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 |
|
A34 F5 I0 R1
|
408 |
67.6 |
2494072 |
96.8% |
2414261 |
139.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_000913 |
1,890,943 |
T→C |
100% |
T109A (ACC→GCC) |
tsaB ← |
tRNA(ANN) t(6)A37 threonylcarbamoyladenosine modification protein; binding partner and protease for TsaD |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,890,943 | 0 | T | C | 96.9%
| 109.3
/ ‑3.8
| 32 | T109A (ACC→GCC) | tsaB | tRNA(ANN) t(6)A37 threonylcarbamoyladenosine modification protein; binding partner and protease for TsaD |
| Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (13/18); total (14/18) |
| Fisher's exact test for biased strand distribution p-value = 4.38e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.83e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CTGTTGCATTCGTTCATGGACGATTTCGGGTTTGAGTACGGCTTCGGTTTCTTCACCGTGCCAGATACCGTTTTCATCACGCTGATATTCGGCCCAGTAAACTTCGCCCATTCGCGCGTCAATGGCTGCCAGCACGCGGGTTGCGCCGTTTTTGCGCCACGCCCCTTGCGCCATCGTCATTAGCGTGGAGACGCCAATCATCGGTAATTCCGCGCCAAGCGCCAGCCCTTGCGCGATGCCAATACCAATGCGCACGCCAGTAAAGCTACCGGGGCCGCGCCC > NC_000913/1890803‑1891084
|
cTGTTGCATTCGTTCATGGACGATTTCGGGTTTGAGTACGGCTTCGGTTTCTTCACCGTGCCAGATACCGTTTTCATCACGCTGATATTCGGCCCAGTAAACTTCGCCCATTCGCGCGTCAATGGCTGCCAGCACGCGGGCTGCGCCGt > 3:315326/1‑149 (MQ=255)
ttCGTTCATGGACGATTTCGGGTTTGAGTACGGCTTCGGTTTCTTCACCGTGCCAGATACCGTTTTCATCACGCTGATATTCGGCCCAGTAAACTTCGCCCATTCGCGCGTCAATGGCTGCCAGCACGCGGGCTGCGCCGTTTTTgcgc > 3:619096/1‑149 (MQ=255)
tGGACGATTTCGGGTTTGAGTACGGCTTCGGTTTCTTCACCGTGCCAGATACCGTTTTCATCACGCTGATATTCGGCCCAGTAAACTTCGCCCATTCGCGCGTCAATGGCTGCCAGCACGCGGGCTGCGCCGTTTTTGCGCCACGcccc < 2:160461/149‑1 (MQ=255)
tttCGGGTTTGAGTACGGCTTCGGTTTCTTCACCGTGCCAGATACCGTTTTCATCACGCTGATATTCGGCCCAGTAAACTTCGCCCATTCGCGCGTCAATGGCTGCCAGCACGCGGGCTGCGCCGTTTTTGCGCCACGCCCCTTGCGcc > 2:398624/1‑149 (MQ=255)
ttCGGGTTTGAGTACGGCTTCGGTTTCTTCACCGTGCCAGATACCGTTTTCATCACGCTGATATTCGGCCCAGTAAACTTCGCCCATTCGCGCGTCAATGGCTGCCAGCACGCGGGTTGCGCCGTTTTTGCGCCACGCCCCTTGCGCCa > 4:492013/1‑149 (MQ=255)
ttGAGTACGGCTTCGGTTTCTTCACCGTGCCAGATACCGTTTTCATCACGCTGATATTCGGCCCAGTAAACTTCGCCCATTCGCGCGTCAATGGCTGCCAGCACGCGGGCTGCGCCGTTTTTGCGCCACGCCCCTTGCGCCATCGTCAt < 3:231396/149‑1 (MQ=255)
gCTTCGGTTTCTTCACCGTGCCAGATACCGTTTTCATCACGCTGATATTCGGCCCAGTAAACTTCGCCCATTCGCGCGTCAATGGCTGCCAGCACGCGGGCTGCGCCGTTTTTGCGCCACGCCCCTTGCGCCATCGTCATTAGCGTGga > 1:336664/1‑149 (MQ=255)
ttCGGTTTCTTCACCGTGCCAGATACCGTTTTCATCACGCTGATATTCGGCCCAGTAAACTTCGCCCATTCGCGCGTCAATGGCTGCCAGCACGCGGGCTGCGCCGTTTTTGCGCCACGCCCCTTGCGCCATCGTCATTAGCGTGgaga > 2:417445/1‑149 (MQ=255)
cttcACCGTGCCAGATACCGTTTTCATCACGCTGATATTCGGCCCAGTAAACTTCGCCCATTCGCGCGTCAATGGCTGCCAGCACGCGGGCTGCGCCGTTTTTGCGCCACGCCCCTTGCGCCATCGTCATTAGCGTGGAGACGCCAatc > 4:54680/1‑149 (MQ=255)
cACCGTGCCAGATACCGTTTTCATCACGCTGATATTCGGCCCAGTAAACTTCGCCCATTCGCGCGCCAATGGCTGCCAGCACGCGGGCTGCGCCGTTTTTGCGCCACGCCCCTTGCGCCATCGTCATTAGCGTGGAGACGCCAatcatc < 3:398746/149‑1 (MQ=255)
aCCGTGCCAGATACCGTTTTCATCACGCTGATATTCGGCCCAGTAAACTTCGCCCATTCGCGCGTCAATGGCTGCCAGCACGCGGGCTGCGCCGTTTTTGCGCCACGCCCCTTGCGCCATCGTCATTAGCGTGGAGACGCCAATCATCg < 4:392165/149‑1 (MQ=255)
aCCGTGCCAGATACCGTTTTCATCACGCTGATATTCGGCCCAGTAAACTTCGCCCATTCGCGCGTCAATGGCTGCCAGCACGCGGGCTGCGCCGTTTTTGCGCCACGCCCCTTGCGCCATCGTCATTAGCGTGGAGACGCCAATCATCg < 1:500364/149‑1 (MQ=255)
ccGTGCCAGATACCGTTTTCATCACGCTGATATTCGGCCCAGTAAACTTCGCCCATTCGCGCGTCAATGGCTGCCAGCACGCGGGCTGCGCCGTTTTTGCGCCACGCCCCTTGCGCCATCGTCATTAGCGTGGAGACGCCAATCATCgg < 3:339054/149‑1 (MQ=255)
tGCCAGATACCGTTTTCATCACGCTGATATTCGGCCCAGTAAACTTCGCCCATTCGCGCGTCAATGGCTGCCAGCACGCGGGCTGCGCCGTTTTTGCGCCACGCCCCTTGCGCCATCGTCATTAGCGTGGAGACGCCAATCATCGGTaa < 4:19161/149‑1 (MQ=255)
tACCGTTTTCATCACGCTGATATTCGGCCCAGTAAACTTCGCCCATTCGCGCGTCAATGGCTGCCAGCACGCGGGCTGCGCCGTTTTTGCGCCACGCCCCTTGCGCCATCGTCATTAGCGTGGAGACGCCAATCATCGGTAATTCcgcg < 2:375276/149‑1 (MQ=255)
ttttCATCACGCTGATATTCGGCCCAGTAAACTTCGCCCATTCGCGCGTCAATGGCTGCCAGCACGCGGGCTGCGCCGTTTTTGCGCCACGCCCCTTGCGCCATCGTCATTAGCGTGGAGACGCCAATCATCGGTAATTCCGCGCCAAg > 1:315394/1‑149 (MQ=255)
catcaCGCTGATATTCGGCCCAGTAAACTTCGCCCATTCGCGCGTCAATGGCTGCCAGCACGCGGGCTGCGCCGTTTTTGCGCCACGCCCCTTGCGCCATCCTCATTAGCGTGGAGACGCCAATCATCGGTAATTCCGCGCCAAGCGcc < 4:121931/149‑1 (MQ=255)
tcaCGCTGATATTCGGCCCAGTAAACTTCGCCCATTCGCGCGTCAATGGCTGCCAGCACGCGGGCTGCGCCGTTTTTGCGCCACGCCCCTTGCGCCATCGTCATTa > 3:23552/1‑106 (MQ=255)
tcaCGCTGATATTCGGCCCAGTAAACTTCGCCCATTCGCGCGTCAATGGCTGCCAGCACGCGGGCTGCGCCGTTTTTGCGCCACGCCCCTTGCGCCATCGTCATTa < 4:23552/106‑1 (MQ=255)
gCTGATATTCGGCCCAGTAAACTTCGCCCATTCGCGCGTCAATGGCTGCCAGCACGCGGGCTGCGCCGTTTTTGCGCCACGCCCCTTGCGCCATCGTCATTAGCGTGGAGACGCCAATCATCGGTAATTCCGCGCCAAGCGCCAGCCCt > 2:486744/1‑149 (MQ=255)
gCTGATATTCGGCCCAGTAAACTTCGCCCATTCGCGCGTCAATGGCTGCCAGCACGCGGGCTGCGCCGTTTTTGCGCCACGCCCCTTGCGCCATCGTCATTAGCGTGGAGACGCCAATCATCGGTAATTCCGCGCCAAGCGCCAGCCCt < 1:486744/149‑1 (MQ=255)
cTGATATTCGGCCCAGTAAACTTCGCCCATTCGCGCGTCAATGGCTGCCAGCACGCGGGCTGCGCCGTTTTTGCGCCACGCCCCTTGCGCCATCGTCATTAGCGTGGAGACGCCAATCATCGGTAATTCCGCGCCAAGCGCCAGCCCtt > 2:298542/1‑149 (MQ=255)
gATATTCGGCCCAGTAAACTTCGCCCATTCGCGCGTCAATGGCTGCCAGCACGCGGGCTGCGCCGTTTTTGCGCCACGCCCCTTGCGCCATCGTCATTAGCGTGGAGACGCCAATCATCGGTAATTCCGCGCCAAGCGCCAGCCCTTgc < 1:417445/149‑1 (MQ=255)
cGGCCCAGTAAACTTCGCCCATTCGCGCGTCAATGGCTGCCAGCACGCGGGCTGCGCCGTTTTTGCGCCACGCCCCTTGCGCCATCGTCATTAGCGTGGAGACGCCAATCATCGGTAATTCCGCGCCAAGCGCCAGCCCTTGCGCGATg < 1:95889/149‑1 (MQ=255)
cGGCCCAGTAAACTTCGCCCATTCGCGCGTCAATGGCTGCCAGCACGCGGGCTGCGCCGTTTTTGCGCCACGCCCCTTGCGCCATCGTCATTAGCGTGGAGACGCCAATCATCGGTAATTCCGCACCAAGCGCCAGCCCTTGCGCGATg < 1:530217/149‑1 (MQ=255)
gCCCAGTAAACTTCGCCCATTCGCGCGTCAATGGCTGCCAGCACGCGGGCTGCGCCGTTTTTGCGCCACGCCCCTTGCGCCATCGTCATTAGCGTGGAGACGCCAATCATCGGTAATTCCGCGCCAAGCGCCAGCCCTTGCGCGATGcc > 4:20225/1‑149 (MQ=255)
cccAGTAAACTTCGCCCATTCGCGCGTCAATGGCTGCCAGCACGCGGGCTGCGCCGTTTTTGCGCCACGCCCCTTGCGCCATCGTCATTAGCGTGGAGACGCCAATCATCGGTAATTCCGCGCCAAGCGCCAGCCCTTGCGCGATGCCa < 1:398624/149‑1 (MQ=255)
aGTAAACTTCGCCCATTCGCGCGTCAATGGCTGCCAGCACGCGGGCTGCGCCGTTTTTGCGCCACGCCCCTTGCGCCATCGTCATTAGCGTGGAGACGCCAATCATCGGTAATTCCGCGCCAAGCGCCAGCCCTTGCGCGATGCCAATa < 3:54680/149‑1 (MQ=255)
aGTAAACTTCGCCCATTCGCGCGTCAATGGCTGCCAGCACGCGGGCTGCGCCGTTTTTGCGCCACGCCCCTTGCGCCATCGTCATTAGCGTGGAGACGCCAATCATCGGTAATTCCGCGCCAAGCGCCAGCCCTTGCGCGATGCCAATa < 2:315394/149‑1 (MQ=255)
ttCGCCCATTCGCGCGTCAATGGCTGCCAGCACGCGGGCTGCGCCGTTTTTGCGCCACGCCCCTTGCGCCATCGTCATTAGCGTGGAGACGCCAATCATCGGTAATTCCGCGCCAAGCGCCAGCCCTTGCGCGATGCCAATACCAATgc > 2:300017/1‑149 (MQ=255)
tGCCAGCACGCGGGCTGCGCCGTTTTTGCGCCACGCCCCTTGCGCCATCGTCATTAGCGTGGAGACGCCAATCATCGGTAATTCCGCGCCAAGCGCCAGCCCTTGCGCGATGCCAATACCAATGCGCACGCCAGTAAAGCTACCGGGGc > 4:451633/1‑149 (MQ=255)
aCGCGGGCTGCGCCGTTTTTGCGCCACGCCCCTTGCGCCATCGTCATTAGCGTGGAGACGCCAATCATCGGTAATTCCGCGCCAAGCGCCAGCCCTTGCGCGATGCCAATACCAATGCGCACGCCAGTAAAGCTACCGGGGCCGCGccc < 2:37501/149‑1 (MQ=255)
|
CTGTTGCATTCGTTCATGGACGATTTCGGGTTTGAGTACGGCTTCGGTTTCTTCACCGTGCCAGATACCGTTTTCATCACGCTGATATTCGGCCCAGTAAACTTCGCCCATTCGCGCGTCAATGGCTGCCAGCACGCGGGTTGCGCCGTTTTTGCGCCACGCCCCTTGCGCCATCGTCATTAGCGTGGAGACGCCAATCATCGGTAATTCCGCGCCAAGCGCCAGCCCTTGCGCGATGCCAATACCAATGCGCACGCCAGTAAAGCTACCGGGGCCGCGCCC > NC_000913/1890803‑1891084
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
