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 I122 R1
|
193 |
20.9 |
1228102 |
94.7% |
1163012 |
84.0 |
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%
| 44.7
/ NA
| 14 | intergenic (‑43/+62) | celF/chbR | 6‑phospho‑beta‑glucosidase/transcriptional regulator ChbR |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (6/8); total (6/8) |
CCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAATT > NZ_CP009273/1812719‑1812884
|
cccGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑‑cccccccc < 1:331557/90‑2 (MQ=255)
cccGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑‑cccccccc < 1:467343/90‑2 (MQ=255)
gacgacTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATcc > 1:531224/1‑90 (MQ=255)
acgacTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCa < 1:436537/90‑1 (MQ=255)
gacTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGc > 2:498332/1‑90 (MQ=255)
ttAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAg > 2:74406/1‑90 (MQ=255)
aTTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGAc < 1:171199/90‑1 (MQ=255)
aTTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGAc < 1:498332/90‑1 (MQ=255)
tttCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGt < 2:153982/90‑1 (MQ=255)
tctcCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTc < 2:539331/90‑1 (MQ=255)
cTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGAc < 1:288442/53‑1 (MQ=255)
cTGATATCTGGCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGAc > 2:288442/1‑53 (MQ=255)
ggCATATCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAgc > 2:609987/1‑89 (MQ=255)
tatCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAAt < 2:100564/90‑1 (MQ=255)
tatCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAAt < 2:487615/90‑1 (MQ=255)
atCTGC‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAAtt > 1:252300/1‑90 (MQ=255)
|
CCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAATT > NZ_CP009273/1812719‑1812884
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 30 ≤ 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
TATAGCTGCTCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAATT > NZ_CP009273/1812709‑1812884
|
TATAGCTGCTCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑CCCCCCCC < SRR3721989.534819/100‑1 (MQ=60)
CCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAAT < SRR3721989.337883/100‑1 (MQ=60)
CCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAAT < SRR3721989.477163/100‑1 (MQ=60)
CACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCC > SRR3721989.542616/1‑100 (MQ=60)
ACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGAC < SRR3721989.445613/100‑1 (MQ=60)
gcagcgtcagatgtgtataagagacagGTACAGAATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGA < SRR3721989.293765/73‑1 (MQ=60)
cgaccaccgagatctacactccttacgtcgtcggcagcgtcagatgtgtataagagacagCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGA < SRR3721989.275680/40‑1 (MQ=60)
ATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGA < SRR3721989.174344/100‑1 (MQ=60)
ATTTCTGGCTCATAATTTCTCCCTTCAGTACAAAATACTGATATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGA < SRR3721989.508911/100‑1 (MQ=60)
TATCTGGCATATCTGCCCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAATT > SRR3721989.256789/1‑100 (MQ=60)
|
TATAGCTGCTCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑CCCCCCCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAATT > NZ_CP009273/1812709‑1812884
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
