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 F3 I95 R1
|
196 |
14.2 |
808436 |
96.0% |
776098 |
85.4 |
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%
| 45.0
/ NA
| 15 | intergenic (‑43/+62) | celF/chbR | 6‑phospho‑beta‑glucosidase/transcriptional regulator ChbR |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (8/7); total (8/7) |
GCTGCTCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAA > NZ_CP009273/1812713‑1812882
|
gctgctCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑cc < 1:85051/90‑1 (MQ=255)
ctgctCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑ccc < 1:328089/90‑1 (MQ=255)
acgacTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCa < 2:382024/90‑1 (MQ=255)
ttttAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAAc < 1:201103/90‑1 (MQ=255)
aTTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGAc < 2:131770/90‑1 (MQ=255)
tAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAAt < 2:52439/90‑1 (MQ=255)
tctcCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGCCa > 1:96238/1‑90 (MQ=255)
ctcCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAg < 1:14632/90‑1 (MQ=255)
cTTCAGTACAGAATACTCATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAg < 1:173782/70‑1 (MQ=255)
cTTCAGTACAGAATACTCATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAg > 2:173782/1‑70 (MQ=255)
cTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATaa < 2:30513/77‑1 (MQ=255)
cTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATaa > 1:30513/1‑77 (MQ=255)
gATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTaa > 2:298/1‑90 (MQ=255)
gATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTaa > 1:193138/1‑90 (MQ=255)
atCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAAtt > 1:5929/1‑90 (MQ=255)
atCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAAtt > 2:396936/1‑90 (MQ=255)
atatCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCaa > 2:83330/1‑90 (MQ=255)
|
GCTGCTCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAA > NZ_CP009273/1812713‑1812882
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 33 ≤ 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
GCTGCTCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATT > NZ_CP009273/1812713‑1812875
|
GCTGCTCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCCCCGGAC < SRR3722235.86046/100‑1 (MQ=60)
CTGCTCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCCCCGGACA < SRR3722235.332765/100‑1 (MQ=60)
TTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATA < SRR3722235.203561/100‑1 (MQ=60)
taagagacagTAATTTCTCCCTTCAGTACAGAATACTCATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAAT < SRR3722235.175778/90‑1 (MQ=60)
GCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGCCA > SRR3722235.97365/1‑100 (MQ=60)
tcttgtctcgtgggctcggagatgtgtataagagacagtatctgcCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTAT < SRR3722235.109432/55‑1 (MQ=60)
CTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGAC < SRR3722235.14799/100‑1 (MQ=60)
GTACAGAATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGctg > SRR3722235.30856/1‑97 (MQ=60)
ACAGAATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAA > SRR3722235.195456/1‑100 (MQ=60)
GAATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATT > SRR3722235.5996/1‑100 (MQ=60)
|
GCTGCTCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATT > NZ_CP009273/1812713‑1812875
|
| 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: ‑ |
