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 I211 R1
|
223 |
18.0 |
1007644 |
96.3% |
970361 |
85.7 |
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 | 94.1%
| 49.4
/ ‑2.4
| 17 | intergenic (‑43/+62) | celF/chbR | 6‑phospho‑beta‑glucosidase/transcriptional regulator ChbR |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base C (9/7); total (10/7) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.79e-01 |
TCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑CCCCC‑CCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGT > NZ_CP009273/1812718‑1812879
|
tCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑ccccc‑cc > 2:238190/1‑90 (MQ=255)
tCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑ccccc‑cc > 2:151141/1‑90 (MQ=255)
gacgacTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCC‑CCGGACATAAATAATcc > 1:414931/1‑90 (MQ=255)
cgacTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCC‑CCGGACATAAATAATCCAg > 1:207289/1‑90 (MQ=255)
cTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCC‑CCGGACATAAATAATCCa < 2:389683/76‑1 (MQ=255)
cTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCC‑CCGGACATAAATAATCCa > 1:389683/1‑76 (MQ=255)
tAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCC‑CCGGACATAAATAATCCAGCAACAGGACAGATATGTGAAt < 1:151141/90‑1 (MQ=255)
tctcCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCC‑CCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCa < 2:207289/90‑1 (MQ=255)
ctcCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCC‑CCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAg < 1:134715/90‑1 (MQ=255)
ctcCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCC‑CCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAg < 1:124679/90‑1 (MQ=255)
tCAGTACAGAATACTGATATCTGGCATATCTGCCCCCC‑CCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATaa < 2:116774/90‑1 (MQ=255)
gAATACTGATATCTGGCATATCTGCCCCCC‑CCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTAc > 1:76789/1‑90 (MQ=255)
cTGATATCTGGCATATCTGCCCCCC‑CCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGAtt > 1:496802/1‑90 (MQ=255)
atCTGGCATATCTGCCCCCC‑CCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGtat < 2:232511/70‑1 (MQ=255)
atCTGGCATATCTGCCCCCC‑CCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGtat > 1:232511/1‑70 (MQ=255)
atCTGGCATATCTGCCCCCC‑CCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAAtt > 2:116639/1‑90 (MQ=255)
atCTGGCATATCTGCCCCCC‑CCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAAtt > 2:117301/1‑90 (MQ=255)
cTGGCATATCTG‑CCCCCTCCGGACATAAATAATCAAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCa > 1:463365/1‑90 (MQ=255)
ggCATATCTGCCCCCC‑CCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGt > 2:107621/1‑90 (MQ=255)
|
TCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑CCCCC‑CCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGT > NZ_CP009273/1812718‑1812879
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ 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
CACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑CCCCC‑CCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAATTTCT > NZ_CP009273/1812724‑1812887
|
CACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCC‑CCGGACATAAATAATCC > SRR3722094.422154/1‑100 (MQ=60)
CCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCC‑CCGGACATAAATAATCCAG > SRR3722094.210090/1‑100 (MQ=60)
CTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCC‑CCGGACATAAATAATCCAGCAACAGGACctgt > SRR3722094.396375/1‑96 (MQ=60)
TAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCC‑CCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTAT < SRR3722094.153253/100‑1 (MQ=60)
CTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCC‑CCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGAC < SRR3722094.126470/100‑1 (MQ=60)
CTCCCTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCC‑CCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGAC < SRR3722094.136644/100‑1 (MQ=60)
CTTCAGTACAGAATACTGATATCTGGCATATCTGCCCCCC‑CCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTAC > SRR3722094.77891/1‑100 (MQ=60)
GTACAGAATACTGATATCTGGCATATCTGCCCCCC‑CCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATT > SRR3722094.505561/1‑100 (MQ=60)
GAATACTGATATCTGGCATATCTGCCCCCC‑CCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACctgtctctta > SRR3722094.235765/1‑90 (MQ=60)
ATACTGATATCTGGCATATCTG‑CCCCCTCCGGACATAAATAATCAAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCA > SRR3722094.471519/1‑100 (MQ=60)
CTGGCATATCTGCCCCCC‑CCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAATTTCT > SRR3722094.300361/1‑100 (MQ=60)
|
CACCAATAGTGACGACTTTTAATTTCTGGCTCATAATTTCTCCCTTCAGTACAGAATACTGATATCTGGCATATCTG‑CCCCC‑CCGGACATAAATAATCCAGCAACAGGACAGATATGTGAATTGTCAGGTATAACGACTTACTGATTAAATTCAGTCAATTTCT > NZ_CP009273/1812724‑1812887
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
