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 I177 R1
|
141 |
27.5 |
996908 |
97.7% |
973979 |
124.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
525,225 |
A→G |
pseudogene (248/366 nt) |
ylbG ← |
helix‑turn‑helix domain‑containing protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 525,225 | 0 | A | G | 100.0%
| 77.3
/ NA
| 22 | pseudogene (248/366 nt) | ylbG | helix‑turn‑helix domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (13/9); total (13/9) |
GTTCAGTATCGTCTTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGAAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGTAACGAT > NZ_CP009273/525099‑525354
|
gTTCAGTATCGTCTTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCg < 2:468673/138‑1 (MQ=255)
ttCAGTATCGTCTTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGt > 1:76419/1‑138 (MQ=255)
tCGTCTTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATcaaca < 1:277520/139‑1 (MQ=255)
gAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTa < 1:108529/139‑1 (MQ=255)
aCCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGtt > 1:230569/1‑139 (MQ=255)
agacagaACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCtt < 2:262586/139‑1 (MQ=255)
cGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCaacaac > 1:400432/1‑98 (MQ=255)
cGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCaacaac < 2:400432/98‑1 (MQ=255)
acTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCgcgg > 1:350119/1‑139 (MQ=255)
acTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCgcgg > 1:111543/1‑139 (MQ=255)
cccccTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGCCTACGATTAATCTg < 2:301895/139‑1 (MQ=255)
cGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCacac > 1:393864/1‑139 (MQ=255)
gCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCtt > 1:238984/1‑91 (MQ=255)
gCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCtt < 2:238984/91‑1 (MQ=255)
gCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGAc < 2:414402/137‑1 (MQ=255)
gCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGAc > 1:40803/1‑137 (MQ=255)
aCCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGt < 2:111543/137‑1 (MQ=255)
gtgtCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGTAACGAt > 2:183562/1‑138 (MQ=255)
gtgtCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGTAACGAt > 2:112985/1‑138 (MQ=255)
gtgtCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGTAACGAt > 1:497134/1‑138 (MQ=255)
gtgtCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGTAACGAt > 2:394295/1‑138 (MQ=255)
gtgtCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGTAACGAt > 1:421727/1‑138 (MQ=255)
|
GTTCAGTATCGTCTTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGAAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGTAACGAT > NZ_CP009273/525099‑525354
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ 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
GATAAAATTTGTTCAGTATCGTCTTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGAAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGTAACGATA > NZ_CP009273/525089‑525355
|
GATAAAATTTGTTCAGTATCGTCTTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTA > SRR3722131.77266/1‑150 (MQ=60)
ATCGTCTTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTC < SRR3722131.280734/151‑1 (MQ=60)
GTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTC > SRR3722131.233300/1‑151 (MQ=60)
GGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAG < SRR3722131.109717/151‑1 (MQ=60)
ACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGctgtctcttatacacatctccgagcccacg > SRR3722131.404786/1‑120 (MQ=60)
GAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGC > SRR3722131.112787/1‑151 (MQ=60)
GAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGC > SRR3722131.354031/1‑151 (MQ=60)
CCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACC > SRR3722131.398186/1‑151 (MQ=60)
CTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCtgtctcttatacacatctccgagcccacgagaccgt > SRR3722131.241811/1‑114 (MQ=60)
GCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACC > SRR3722131.41224/1‑149 (MQ=60)
GTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGTAACGATA > SRR3722131.426281/1‑150 (MQ=60)
GTGCTGACCATGTGTCGGGGAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGTAACGATA > SRR3722131.502434/1‑150 (MQ=60)
|
GATAAAATTTGTTCAGTATCGTCTTTTGAGATTCTCAAGGTTATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAAACCCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGAAAGCGACGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTCAGCGACCAGTTCGCGGTAACGATA > NZ_CP009273/525089‑525355
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
