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 |
|
A11 F1 I1 R1
|
21 |
62.2 |
4089897 |
94.3% |
3856772 |
75.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
4,262,746 |
C→A |
A364S (GCT→TCT) |
actP ← |
acetate permease |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 4,262,746 | 0 | C | A | 97.7%
| 140.3
/ ‑2.4
| 44 | A364S (GCT→TCT) | actP | acetate permease |
| Reads supporting (aligned to +/- strand): ref base C (0/1); new base A (23/19); total (24/20) |
| Fisher's exact test for biased strand distribution p-value = 4.65e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.42e-01 |
TACAAGTCATGCGAAACCGCGGATGCGCCCGCCAGCGTCAGACCCGCAACCACCGCGAGGATAGTGGCGAAAGCAACCGCTGAAATAAAACCGAGGAACAGGTTGCCGCCCACTGCATTCGCCAGGTGAACGGCCGCCATGTTGT > REL606/4262673‑4262817
|
tACAAGTCATGCGAAACCGCGGATGCGCCCGCCAGCGTCAGACCCGCAACCACCGCGAGGATAGTGGCgaaagaaa > 1:1472932/1‑76 (MQ=255)
cAAGTCATGCGAAACCGCGGATGCGCCCGCCAGCGTCAGACCCGCAACCACCGCGAGGATAGTGGCGAAAGAAAcc > 2:1802416/1‑76 (MQ=255)
cAAGTCATGCGAAACCGCGGATGCGCCCGCCAGCGTCAGACCCGCAACCACCGCGAGGATAGTGGCGAAAGAAAcc > 2:1606184/1‑76 (MQ=255)
cAAGTCATGCGAAACCGCGGATGCGCCCGCCAGCGTCAGACCCGCAACCACCGCGAGGATAGTGGCGAAAGAAAcc > 2:1396322/1‑76 (MQ=255)
aGTCATGCGAAACCGCGGATGCGCCCGCCAGCGTCAGACCCGGAACCACCGCGAGGATAGTGGCGAAAGAAACCGc > 1:1493055/1‑76 (MQ=255)
gagAACCCGCGGAGGCCCCCGCCAGCGTCAGACCCGCAACCACCGCGAGGATAGTGGCGAAAGAAACCGCTGAAAt < 2:1116963/74‑1 (MQ=255)
cGAAACCGCGGATGCGCGCGCCAGCGTCAGACCCGCAACCACCGCGAGGATAGTGGCGAAAGAAACCGCTGAAATa > 1:2029679/1‑76 (MQ=255)
aaaaCCGCGGGGGCCCCCGCCAGCGTCAGACCCGCAACCACCGCGAGGATAGTGGCGAAAGAAACCGCTGAAATaa < 2:1907844/75‑1 (MQ=255)
cgcgGATGCGCCCGCCAGCGCCAGACCCGCAACCACCGCGAGGATAGTGGCGAAAGAAACCGCTGAAATAAAACCg > 2:174063/1‑76 (MQ=255)
cgGATGCGCCCGCCAGCGTCAGACCCGCAACCACCGCGAGGATAGTGGCGAAAGAAACCGCTGAAATAAAACCGAg > 1:842990/1‑76 (MQ=255)
cgGACGCGCCCGCCAGCGTCAGACCCGCAACCACCGCGAGGATAGTGGCGAAAGAAACCGCTGAAATAAAACCGAg < 2:1017943/76‑1 (MQ=255)
gATGCCCCCGCCAGTGTCAGACCCGCAACCACCGCGAGGATAGTGGCGAAAGAAACCGCTGAAATCAAACCGAGGa < 1:163562/76‑1 (MQ=255)
aTGCGCCCGCCAGCGTCAGACCCGCAACCACCGCGAGGATAGTGGCGAAAGAAACCGCTGAAATAAAACCGAGGaa > 2:1205477/1‑76 (MQ=255)
tGCGCCCGCCAGCGTCAGACCCGCAACCACCGCGAGGATAGTGGCGAAAGAAACCGCTGAAATAAAACCGAGGAAc > 1:761520/1‑76 (MQ=255)
ggcgcCCGCCAGCGTCAGACCCGCAACCACCGCGAGGATAGTGGCGAAAGAAACCGCTGAAATAAAACCGAGNAAc < 1:1832013/75‑1 (MQ=255)
cgcgcCCGCCAGCGTCAGACCCGCAACCACCGCGAGGATAGTGGCGAAAGAAACCGCTGAAATAAAACCGAGGAAc < 2:948482/75‑1 (MQ=255)
gcgcCCGCCAGCGTCAGACCCGCAACCACCGCGAGGATAGTGGCGAAAGAAACCGCTGAAATAAAACCGAGGAACa > 1:1808994/1‑76 (MQ=255)
cgcccgccAGCGTCAGACCCGCAACCACCGCGAGGATAGTGGCGAAAGAAACCGCTGAAATAAAACCGAGGAACAg < 2:1879989/76‑1 (MQ=255)
cccgccAGCGTCAGACCCGCAACCACCGCGAGGATAGTGGCGAAAGAAACCGCTGAAATAAAACCGAGGAACAGGt > 2:1532152/1‑76 (MQ=255)
gccAGCGTCAGACCCGCAACCACCGCGAGGATAGAGGCGAANGGAACCGCTGAAATAAAANCGNGGAACAGGTTgc > 1:1663050/1‑76 (MQ=255)
ccAGCGTCAGACCCTCAACCACCGCGAGGATAGTGGCGAAAGAAACCGCTGAAATAAACCCGAGGTACAGGTTgcc < 1:174063/76‑1 (MQ=255)
aGCGTCAGACCCGCAACCACCGCGAGGATAGTGGCGAAAGAAACCGCTGAAATAAAACCGAGGAACAGGTTgccgc > 1:1329004/1‑76 (MQ=255)
aGCGTCAGACCCGCAACCACCGCGAGGATAGTGGCGAAAGAAACCGCTGAAATAAAACCGAGGAACAGGTTgccgc > 2:1327567/1‑76 (MQ=255)
gCGTCAGACCCGCAACCACCGCGAGGATAGTGGCGAAAGAAACCGCTGAAATAAAACCGAGGAACAGGTTgccgcc < 1:146844/76‑1 (MQ=255)
gTCAGACCCGCAACCACCGCGAGGATAGTGGCGAAAGAAACCGCTGAAATAAAACCGAGGAACAGGTTGCCGCCCa > 1:1084613/1‑76 (MQ=255)
tCAGACCCGCAACCACCGCGAGGATAGTGGCGAAAGAAACCGCTGAAATAAAACCGAGGAACAGGTTGCCGCCCAc < 1:473233/76‑1 (MQ=255)
cAGACCCGCAACCACCGCGAGGATAGTGGCGAAAGAAACCGCTGAAATAAAACCGAGGAACAGGTTGCCGCCCACt > 1:1599933/1‑76 (MQ=255)
cAGACCCGCAACCACCGCGAGGATAGTGGCGAAAGAAACCGCTGAAATAAAACCGAGGAACAGGTTGCCGCCCACt > 2:1416964/1‑76 (MQ=255)
gACCCGCAACCACCGCGAGGATAGTGGCGAAAGAAACCGCTGAAATAAAACCGAGGAACAGGTTGCCGCCCACTGc < 1:364782/76‑1 (MQ=255)
gACCCGCAACCACCGCGAGGATAGTGGCGAAAGAAACCGCTGAAATAAAACCGAGGAACAGGTTGCCGCCCACTGc < 1:858413/76‑1 (MQ=255)
cGCAACCACCGCGAGGATAGTGGCGAAAGAAACCGCTGAAATAAAACCGAGGAACAGGTTGCCGCCCACTGCATTc < 1:961653/76‑1 (MQ=255)
cGCAACCACCGCGAGGATAGTGGCGAAAGAAACCGCTGAAATAAAACCGAGGAACAGGTTGCCGCCCACTGCATTc > 1:1312034/1‑76 (MQ=255)
cGCAACCACCGCGAGGATAGTGGCGAAAGAAACCGCTGAAATAAAACCGAGGAACAGGTTGCCGCCCACTGCATTc > 2:1236447/1‑76 (MQ=255)
aaCCACCGCGAGTATCGTGGCGAAAGAAACCGCTGAAATAAAACCGAGGAACAGGTTGCCGNCCACTGCATTCGcc > 1:1752298/1‑76 (MQ=255)
aaCCACCGCGAGGATAGTGGCGAAAGAAACCGCTGAAATAAAACCGAGGAACAGGTTGCCGCCCACTGCATTCGcc > 2:693440/1‑76 (MQ=255)
accaccGCGAGGATAGTGGCGAAAGAAACCGCTGAAATAAGCTCGAGGCACTGGCTGCCGCCCCCTGNATTCGCCa > 2:331018/1‑76 (MQ=255)
accaccGCGAGGATAGTGGCGAAAGAAACCGCTGAAATAAAACCGAGGAACAGGTTGCCGCCCACTGCATTCGCCa < 2:1289548/76‑1 (MQ=255)
ccGCGAGGATAGTGGCGAAAGCAACCGCTGAAATAAAACCGAGGAACAGGTTGCCGCCCACTGCATTCGCCAGGTg < 2:761294/76‑1 (MQ=255)
ccGCGAGGATAGTGGCGAAAGAAACCGCTGAAATAAAACCGAGGAACAGGTTGCCGCCCACTGCATTCGCCAGGTg < 2:864217/76‑1 (MQ=255)
cgAGGATAGTGGCGAAAGAAACCGCTGAAATAAAACTGAAGAACAGGTNGCCGCCCACTGCATTCGCCAGGTGAAc < 1:1778974/76‑1 (MQ=255)
cgAGGATAGTGGCGAAAGAAACCGCTGAAATAAAACCGAGGAACAGGTTGCCGCCCACTGCATTCGCCAGGTGAAc < 1:972941/76‑1 (MQ=255)
gATAGTGGCGAAAGAAACCGCTGAAATAAAACCGAGGAACAGGTTGCCGCCCACTGCATTCGCCAGGTGAACGgcc < 2:634826/76‑1 (MQ=255)
gTGGCGAAAGAAACCGCTGAAATAAAACCGAGGAACAGGTTGCCGCCCACTGCATTCGCCAGGTGAACGGCCGCCa < 2:1126492/76‑1 (MQ=255)
cGAAAGAAACCGCTGAAATAAAACCGAGGAACAGGTTGCCGCCCACTGCATTCGCCAGGTGAACGGCCGCCAtgtt > 2:413740/1‑76 (MQ=255)
aaaGAAACCGCTGAAATAAAACCGAGGAACAGGTTGCCGCCCACTGCATTCGCCAGGTGAACGGCCGCCAtgttgt > 2:446579/1‑76 (MQ=255)
aaaGAAACAGCTGAAATAAAACCGAGGAACAGGTTCCCGCCCACTGAATTCGCCAGATGAAGGGCCGCCAtgttgt > 2:45753/1‑76 (MQ=255)
|
TACAAGTCATGCGAAACCGCGGATGCGCCCGCCAGCGTCAGACCCGCAACCACCGCGAGGATAGTGGCGAAAGCAACCGCTGAAATAAAACCGAGGAACAGGTTGCCGCCCACTGCATTCGCCAGGTGAACGGCCGCCATGTTGT > REL606/4262673‑4262817
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
