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 F1 I1 R1
|
66 |
20.9 |
912876 |
97.7% |
891879 |
114.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
1,910,043 |
A→C |
V19V (GTT→GTG) |
kdgR ← |
KDG regulon transcriptional repressor |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,910,043 | 0 | A | C | 92.0%
| 84.4
/ 0.6
| 25 | V19V (GTT→GTG) | kdgR | KDG regulon transcriptional repressor |
| Reads supporting (aligned to +/- strand): ref base A (1/1); new base C (12/11); total (13/12) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.40e-01 |
CATAACCTAAGGTTTTCATGGTCTGTAAAAAGCGATAAACGGTGCTTTTTGACATCATGACGCGCTGCGACAGCTCGGTTATCCCTATTTCGCGCTCTTCACCCAGCGCCTGCAAAATGCCAAAAACTTTTAGCACGGAAGATACAGAATCAGGCTGTTTATCCAGATCTGCGTTAGCCATTTATCACCTCATTGCGAGTGTTTTATAAAAATCAGAACTGTTTTTTATTATAATTTCGCACCAGGGTGGTCGCAAT > NC_000913/1909919‑1910175
|
caTAACCTAAGGTTTTCATGGTCTGTAAAAAGCGATAAACGGTGCTTTTTGACATCATGACGCGCTGCGACAGCTCGGTTATCCCTATTTCGCGCTCTTCACCCAGCGCCTGCAAAATGCCAAAAACTTTTAGCACGGa > 2:239122/1‑139 (MQ=255)
ccTAAGGTTTTCATGGTCTGTAAAAAGCGATAAACGGTGCTTTTTGACATCATGACGCGCTGCGACAGCTCGGTTATCCCTATTTCGCGCTCTTCACCCAGCGCCTGCAAAATGCCAAACACTTTTAGCACGGAAGATa > 2:261011/1‑139 (MQ=255)
tCATGGTCTGTAAAAAGCGATAAACGGTGCTTTTTGACATCATGACGCGCTGCGACAGCTCGGTTATCCCTATTTCGCGCTCTTCACCCAGCGCCTGCAAAATGCCAAAAACTTTTAGCACGGAAGATACAGAATCAgg < 1:239122/139‑1 (MQ=255)
gTAAAAAGCGATAAACGGTGCTTTTTGACATCATGACGCGCTGCGACAGCTCGGTTATCCCTATTTCGCGCTCTTCACCCAGCGCCTGCAAAATGCCAAACACTTTTAGCACGGAAGATACAGAATCAGGCTGTTTATc < 1:365457/139‑1 (MQ=255)
aaGCGATAAACGGTGCTTTTTGACATCATGACGCGCTGCGACAGCTCGGTTATCCCTATTTCGCGCTCTTCACCCAGCGCCTGCAAAATGCCAAACACTTTTAGCACGGAAGATACAGAATCAGGCTGTTTATCCAGAt < 1:261011/139‑1 (MQ=255)
tAAACGGTGCTTTTTGACATCATGACGCGCTGCGACAGCTCGGTTATCCCTATTTCGCGCTCTTCACCCAGCGCCTGCAAAATGCCAAACACTTTTAGCACGGAAGATACAGAATCAg < 1:69403/118‑1 (MQ=255)
tAAACGGTGCTTTTTGACATCATGACGCGCTGCGACAGCTCGGTTATCCCTATTTCGCGCTCTTCACCCAGCGCCTGCAAAATGCCAAACACTTTTAGCACGGAAGATACAGAATCAg > 2:69403/1‑118 (MQ=255)
tcatGACGCGCTGCGACAGCTCGGTTATCCCTATTTCGCGCTCTTCACCCAGCGCCTGCAAAATGCCAAACACTTTTAGCACGGAAGATACAGAATCAGGCTGt < 1:135538/104‑1 (MQ=255)
tcatGACGCGCTGCGACAGCTCGGTTATCCCTATTTCGCGCTCTTCACCCAGCGCCTGCAAAATGCCAAACACTTTTAGCACGGAAGATACAGAATCAGGCTGt > 2:135538/1‑104 (MQ=255)
atGACGCGCTGCGACAGCTCGGTTATCCCTATTTCGCGCTCTTCACCCAGCGCCTGCAAAATGCCAAACACTTTTAGCACGGAAGATACAGAATCAGGCTGTTTATCCAGATCTGCGTTAGCCATTTATCACCTCATTg > 1:299678/1‑139 (MQ=255)
gcTGCGACAGCTCGGTTATCCCTATTTCGCGCTCTTCACCCAGCGCCTGCAAAATGCCAAACACTTTTAGCACGGAAGATACAGAATCAGGCTGt < 1:340423/95‑1 (MQ=255)
gcTGCGACAGCTCGGTTATCCCTATTTCGCGCTCTTCACCCAGCGCCTGCAAAATGCCAAACACTTTTAGCACGGAAGATACAGAATCAGGCTGt > 2:340423/1‑95 (MQ=255)
tGCGACAGCTCGGTTATCCCTATTTCGCGCTCTTCACCCAGCGCCTGCAAAATGCCAAACACTTTTAGCACGGAAGATACAGAATCAg < 1:429853/88‑1 (MQ=255)
tGCGACAGCTCGGTTATCCCTATTTCGCGCTCTTCACCCAGCGCCTGCAAAATGCCAAACACTTTTAGCACGGAAGATACAGAATCAg > 2:429853/1‑88 (MQ=255)
cTCGGTTATCCCTATTTCGCGCTCTTCACCCAGCGCCTGCAAAATGCCAAACACTTTTAGCACGGAAGATACAGAATCAGGCTGTTTATCCAGATCTGCGTTAGCCATTTATCACCTCATTGCGAGTGTTTTATaaaaa > 2:367307/1‑139 (MQ=255)
aTTTCGCGCTCTTCACCCAGCGCCTGCAAAATGCCAAACACTTTTAGCACGGAAGATACAGAATCAGGCTGTTTATCCAGATCTGCGTTAGCCATTTATCACCTCATTGCGAGTGTTTTATAAAAATCAGAACTGtttt > 2:119232/1‑139 (MQ=255)
cgcTCTTCACCCAGCGCCTGCAAAATGCCAAACACTTTTAGCa > 2:297604/1‑43 (MQ=255)
cgcTCTTCACCCAGCGCCTGCAAAATGCCAAACACTTTTAGCa < 1:297604/43‑1 (MQ=255)
cgcTCTTCACCCAGCGCCTGCAAAATGCCAAACACTTTTAGCACGGAAGATACAGAATCAg > 2:158154/1‑61 (MQ=255)
cgcTCTTCACCCAGCGCCTGCAAAATGCCAAACACTTTTAGCACGGAAGATACAGAATCAg < 1:158154/61‑1 (MQ=255)
cgcTCTTCACCCAGCGCCTGCAAAATGCCAAACACTTTTAGCACGGAAGATACAGAATCAGGCTGTTTATCCAGATCTGCGTTAGCCATTTATCACCTCATTGCGAGTGTTTTATAAAAATCAGAACTGTTTTttatta > 2:214575/1‑139 (MQ=255)
gcTCTTCACCCAGCGCCTGCAAAATGCCAAACACTTTTAGCACGGAAGATACAGAATCAGGCTGTTTATCCAGATCTGCGTTAGCCATTTATCACCTCATTGCGAGTGTTTTATAAAAATCAGAACTGTTTTTtattat < 1:214575/139‑1 (MQ=255)
gCAAAATGCCAAACACTTTTAGCACGGAAGATACAGAATCAGGCTGTTTATCCAGATCTGCGTTAGCCATTTATCACCTCATTGCGAGTGTTTTATAAAAATCAGAACTGTTTTTTATTATAATTTCGCACCAGggtgg > 2:330927/1‑139 (MQ=255)
gCCAAACACTTTTAGCACGGAAGATACAGAATCAGGCTGTTTATCCAGATCTGCGTTAGCCATTTATCACCTCATTGCGAGTGTTTTATAAAAATCAGAACTGTTTTTTATTATAATTTCGCACCAGGGTGGTCGCAAt < 1:119232/139‑1 (MQ=255)
gCCAAACACTTTTAGCACGGAAGATACAGAATCAGGCTGTTTATCCAGATCTGCGTTAGCCATTTATCACCTCATTGCGAGTGTTTTATAAAAATCAGAACTGTTTTTTATTATAATTTCGCACCAGGGTGGTCGCAAt < 1:416664/139‑1 (MQ=255)
|
CATAACCTAAGGTTTTCATGGTCTGTAAAAAGCGATAAACGGTGCTTTTTGACATCATGACGCGCTGCGACAGCTCGGTTATCCCTATTTCGCGCTCTTCACCCAGCGCCTGCAAAATGCCAAAAACTTTTAGCACGGAAGATACAGAATCAGGCTGTTTATCCAGATCTGCGTTAGCCATTTATCACCTCATTGCGAGTGTTTTATAAAAATCAGAACTGTTTTTTATTATAATTTCGCACCAGGGTGGTCGCAAT > NC_000913/1909919‑1910175
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
