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 F2 I206 R1
|
206 |
23.7 |
1314362 |
96.8% |
1272302 |
86.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,269,793 |
G→C |
intergenic (+37/‑115) |
ghxP → / → yjcE |
guanine/hypoxanthine transporter GhxP/Na+/H+ antiporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,269,793 | 0 | G | C | 100.0%
| 57.2
/ NA
| 19 | intergenic (+37/‑115) | ghxP/yjcE | guanine/hypoxanthine transporter GhxP/Na+/H+ antiporter |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base C (14/5); total (14/5) |
TATCGCCGTGGCGCTGGTGACCTTCTATGCGGGTGGCTGGGCTATCTAATCTTTCATCGGATTCTGAAAACGGGTGGCAATGGCTGCCCGTTTTTATTTTCTCCGCACATTGTGTGAGCTTTTGCGATATTCTGAAAAAAATGAGAATTCAGGCATAACGT > NZ_CP009273/4269708‑4269868
|
tATCGCCGTGGCGCTGGTGACCTTCTATGCGGGTGGCTGGGCTATCTAATCTTTCATCGGATTCTGAAAACGGGTGGCAATGGCTCCCCg > 1:322957/1‑90 (MQ=255)
ccGTGGCGCTGGTGACCTTCTATGCGGGTGGCTGGGCTATCTAATCTTTCATCGGATTCTGAAAACGGGTGGCAATGGCTCCCCGttttt > 1:174118/1‑90 (MQ=255)
ccGTGGCGCTGGTGACCTTCTATGCGGGTGGCTGGGCTATCTAATCTTTCATCGGATTCTGAAAACGGGTGGCAATGGCTCCCCGttttt > 2:648109/1‑90 (MQ=255)
ccGTGGCGCTGGTGACCTTCTATGCGGGTGGCTGGGCTATCTAATCTTTCATCGGATTCTGAAAACGGGTGGCAATGGCTCCCCGttttt > 1:50455/1‑90 (MQ=255)
ccGTGGCGCTGGTGACCTTCTATGCGGGTGGCTGGGCTATCTAATCTTTCATCGGATTCTGAAAACGGGTGGCAATGGCTCCCCGttttt > 2:533043/1‑90 (MQ=255)
ccGTGGCGCTGGTGACCTTCTATGCGGGTGGCTGGGCTATCTAATCTTTCATCGGATTCTGAAAACGGGTGGCAATGGCTCCCCGttttt > 2:304847/1‑90 (MQ=255)
gTGGCGCTGGTGACCTTCTATGCGGGTGGCTGGGCTATCTAATCTTTCATCGGATTCTGAAAACGGGTGGCAATGGCTCCCCGTTTTTAt > 1:257737/1‑90 (MQ=255)
gTGACCTTCTATGCGGGTGGCTGGGCTATCTAATCTTTCATCGGATTCTGAAAACGGGTGGCAATGGCTCCCCGTTTTTATTTTCTCCGc < 2:606058/90‑1 (MQ=255)
ccTTCTATGCGGGTGGCTGGGCTATCTAATCTTTCATCGGATTCTGAAAACGGGTGGCAATGGCTCCCCGTTTTTATTTTCTCCGCACAt < 1:648109/90‑1 (MQ=255)
ccTTCTATGCGGGTGGCTGGGCTATCTAATCTTTCATCGGATTCTGAAAACGGGTGGCAATGGCTCCCCGTTTTTATTTTCTCCGCACAt < 2:354403/90‑1 (MQ=255)
gggTGGCTGGGCTATCTAATCTTTCATCGGATTCTGAAAACGGGTGGCAATGGCTCCCCGTTTTTATTTTCTCCGCACATTGTGTGAGCt > 2:525710/1‑90 (MQ=255)
ggCTATCTAATCTTTCATCGGATTCTGAAAACGGGTGGCAATGGCTCCCCGTTTTTATTTTCTCCGCACATTGTGTGAGCTTTTGCGata > 2:217433/1‑90 (MQ=255)
aTCTAATCTTTCATCGGATTCTGAAAACGGGTGGCAATGGCTCCCCGTTTTTATTTTCTCCGCACATTGTGTGAGCTTTTGCGATATTCt > 2:55388/1‑90 (MQ=255)
aTCTTTCATCGGATTCTGAAAACGGGTGGCAATGGCTCCCCGTTTTTATTTTCTCCGCACATTGTGTGAGCTTTTGCGATATTCTGaaaa < 1:267529/90‑1 (MQ=255)
tCATCGGATTCTGAAAACGGGTGGCAATGGCTCCCCGTTTTTATTTTCTCCGCACATTGTGTGAGCTTTTGCGATATTCTGAAAAAAATg > 2:476052/1‑90 (MQ=255)
tCATCGGATTCTGAAAACGGGTGGCAATGGCTCCCCGTTTTTATTTTCTCCGCACATTGTGTGAGCTTTTGCGATATTCTGAAAAAAATg > 2:495719/1‑90 (MQ=255)
tCATCGGATTCTGAAAACGGGTGGCAATGGCTCCCCGTTTTTATTTTCTCCGCACATTGTGTGAGCTTTTGCGATATTCTGAAAAAAATg > 1:535431/1‑90 (MQ=255)
gATTCTGAAAACGGGTGGCAATGGCTCCCCGTTTTTATTTTCTCCGCACATTGTGTGAGCTTTTGCGATATTCTGAAAAAAATGAGAAtt > 2:552298/1‑90 (MQ=255)
gggTGGCAATGGCTCCCCGTTTTTATTTTCTCCGCACATTGTGTGAGCTTTTGCGATATTCTGAAAAAAATGAGAATTCAGGCATAACGt < 2:557819/90‑1 (MQ=255)
|
TATCGCCGTGGCGCTGGTGACCTTCTATGCGGGTGGCTGGGCTATCTAATCTTTCATCGGATTCTGAAAACGGGTGGCAATGGCTGCCCGTTTTTATTTTCTCCGCACATTGTGTGAGCTTTTGCGATATTCTGAAAAAAATGAGAATTCAGGCATAACGT > NZ_CP009273/4269708‑4269868
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ 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
GTACGGTCGTTATCGCCGTGGCGCTGGTGACCTTCTATGCGGGTGGCTGGGCTATCTAATCTTTCATCGGATTCTGAAAACGGGTGGCAATGGCTGCCCGTTTTTATTTTCTCCGCACATTGTGTGAGCTTTTGCGATATTCTGAAAAAAATGAGAATTCAGGCATAACGTCTTTCTC > NZ_CP009273/4269698‑4269875
|
GTACGGTCGTTATCGCCGTGGCGCTGGTGACCTTCTATGCGGGTGGCTGGGCTATCTAATCTTTCATCGGATTCTGAAAACGGGTGGCAATGGCTCCCCG > SRR3722088.326261/1‑100 (MQ=60)
GTCGTTATCGCCGTGGCGCTGGTGACCTTCTATGCGGGTGGCTGGGCTATCTAATCTTTCATCGGATTCTGAAAACGGGTGGCAATGGCTCCCCGTTTTT > SRR3722088.175864/1‑100 (MQ=60)
GTCGTTATCGCCGTGGCGCTGGTGACCTTCTATGCGGGTGGCTGGGCTATCTAATCTTTCATCGGATTCTGAAAACGGGTGGCAATGGCTCCCCGTTTTT > SRR3722088.50988/1‑100 (MQ=60)
CGTTATCGCCGTGGCGCTGGTGACCTTCTATGCGGGTGGCTGGGCTATCTAATCTTTCATCGGATTCTGAAAACGGGTGGCAATGGCTCCCCGTTTTTAT > SRR3722088.260241/1‑100 (MQ=60)
CCTTCTATGCGGGTGGCTGGGCTATCTAATCTTTCATCGGATTCTGAAAACGGGTGGCAATGGCTCCCCGTTTTTATTTTCTCCGCACATTGTGTGAGCT < SRR3722088.656139/100‑1 (MQ=60)
ATCTAATCTTTCATCGGATTCTGAAAACGGGTGGCAATGGCTCCCCGTTTTTATTTTCTCCGCACATTGTGTGAGCTTTTGCGATATTCTGAAAAAAATG > SRR3722088.541935/1‑100 (MQ=60)
ATCTTTCATCGGATTCTGAAAACGGGTGGCAATGGCTCCCCGTTTTTATTTTCTCCGCACATTGTGTGAGCTTTTGCGATATTCTGAAAAAAATGAGAAT < SRR3722088.270120/100‑1 (MQ=60)
AACGGGTGGCAATGGCTCCCCGTTCTTATTTTCTCCGCACATTGTGTGAGCTTTTGCGATATTCTGAAAAAAATGAGAATTCAGGCATAACGTCTTTCTC < SRR3722088.449843/100‑1 (MQ=60)
|
GTACGGTCGTTATCGCCGTGGCGCTGGTGACCTTCTATGCGGGTGGCTGGGCTATCTAATCTTTCATCGGATTCTGAAAACGGGTGGCAATGGCTGCCCGTTTTTATTTTCTCCGCACATTGTGTGAGCTTTTGCGATATTCTGAAAAAAATGAGAATTCAGGCATAACGTCTTTCTC > NZ_CP009273/4269698‑4269875
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
