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 |
|
A8 F1 I1 R1
|
15 |
61.9 |
4096487 |
94.5% |
3871180 |
75.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
3,145,869 |
G→T |
E2D (GAG→GAT) |
rpoD → |
RNA polymerase sigma factor |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 3,145,869 | 0 | G | T | 98.0%
| 174.0
/ ‑2.9
| 51 | E2D (GAG→GAT) | rpoD | RNA polymerase sigma factor |
| Reads supporting (aligned to +/- strand): ref base G (1/0); new base T (25/24); total (27/24) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.68e-01 |
AACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACCTATGCCGAG > REL606/3145797‑3145941
|
aaCGGCTGAAGGACATCGGGTCAATCGCCCAACACCACCCTCATGAAATAAGTGTGGATACCGTCTTATGGATCaa > 1:1714532/1‑76 (MQ=255)
aaCGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGATCaa > 1:1118789/1‑76 (MQ=255)
aCGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATGAGTGTGGATACCGTCTTATGGATCaaa < 1:1812560/76‑1 (MQ=255)
cGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGATCaaaa < 1:970937/76‑1 (MQ=255)
cGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGATCaaaa > 1:969798/1‑76 (MQ=255)
cTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGATCAAAAccc > 2:1125814/1‑76 (MQ=255)
cTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGATCAAAAccc < 1:869618/76‑1 (MQ=255)
cTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGATCAAAAccc < 1:1941276/76‑1 (MQ=255)
gAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAGATAAGTGTNGATACCGTCTTATGGATCAAAACCCGc < 1:1802745/76‑1 (MQ=255)
gAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGATCAAAACCCGc > 1:1023194/1‑76 (MQ=255)
gAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGATCAAAACCCGc > 1:643640/1‑76 (MQ=255)
gAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGATCAAAACCCGc > 2:506975/1‑76 (MQ=255)
aaGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGATCAAAACCCGCa > 2:1751454/1‑76 (MQ=255)
aaGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGATCAAAACCCGCa > 2:544802/1‑76 (MQ=255)
gACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGATCAACACCCGCAGTc < 1:1947122/76‑1 (MQ=255)
gACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGATCAAAACCCGCAGTc < 2:1755201/76‑1 (MQ=255)
aCATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGATCAAAACCCGCAGTca < 2:471841/76‑1 (MQ=255)
tCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGATCAAAACCCGCAGTCACAg < 2:700501/76‑1 (MQ=255)
gggTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGATCAAAACCCGCAGTCACAGCt < 2:1130067/76‑1 (MQ=255)
aaTCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGATCAAAACCCGCAGTCACAGCTGAAAc > 2:373190/1‑76 (MQ=255)
cGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCAGAGCTGAAActtc > 1:787266/1‑76 (MQ=255)
ccAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGATCAAAACCCGCAGTCACAGCTGAAACTTCTTg > 2:412697/1‑76 (MQ=255)
cAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGATCAAAACCCGCAGTCACAGCTGAAACTTCTTGt > 1:485600/1‑76 (MQ=255)
aaCACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGATCAAAACCCGCAGTCACAGCTGAAACTTCTTGTc > 1:1323818/1‑76 (MQ=255)
ccTCATGAAATAAGTGTGGATACCGTCTTATGGATCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTgg < 1:1534943/76‑1 (MQ=255)
cATGAAATAAGTGTGGATACCGTCTTATGGATCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTaa < 1:1273290/76‑1 (MQ=255)
cATGAAATAAGTGTGGATACCGTCTTATGGATCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTaa < 1:1442447/76‑1 (MQ=255)
aTGAAATAAGTGTGGATACCGTCTTATGGATCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAg < 1:837214/76‑1 (MQ=255)
tGAAATAAGTGTGGATANCGTCTTATGGATCAAAACCCGCAGTCACAGCTGAGACTTCTTGTCCCCCGTGGTAAgg > 1:263101/1‑76 (MQ=255)
gAAATAAGTGTGGATACCGTCTTATGGATCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGa > 1:1645712/1‑76 (MQ=255)
gAAATAAGTGTGGATACCGTCTTATGGATCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGa > 2:1217355/1‑76 (MQ=255)
aaGTGTGGATACAGTATTATGGATCAAAACCCGTAGTCACAGCTGAAACTTCTTGTCACCCNTGGTAAGGAGCAAg > 1:1752996/1‑76 (MQ=255)
aGTGTGGATACCGTCTTATGGATCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAgg > 1:567982/1‑76 (MQ=255)
gtgGATACCGTCTTATGGATCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTa < 1:1557803/76‑1 (MQ=255)
tgGATACCGTCTTATGGATCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTAt > 2:1354358/1‑76 (MQ=255)
tgGATACCGTCTTATGGATCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTAt < 2:369274/76‑1 (MQ=255)
ggATACCGTCTTATGGATCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATc > 2:1346175/1‑76 (MQ=255)
ggATACCGTCTTATGGATCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATc > 1:1397413/1‑76 (MQ=255)
ggATACCGTCTTATGGATCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATc > 1:1531760/1‑76 (MQ=255)
ggATACCGTCTTATGGATCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATc > 1:1815564/1‑76 (MQ=255)
aTACCGTCTTATGGATCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTg < 1:1341088/76‑1 (MQ=255)
tACCGTCTCATGGATCAAAACCCGCAGCTACTTCTGAGACTTTTTGTCACCCGTGGTAAGGAGGAAGGCTATCTGa < 1:1972911/76‑1 (MQ=255)
aCCGTCTTATGGATCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGAc > 1:1064064/1‑76 (MQ=255)
cGTCTTATGGATCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACCt < 2:1048428/76‑1 (MQ=255)
cGTCTTATGGATCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACCt > 1:1557746/1‑76 (MQ=255)
cGTCTTATGGATCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACCt < 1:1471854/76‑1 (MQ=255)
cGTCTTATGGATCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACCt < 2:567932/76‑1 (MQ=255)
cGTCTTATGGATCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACCt < 2:588096/76‑1 (MQ=255)
cGTCTTATGGATCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACCt < 2:719404/76‑1 (MQ=255)
tCTTATCGAACAAAACCGGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAANGCNATCTGACCTAt > 2:310401/1‑76 (MQ=255)
cTTATGGATCAAATCCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACCTATg < 1:1346502/76‑1 (MQ=255)
aTGGATCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACCTATGCCg < 2:1954993/76‑1 (MQ=255)
ggATCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACCTATGCCGAg < 2:1306871/76‑1 (MQ=255)
|
AACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACCTATGCCGAG > REL606/3145797‑3145941
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
