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 |
|
A13 F69 I0 R1
|
1426 |
148.0 |
5875178 |
97.4% |
5722423 |
123.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_000913 |
1,169,384 |
G→A |
30.4% |
intergenic (+54/+28) |
bhsA → / ← ldtC |
biofilm, cell surface and signaling protein/L,D‑transpeptidase linking Lpp to murein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,169,384 | 0 | G | A | 30.4%
| 28.9
/ 15.9
| 23 | intergenic (+54/+28) | bhsA/ldtC | biofilm, cell surface and signaling protein/L,D‑transpeptidase linking Lpp to murein |
| Reads supporting (aligned to +/- strand): ref base G (9/7); new base A (4/3); total (13/10) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.81e-01 |
GAATACCCTCCATGGAACAGCAGTAATTTATAAATAAGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAACGGACATCCATCACATGTTGCATCACTTCAGCGTCAGTTTGTGCTGCATCTTTAAATGATTGCAT > NC_000913/1169294‑1169531
|
gAATACCCTCCATGGAACAGCAGTAATTTATAAATAAGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGAcgg > 2:1302611/1‑149 (MQ=255)
tCCATGGAACAGCAGTAATTTATAAATAAGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACACGGCATGTCGCggg > 4:1372526/1‑92 (MQ=39)
tCCATGGAACAGCAGTAATTTATAAATAAGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACACGGCATGTCGCggg < 3:1372526/92‑1 (MQ=39)
tAATTTATAAATAAGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGa > 3:539736/1‑149 (MQ=255)
ataaGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAAc < 1:492548/141‑1 (MQ=255)
ataaGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAAc > 2:492548/1‑141 (MQ=255)
aaGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAACGGAcatccat < 1:1302611/149‑1 (MQ=255)
tCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAACGGACATCCATCACATGTTGCAt < 4:539736/149‑1 (MQ=255)
cTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAACGGACATCCATCACATGTTGCATCACTTCAGCg > 4:592483/1‑149 (MQ=255)
gCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCgg < 4:834273/104‑1 (MQ=255)
gCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCgg > 3:834273/1‑104 (MQ=255)
ccGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAACGGACATCCATCACATGTTGCATCACTTCAGCGTCAGTTTGTGCTGCATCTTTa > 3:1269129/1‑149 (MQ=255)
ccGCGACACGGCATGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAACGGAcatccatc < 2:393887/107‑1 (MQ=255)
ccGCGACACGGCATGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAACGGAcatccatc > 1:393887/1‑107 (MQ=255)
ccGCGACACGGCATGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAACGGACATCCATCACATGTTGCa > 2:182216/1‑117 (MQ=255)
ccGCGACACGGCATGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAACGGACATCCATCACATGTTGCa < 1:182216/117‑1 (MQ=255)
ccGCGACACGGCATGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAACGGACATCCATCACATGTTGCATCACTTCAGCGTCAGTTTGTGCTGCATCTTTa > 2:47264/1‑149 (MQ=255)
cATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAACGGACATCCATCACATGTTGCATCACTTCAGCGTCAGTTTGTGCTGCATCTTTAAATGat < 4:1269129/149‑1 (MQ=255)
tGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAACGGACATCCATCACATGTTGCATCACTTCAGCGTCAGTTTGTGCTGCATCTTTAAATGattg > 2:1395544/1‑149 (MQ=255)
tGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAACGGACATCCATCACATGTTGCATCACTTCAGCGTCAGTTTGTGCTGCATCTTTAAATGattg < 3:592483/149‑1 (MQ=255)
ccGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAACGGACATCCATCACATGTTGCATCACTTCAGCGTCAGTTtg < 2:1218908/126‑1 (MQ=255)
ccGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAACGGACATCCATCACATGTTGCATCACTTCAGCGTCAGTTtg > 1:1218908/1‑126 (MQ=255)
cGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAACGGACATCCATCACATGTTGCATCACTTCAGCGTCAGTTTGTGCTGCATCTTTAAATGattgcat > 1:1333272/1‑149 (MQ=255)
|
GAATACCCTCCATGGAACAGCAGTAATTTATAAATAAGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAACGGACATCCATCACATGTTGCATCACTTCAGCGTCAGTTTGTGCTGCATCTTTAAATGATTGCAT > NC_000913/1169294‑1169531
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
