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 F218 I0 R1
|
1506 |
278.7 |
9275112 |
94.5% |
8764980 |
150.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
CP009273 |
1,196,660 |
G→T |
46.1% |
intergenic (‑172/‑293) |
xisE ← / → ymfI |
e14 prophage; putative excisionase/e14 prophage; uncharacterized protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | CP009273 | 1,196,660 | 0 | G | T | 46.1%
| 12.5
/ 30.9
| 26 | intergenic (‑172/‑293) | xisE/ymfI | e14 prophage; putative excisionase/e14 prophage; uncharacterized protein |
| Reads supporting (aligned to +/- strand): ref base G (9/5); new base T (8/4); total (17/9) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.36e-01 |
ACTGCTTAGTCTCAGCATATCGACCCTGCACGGTCGGTTAGTTTCTCCACAAAACAGAGAAGAGCACCTGTGGCCACAGCTATCAGGATGGGTCGGGTTATTAACCCGTCATCCGGGGATACTCTTCTCTGTTTTGTAAAAAGGGCGGTACCAGAAAGGACTAAGGAAAAAACTGGTACCGCCAAGACTACACACAGCATAAAGTTGTGGTGTCGGGTGCCCCCGGTGCCTGGCGAAGGTTGCACACCAGGCGGGTGGGTATCCACAGAAGGTCGATTGTCAGCCTCAA > CP009273/1196514‑1196802
|
aCTGCTTAGTCTCAGCATATCGACCCTGCACGGTCGGTTAGTTTCTCCACAAAACAGAGAAGAGCACCTGTGGCCACAGCTATCAGGATGGGTCGGGTTATTAACCCGTCATCCGGGGATACTCTTCTCTGTTTTGTAAAAAGGGCGGTa < 2:2021260/150‑1 (MQ=255)
ttAGTCTCAGCATATCGACCCTGCACGGTCGGTTAGTTTCTCCACAAAACAGAGAAGAGCACCTGTGGCCACAGCTATCAGGATGGGTCGGGTTATTAACCCGTCATCCGGGGATACTCTTCTCTGTTTTGTAAAAAGGGCTGTACCAGa > 2:3840220/1‑150 (MQ=255)
tAGTCTCAGCATATCGACCCTGCACGGTCGGTTAGTTTCTCCACAAAACAGAGAAGAGCACCTGTGGCCACAGCTATCAGGATGGGTCGGGTTATTAACCCGTCATCCGGGGATACTCTTCTCTGTTTTGTAAAAAGGGCTGTACCAGaa < 2:2574630/150‑1 (MQ=255)
tAGTCTCAGCATATCGACCCTGCACGGTCGGTTAGTTTCTCCACAAAACAGAGAAGAGCACCTGTGGCCACAGCTATCAGGATGGGTCGGGTTATTAACCCGTCATCCGGGGATACTCTTCTCTGTTTTGTAAAAAGGGCTGTACCAGaa < 2:2574584/150‑1 (MQ=255)
tAGTCTCAGCATATCGACCCTGCACGGTCGGTTAGTTTCTCCACAAAACAGAGAAGAGCACCTGTGGCCACAGCTATCAGGATGGGTCGGGTTATTAACCCGTCATCCGGGGATACTCTTCTCTGTTTTGTAAAAAGGGCTGTACCAGaa < 2:2574583/150‑1 (MQ=255)
ctcAGCATATCGACCCTGCACGGTCGGTTAGTTTCTCCACAAAACAGAGAAGAGCACCTTTGGCCACAGCTATCAGGATGGGTCGGGTTATTAACCCGTCATCCGGGGATACTCTTCTCTGTTTTGTAAAAAGGGCGGTACCAGAAAGGa > 1:658507/1‑150 (MQ=255)
ctcAGCATATCGACCCTGCACGGTCGGTTAGTTTCTCCACAAAACAGAGAAGAGCACCTGTGGCCACAGCTATCAGGATGGGTCGGGTTATTAACCCGTCATCCGGGGATACTCTTCTCTGTTTTGTAAAAAGGGCGGTACCAGAAAGGa > 1:1899151/1‑150 (MQ=255)
aGCATATCGACCCTGCACGGTCGGTTAGTTTCTCCACAAAACAGAGAAGAGCACCTGTGGCCACAGCTATCAGGATGGGTCGGGTTATTAACCCGTCATCCGGGGATACTCTTCTCTGTTTTGTAAAAAGGGCGGTACCAGAAAGGACTa > 1:658553/1‑150 (MQ=255)
cGACCCTGCACGGTCGGTTAGTTTCTCCACAAAACAGAGAAGAGCACCTGTGGCCACAGCTATCAGGATGGGTCGGGTTATTAACCCGTCATCCGGGGATACTCTTCTCTGTTTTGTAAAAAGGGCTGTACCAGAAAGGACTAAGGaaaa < 2:1424935/150‑1 (MQ=255)
cccTGCACGGTCGGTTAGTTTCTCCACAAAACAGAGAAGAGCACCTGTGGCCACAGCTATCAGGATGGGTCGGGTTATTAACCCGTCATCCGGGGATACTCTTCTCTGTTTTGTAAAAATGGCGGTACCAGAAAGGACTAAGGAAAAAAc > 1:3711558/1‑150 (MQ=255)
cccTGCACGGTCGGTTAGTTTCTCCACAAAACAGAGAAGAGCACCTGTGGCCACAGCTATCAGGATGGGTCGGGTTATTAACCCGTCATCCGGGGATACTCTTCTCTGTTTTGTAAAAAGGGCGGTACCAGAAAGGACTAAGGAAAAAAc > 1:3711559/1‑150 (MQ=255)
cccTGCACGGTCGGTTAGTTTCTCCACAAAACAGAGAAGAGCACCTGTGGCCACAGCTATCAGGATGGGTCGGGTTATTAACCCGTCAACCGGGGATACTCATCTCTGTTTTGTAAAAAGGGCGGTACCAGAAAGGACTAAGGAAAAAAc > 1:3711575/1‑150 (MQ=255)
cccTGCACGGTCGGTTAGTTTCTCCACAAAACAGAGAAGAGCACCAGTGGCCACAGCTATCAGGATGGGTCGGGTTATTAACCCGTCAACCCGGGATACTCTTCTCTGTTTTTTAAAAAGGGCGGTACCAGAAAGGACTAAGGAAAAAAc > 1:3711594/1‑150 (MQ=255)
ttCTCCACAAAACAGAGAAGAGCACCTGTGGCCACAGCTATCAGGATGGGTCGGGTTATTAACCCGTCATCCGGGGATACTCTTCTCTGTTTTGTAAAAAGGGCGGTACCAGAAAGGACTAAGGAAAAAACTGGTACCGCCAAGACTaca < 1:1382766/150‑1 (MQ=255)
ggCCACAGCTATCAGGATGGGTCGGGTTATTAACCCGTCATCCGGGGATACTCTTCTCTGTTTTGTAAAAAGGGCGGTACCAGAAAGGACTAAGTAAAAAACTGGTACCGCCAAGACTACACACAGCATAAAGTTGTGGTGTCGGGTGcc > 2:696595/1‑150 (MQ=255)
caGCTATCAGGATGGGTCGGGTTATTAACCCGTCATCCGGGGATACTCTTCTCTGTTTTGTAAAAAGGGCTGTACCAGAAAGGACTAAGGAAAAAACTGGTACCGCCAAGACTACACACAGCATAAAGTTGTGGTGTCGGGTGCCCCCgg > 2:2155347/1‑150 (MQ=255)
aTGGGTCGGGTTATTACCCCGTCATCCGGGGATACTCTTCTCTGTTTTGTAAAAAGGGCGGTACCAGAAAGGACTAAGGAAAAAACTGGTACCGCCAAGACTACACACAGCATAAAGTTGTGGTGTCGGGTGCCCCCGGTGCCTGGCGaa < 2:2471503/150‑1 (MQ=255)
attaACCCGTCATCCGGGGATACTCTTCTCTGTTTTGTAAAAAGGGCGGTACCAGAAAGGACTAAGGAAAAAACTGGTACCGCCAAGACTACACACAGCATAAAGTTGTGGTGTCGGGTGCCCCCGGTGCCTGGCGAAGGTTGCACACCa < 2:3951699/150‑1 (MQ=255)
tCCGGGGATACTCTTCTCTGTTTTGTAAAACGGGCGGTACCAGAAAGGACTAAGGAAAAAACTGGTACCGCCAAGACTACACACAGCATAAAGTTGTGGTGTCGGGTGCCCCCGGTGCCTGGCGAAGGTTGCACACCAGGCGGGTGGGTa < 1:1164992/150‑1 (MQ=255)
aCTCTTCTCTGTTTTGTAAAAAGGGCTGTACCAGAAAGGACTAAGGAAAAAACTGGTACCGCCAAGACTACACACAGCATAAAGTTGTGGTGTCGGGTGCCCCCGGTGCCTGGCGAAGGTTGCACACCAGGCGGGTGGGTATCCACAGaa > 2:2845116/1‑150 (MQ=255)
aCTCTTCTCTGTTTTGTAAAAAGGGCTGTACCAGAAAGGACTAAGGAAAAAACTGGTACCGCCAAGACTACACACAGCATAAAGTTGTGGTGTCGGGTGCCCCCGGTGCCTGGCGAAGGTTGCACACCAGGCGGGTGGGTATCCACAGaa > 2:2845162/1‑150 (MQ=255)
aCTCTTCTCTGTTTTGTAAAAAGGGCTGTACCAGAAAGGACTAAGGAAAAAACTGGTACCGCCAAGACTACACACAGCATAAAGTTGTGGTGTCGGGTGCCCCCGGTGCCTGGCGAAGGTTGCACACCAGGCGGGTGGGTATCCACAGaa > 2:4214233/1‑150 (MQ=255)
ctctTCTCTGTTTTGTAAAAAGGGCTGTACCAGAAAGGACTAAGGAAAAAACTGGTACCGCCAAGACTACACACAGCATAAAGTTGTGGTGTCGGGTGCCCCCGGTGCCTGGCGAAGGTTGCACACCAGGCGGGTGGGTATCCACAGAAg > 1:671261/1‑150 (MQ=255)
tctGTTTTGTAAAAAGGGCGGTACCAGAAAGGACTAAGGAAAAAACTGGTACCGCCAAGACTACACACAGCATAAAGTTGTGGTGTCGGGTGCCCCCGGTGCCTGGCGAAGGTTGCACACCAGGCGGGTGGGTATCCACAGAAGGTCGAt > 1:3749438/1‑150 (MQ=255)
aaaaGGGCTGTACCAGAAAGGACTAAGGAAAAAACTGGTACCGCCAAGACTACACACAGCATAAAGTTGTGGTGTCGGGTGCCCCCGGTGCCTGGCGAAGGTTACACACCAGGCGGGTGGGTATCCACAGAAGGTCGATTGTCAGCCTCa > 1:4543593/1‑150 (MQ=255)
aaaGGGCTGTACCAGAAAGGACTAAGGAAAAAACTGGTACCGCCAAGACTACACACAGCATAAAGTTGTGGTGTCGGGTGCCCCCGGTGCCTGGCGAAGGTTGCACACCAGGCGGGTGGGTATCCACAGAAGGTCGATTGTCAGCCTCaa > 2:1336695/1‑150 (MQ=255)
|
ACTGCTTAGTCTCAGCATATCGACCCTGCACGGTCGGTTAGTTTCTCCACAAAACAGAGAAGAGCACCTGTGGCCACAGCTATCAGGATGGGTCGGGTTATTAACCCGTCATCCGGGGATACTCTTCTCTGTTTTGTAAAAAGGGCGGTACCAGAAAGGACTAAGGAAAAAACTGGTACCGCCAAGACTACACACAGCATAAAGTTGTGGTGTCGGGTGCCCCCGGTGCCTGGCGAAGGTTGCACACCAGGCGGGTGGGTATCCACAGAAGGTCGATTGTCAGCCTCAA > CP009273/1196514‑1196802
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
