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 |
|
A21 F17 I1 R1
|
11 |
22.6 |
526280 |
94.3% |
496282 |
139.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
USA300TCH1516_ALE |
2,279,705 |
G→A |
A943V (GCA→GTA) |
ebh_3 ← |
Extracellular matrix‑binding protein ebh |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | USA300TCH1516_ALE | 2,279,705 | 0 | G | A | 96.2%
| 66.4
/ NA
| 26 | A943V (GCA→GTA) | ebh_3 | Extracellular matrix‑binding protein ebh |
| Reads supporting (aligned to +/- strand): ref base G (0/1); new base A (12/13); total (12/14) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CGTTATTAGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTGCTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAATTTGCTG > USA300TCH1516_ALE/2279574‑2279840
|
cGTTATTAGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTgttgtt < 2:87322/140‑1 (MQ=255)
ttaGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTACGGTTTATCATTTGCATCATCAATTACTAATGTTACTGTTGTTTCAcc > 1:144573/1‑140 (MQ=255)
tGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATCTTACTGTTGTTTCACCTGtcg > 2:100091/1‑138 (MQ=255)
gATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCAACTGTTGc > 2:83365/1‑140 (MQ=255)
tACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGGCTGTTTGTTGATGTATCTACACTAGAATTGTTATTAGCTTGCGGTTTATACTTTGCATCATCAGTTGCTGATGTTATTGTTGTTTTGTGTGTTGCTGCAt > 2:148368/1‑140 (MQ=255)
cTTCTGGTTTACTAGTTACATCGTTATCCATTTGCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCa < 1:247039/140‑1 (MQ=255)
ggTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCCCtatt > 1:248426/1‑140 (MQ=255)
aTCGTTATCCATTGTCATACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCg < 2:164945/140‑1 (MQ=255)
cGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGAGATTTATCATTTGCATCATCAGTTGCTAATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGga > 2:144824/1‑140 (MQ=255)
ttATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCGTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGgaga > 1:38120/1‑140 (MQ=255)
ttGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGGTACTGTTGTTTCACCTGTTGCCGCATCACTACTATTTGGTGTTCTGGGAGCAGCGCCt > 2:168806/1‑140 (MQ=255)
ttGTCGGACTGTGTGGTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCt < 1:232237/140‑1 (MQ=255)
gTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCCTTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTTTTGCCGCATCACTCTTTTTTTGTATTTTCGGAGACGCGTCCGc > 2:35166/1‑140 (MQ=255)
gACTGGTTGGTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTg < 1:30481/140‑1 (MQ=255)
cTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGcc < 1:167047/140‑1 (MQ=255)
gttgATGGATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGc < 2:49707/140‑1 (MQ=255)
ttGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAgg > 1:153040/1‑140 (MQ=255)
gTTATTAGCTTGCGATTTATCATTTGCATAATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATAAGCTGTCGTCTCAGATACGTGAGGtt > 2:142201/1‑140 (MQ=255)
tttcTTGCGGTTTATCATGTGCATCATCAGTTGCTGATGTTACGGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCa < 1:78538/137‑1 (MQ=255)
gtctATCATTCGCATCATCAGGTGCTGATGTTACTGTTGTTGCACCTGTTGCCGCATCACTATTATTGGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCt < 1:35166/137‑1 (MQ=255)
tttATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGCCGTTGGCGGAGAAGCGTCTGCTCCTCCTTTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTg > 1:165247/1‑140 (MQ=255)
tATCATTTGCATCATTAGTTGTTGATGTTACTGTTGTTTCACTTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGgt < 2:137428/140‑1 (MQ=255)
ttGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATTACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGaa < 1:204125/140‑1 (MQ=255)
gcggATGTGGCTGGGGGTTCACCTGTTGCCGCAGCACTCTTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTTAGTTACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAAtt < 1:38188/137‑1 (MQ=255)
gATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAATTTGc < 1:237975/140‑1 (MQ=255)
tGTTACTGTTGTTTCGCCTGTTGCCGCATCGCTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAATTTGCTg < 2:9627/140‑1 (MQ=255)
|
CGTTATTAGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTGCTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAATTTGCTG > USA300TCH1516_ALE/2279574‑2279840
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
