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 I197 R1
|
189 |
12.7 |
697584 |
97.1% |
677354 |
86.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,812,807 |
(C)7→8 |
intergenic (‑50/+55) |
celF ← / ← chbR |
6‑phospho‑beta‑glucosidase/transcriptional regulator ChbR |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,812,800 | 1 | . | C | 100.0%
| 24.3
/ NA
| 9 | intergenic (‑43/+62) | celF/chbR | 6‑phospho‑beta‑glucosidase/transcriptional regulator ChbR |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (5/4); total (5/4) |
CATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAAT > NZ_CP009273/1812755‑1812883
|
cATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGa < 1:194222/90‑1 (MQ=255)
ttCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTc > 2:73516/1‑90 (MQ=255)
gAATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTAc > 2:194340/1‑90 (MQ=255)
aaTACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACt < 1:194340/90‑1 (MQ=255)
tACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGa > 1:262644/1‑90 (MQ=255)
cTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGtat < 1:336560/75‑1 (MQ=255)
cTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGtat > 2:336560/1‑75 (MQ=255)
cTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCa > 2:45420/1‑90 (MQ=255)
tatCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAAt < 1:73516/90‑1 (MQ=255)
|
CATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAAT > NZ_CP009273/1812755‑1812883
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GTATAGCTGCTCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAATTTCTTACGAT > NZ_CP009273/1812708‑1812893
|
GTATAGCTGCCCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑CCCCCCC < SRR3722076.54117/100‑1 (MQ=60)
CATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGT < SRR3722076.196713/100‑1 (MQ=60)
gacagGTACAGAATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTAC < SRR3722076.341678/95‑1 (MQ=60)
CAGTACAGAATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGA > SRR3722076.266456/1‑100 (MQ=60)
AATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTC < SRR3722076.196831/100‑1 (MQ=60)
TATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAATTTCTTACGAT < SRR3722076.74427/100‑1 (MQ=60)
|
GTATAGCTGCTCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAATTTCTTACGAT > NZ_CP009273/1812708‑1812893
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
