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 |
1,193,873 |
G→T |
70.3% |
intergenic (‑180/‑278) |
ymfE ← / → lit |
e14 prophage; putative inner membrane protein/e14 prophage; cell death peptidase, inhibitor of T4 late gene expression |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | CP009273 | 1,193,873 | 0 | G | T | 70.3%
| 11.8
/ 13.0
| 17 | intergenic (‑180/‑278) | ymfE/lit | e14 prophage; putative inner membrane protein/e14 prophage; cell death peptidase, inhibitor of T4 late gene expression |
| Reads supporting (aligned to +/- strand): ref base G (3/2); new base T (6/6); total (9/8) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.52e-01 |
ATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTGACAGACAATATTGTGATCAGTAGCACGTATCGAGGAGGAGTAGCGCTACAAATTTGACGCTGGGTGAGAATCTGAAATTGATAGAAATGAAATAATGAAATAATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGACAGAGTGTCCAGTGGGCACGGATGGTGTCTTACGACATGCTTACCTTAATCGTTC > CP009273/1193742‑1194016
|
aTTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTGACAGACAATATTGTGATCAGTAGCACGTATCGAGGAGGAGTAGCGCTACAAATTTGACGCTGGGTGAGAATCTGAAATTGATAg > 2:1209856/1‑150 (MQ=255)
tatataCTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTGACAGACAATATTGTGATCAGTAGCACGTATCGAGGAGGAGTAGCGCTACAAATTTGACGCTGGGTTAGAATCTGAAATTGATAgaa > 1:3266219/1‑150 (MQ=255)
ataCTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTGACAGACAATATTGTGATCAGTAGCACGTATCGAGGAGGAGTAGCGCTACAAATTTGACGCTGGGTTAGAATCTGAAATTGATAgaaatg > 2:1075531/1‑150 (MQ=255)
gTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTGACAGACAATATTGTGATCAGTAGCACGTATCGAGGAGGAGTAGCGCTACAAATTTGACGCTGGGTTAGAATCTGAAATTGATAGAaatgaaataatgaa < 1:1931537/150‑1 (MQ=255)
ggTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTGACAGACAATATTGTGATCAGTAGCACGTATCGAGGAGGAGTAGCGCTACAAATTTGACGCTGGGTTAGAATCTGAAATTGATAGAaatgaaataatgaaata > 1:474700/1‑150 (MQ=255)
gACCTAGCTTCGCTGACAGACAATATTGTGATCAGTAGCACGTATCGAGGAGGAGTAGCGCTACAAATTTGACGCTGGGTTAGAATCTGAAATTGATAGAAATGAAATAATGAAATAatgaaatgatgaaatgatgaaatgatgaaatga < 2:1626586/150‑1 (MQ=255)
aCCTAGCTTCGCTGACAGACAATATTGTGATCAGTAGCACGTATCGAGGAGGAGTAGCGCTACAAATTTGACGCTGGGTTAGAATCTGAAATTGATAGAAATGAAATAATGAAATAatgaaatgatgaaatgatgaaatgatgaaatgat > 1:3782693/1‑150 (MQ=255)
aCCTAGCTTCGCTGACAGACAATATTGTGATCAGTAGCACGTATCGAGGAGGAGTAGCGCTACAAATTTGACGCTGGGTTAGAATCTGAAATTGATAGAAATGAAATAATGAAATAatgaaatgatgaaatgatgaaatgatgaaatgat > 1:3782697/1‑150 (MQ=255)
gATCAGTAGCTCGTATCGTGGTGGAGTAGCGCTACAAATTTGTCGCTGGGTTAGAATCTGTATTTGATAGATATTAAATAATGAAATAATGATATGATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGACAGAGTGTcc < 1:3361210/150‑1 (MQ=38)
gATCAGTAGCACGTATCGAGGAGGAGTAGCGCTACAAATTTGACGCTGGGTTAGAATCTGAAATTGATAGAAATGAAATAATGAAATAATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGACAGAGTGTcc < 1:2837900/150‑1 (MQ=255)
gATCAGTAGCACGTATCGAGGAGGAGTAGCGCTACAAATTTGACGCTGGGTTAGAATCTGAAATTGATAGAAATGAAATAATGAAATAATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGACAGAGTGTcc < 1:2837964/150‑1 (MQ=255)
gATCAGTAGCACGTATCGAGGAGGAGTAGCGCTACAAATTTGACGCTGGGTTAGAATCTGAAATTGATAGAAATGAAATAATGAAATAATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGACAGAGTGTcc < 1:3361188/150‑1 (MQ=255)
tCAGTAGCACGTATCGAGGAGGAGTAGCGCTACAAATTTGACGCTGGGTGAGAATCTGAAATTGATAGAAATGAAATAATGAAATAATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGACAGATTTTCCAg > 1:4607361/1‑150 (MQ=255)
tCAGTAGCACGTATCGAGGAGGAGTAGCGCTACAAATTTGACGCTGGGTGAGAATCTGAAATTGATAGAAATGAAATAATGAAATAATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGACAGAGTGTCCAg > 1:4607429/1‑150 (MQ=255)
tCGAGGAGGAGTAGCGCTACAAATTTGACGCTGGGTGAGAATCTGAAATTGATAGAAATGAAATAATGAAATAATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGACAGAGTGTCCAGTGGGCACGGATgg < 2:4611015/150‑1 (MQ=255)
tCGAGGAGGAGTAGCGCTACAAATTTGACGCTGGGTGAGAATCTGAAATTGATAGAAATGAAATAATGAAATAATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGACAGAGTGTCCAGTGGGCACGGATgg < 2:4610982/150‑1 (MQ=255)
cTGGGTTAGAATCTGAAATTGATAGAAATGAAATAATGAAATAATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGACAGAGTGTCCAGTGGGCACGGATGGTGTCTTACGACATGCTTACCTTAATCGTTc > 1:2272690/1‑150 (MQ=255)
|
ATTATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTGACAGACAATATTGTGATCAGTAGCACGTATCGAGGAGGAGTAGCGCTACAAATTTGACGCTGGGTGAGAATCTGAAATTGATAGAAATGAAATAATGAAATAATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGACAGAGTGTCCAGTGGGCACGGATGGTGTCTTACGACATGCTTACCTTAATCGTTC > CP009273/1193742‑1194016
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTGACAGACAATATTGTGATCAGTAGCACGTATCGAGGAGGAGTAGCGCTACAAATTTGACGCTGGGTGAGAATCTGAAATTGATAGAAATGAAATAATGAAATAATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGACAGAGTGTCCAGTGGGCACGGATGGTGTCTTACGACATGCTTACCTTAATCGTTC > CP009273/1193744‑1194016
|
TATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTGACAGACAATATTGTGATCAGTAGCACGTATCGAGGAGGAGTAGCGCTACAAATTTGACGCTGGGTTAGAATCTGAAATTGATAGAA > SRR19973073.3272833/1‑150 (MQ=60)
GTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTGACAGACAATATTGTGATCAGTAGCACGTATCGAGGAGGAGTAGCGCTACAAATTTGACGCTGGGTTAGAATCTGAAATTGATAGAAATGAAATAATGAA < SRR19973073.1935465/150‑1 (MQ=60)
GGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTGACAGACAATATTGTGATCAGTAGCACGTATCGAGGAGGAGTAGCGCTACAAATTTGACGCTGGGTTAGAATCTGAAATTGATAGAAATGAAATAATGAAATA > SRR19973073.475704/1‑150 (MQ=60)
ACCTAGCTTCGCTGACAGACAATATTGTGATCAGTAGCACGTATCGAGGAGGAGTAGCGCTACAAATTTGACGCTGGGTTAGAATCTGAAATTGATAGAAATGAAATAATGAAATAATGAAATGATGAAATGATGAAATGATGAAATGAT > SRR19973073.3790265/1‑150 (MQ=60)
ACCTAGCTTCGCTGACAGACAATATTGTGATCAGTAGCACGTATCGAGGAGGAGTAGCGCTACAAATTTGACGCTGGGTTAGAATCTGAAATTGATAGAAATGAAATAATGAAATAATGAAATGATGAAATGATGAAATGATGAAATGAT > SRR19973073.3790269/1‑150 (MQ=60)
GATCAGTAGCTCGTATCGTGGTGGAGTAGCGCTACAAATTTGTCGCTGGGTTAGAATCTGTATTTGATAGATATTAAATAATGAAATAATGATATGATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGACAGAGTGTCC < SRR19973073.3367989/150‑1 (MQ=60)
GATCAGTAGCACGTATCGAGGAGGAGTAGCGCTACAAATTTGACGCTGGGTTAGAATCTGAAATTGATAGAAATGAAATAATGAAATAATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGACAGAGTGTCC < SRR19973073.2843720/150‑1 (MQ=60)
GATCAGTAGCACGTATCGAGGAGGAGTAGCGCTACAAATTTGACGCTGGGTTAGAATCTGAAATTGATAGAAATGAAATAATGAAATAATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGACAGAGTGTCC < SRR19973073.2843784/150‑1 (MQ=60)
GATCAGTAGCACGTATCGAGGAGGAGTAGCGCTACAAATTTGACGCTGGGTTAGAATCTGAAATTGATAGAAATGAAATAATGAAATAATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGACAGAGTGTCC < SRR19973073.3367967/150‑1 (MQ=60)
TCAGTAGCACGTATCGAGGAGGAGTAGCGCTACAAATTTGACGCTGGGTGAGAATCTGAAATTGATAGAAATGAAATAATGAAATAATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGACAGATTTTCCAG > SRR19973073.4616555/1‑150 (MQ=60)
TCAGTAGCACGTATCGAGGAGGAGTAGCGCTACAAATTTGACGCTGGGTGAGAATCTGAAATTGATAGAAATGAAATAATGAAATAATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGACAGAGTGTCCAG > SRR19973073.4616623/1‑150 (MQ=60)
CTGGGTTAGAATCTGAAATTGATAGAAATGAAATAATGAAATAATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGACAGAGTGTCCAGTGGGCACGGATGGTGTCTTACGACATGCTTACCTTAATCGTTC > SRR19973073.2277342/1‑150 (MQ=60)
|
TATATACTTTTCAGTAGGTTAGTTACAATTTTTTGTATCTGTTCAGGCTGACCTAGCTTCGCTGACAGACAATATTGTGATCAGTAGCACGTATCGAGGAGGAGTAGCGCTACAAATTTGACGCTGGGTGAGAATCTGAAATTGATAGAAATGAAATAATGAAATAATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGAAATGATGACAGAGTGTCCAGTGGGCACGGATGGTGTCTTACGACATGCTTACCTTAATCGTTC > CP009273/1193744‑1194016
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
