255)
attGTTAATAGTAATGTGGCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTAccccc > 1:590390/1‑115 (MQ=255)
tgtgGCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACaa > 1:462895/1‑138 (MQ=255)
gCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAg > 2:363300/1‑138 (MQ=255)
cATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAgg > 1:30228/1‑138 (MQ=255)
cTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAaatgaatg < 1:450609/137‑1 (MQ=255)
ttCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTaaa < 1:611679/138‑1 (MQ=255)
gAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTc > 2:263168/1‑76 (MQ=255)
gAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTc < 1:263168/76‑1 (MQ=255)
ttATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCGTTATGCAATTTAATGGCAAAGGCat < 1:114417/139‑1 (MQ=255)
tttAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCGTTATGCAATTTAATGGCAAAGGCATATg > 2:660764/1‑139 (MQ=255)
cacTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCt < 1:491635/46‑1 (MQ=255)
cacTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCt > 2:491635/1‑46 (MQ=255)
aTCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCGTTATGCAATTTAATGGCAAAGGCATATGCTAAAAACCATTGttat > 2:501529/1‑139 (MQ=255)
tATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCGTTATg < 2:68814/94‑1 (MQ=255)
tATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCGTTATg > 1:68814/1‑94 (MQ=255)
tATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCGTTATGCAATTTAATGGCAAAGGCATATGCTAAAAACCATTGTTATTAGtc > 2:662133/1‑139 (MQ=255)
ttACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCGTTATGCAATTTAATGGCAAAGGCATATGCTAAAAACCATTGTTATTAGTCTCACACtt > 1:333012/1‑139 (MQ=255)
|
CTCATTATTTATTGTTAATAGTAATGTGGCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCTCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCGTTATGCAATTTAATGGCAAAGGCATATGCTAAAAACCATTGTTATTAGTCTCACACTT > NZ_CP009273/1060538‑1060793
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ 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
GATAGCATTTGCTCATTATTTATTGTTAATAGTAATGTGGCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCTCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCGTTATGCAATTTAATGGCAAAGGCATATGCTAAAAACCATTGTTATTAGTCTCACACTTT > NZ_CP009273/1060527‑1060794
|
GATAGCATTTGCTCATTATTTATTGTTAATAGTAATGTGGCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTG > SRR3722133.492207/1‑151 (MQ=60)
GCTCATTATTTATTGTTAATAGTAATGTGGCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTctgtctcttatac > SRR3722133.598189/1‑137 (MQ=60)
gtatttttttttttttcaagcagaagacggcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAA < SRR3722133.498272/68‑1 (MQ=60)
gcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAG < SRR3722133.266760/98‑1 (MQ=60)
GTTAATAGTAATGTGGCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAAT > SRR3722133.469178/1‑150 (MQ=60)
TAGTAATGTGGCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGA > SRR3722133.30621/1‑150 (MQ=60)
CCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGAC < SRR3722133.456734/149‑1 (MQ=60)
TTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCGTTATGCAA < SRR3722133.619752/150‑1 (MQ=60)
GTTATTTAATGAACACTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCGTTATGCAATTTAATGGCAAAGGCATATGCTAAAAAC < SRR3722133.115945/151‑1 (MQ=60)
CTGGCAATCATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCGTTATGCAATTTAATGGCtgtctcttatacacatctccgagcccacgagacc > SRR3722133.69673/1‑117 (MQ=60)
CATTATGACGTTTACCCCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCGTTATGCAATTTAATGGCAAAGGCATATGCTAAAAACCATTGTTATTAGTCTCACACTTT > SRR3722133.337695/1‑151 (MQ=60)
|
GATAGCATTTGCTCATTATTTATTGTTAATAGTAATGTGGCATCAATCTCCTTGGGGAATGAATCCTTTTCAACAGATGAAGATCTTGAGTATGGTTATTTAATGAACACTGGCAATCATTATGACGTTTACCTCCCTCCTGAACTTTTTGCTCAGGCTTACAAGTTAAACAATAAGGAAATGAATGCGCAACTCGACTATTTAAATCGTTATGCAATTTAATGGCAAAGGCATATGCTAAAAACCATTGTTATTAGTCTCACACTTT > NZ_CP009273/1060527‑1060794
|
| 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: ‑ |
