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 F3 I0 R1
|
560 |
56.4 |
4650532 |
94.9% |
4413354 |
59.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
4,325,315 |
T→A |
28.0% |
K10M (AAG→ATG) |
phnI ← |
carbon‑phosphorus lyase complex subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 4,325,315 | 0 | T | A | 28.0%
| 61.9
/ 24.1
| 39 | K10M (AAG→ATG) | phnI | carbon‑phosphorus lyase complex subunit |
| Reads supporting (aligned to +/- strand): ref base T (14/14); new base A (8/3); total (22/17) |
| Fisher's exact test for biased strand distribution p-value = 2.88e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-01 |
AGTTCGGGCAAATCGGTATCGCCTCGGCGTCGGCTCTCTTGCAGGGCGTGGGCGGCGTCGATCGCCTTCTCGCCCCCTTTCACGGCAACGTACATCAGCACACCTCCACATGAGTGGTTCGCGGAATAGCCAGCAGG > W3110S.gb/4325249‑4325385
|
aGTTCGGGCAAATCGGTATCGCCTCGGCGTCGGCTCTCTTGCAGGGCGTGGGCGGCGTCGATCGCCTtc < 1:3095600/69‑1 (MQ=255)
cGGGCAAATCGGTATCGCCTCGGCGTCGGCTCTCTTGCAGGGCGTGGGCGGCGTCGATCGCCTTCTCGccc > 1:2799534/1‑71 (MQ=255)
cGGGCAAATCGGTATCGCCTCGGCGTCGGCTCTCTTGCAGGGCGTGGGCGGCGTCGATCGCCTTCTCGccc > 1:2047447/1‑71 (MQ=255)
aaaTCGGTATCGCCTCGGCGTCGGCTCTCTTGCAGGGCGTGGGCGGCGTCGATCGCCTTCTCGCCCCCttt < 1:4066922/71‑1 (MQ=255)
gCCTCGGCGTCGGCTCTCTTGCAGGGCGTGGGCGGCGTCGATCGCCTTCTCGCCCCCTTTCACGGCAACg < 1:1441130/70‑1 (MQ=255)
gCCTCGGCGTCGGCTCTCTTGCAGGGCGTGGGCGGCGTCGATCGCCTTCTCGCCCCCTTTCACGGCAACg > 1:1610134/1‑70 (MQ=255)
gCCTCGGCGTCGGCTCTCTTGCAGGGCGTGGGCGGCGTCGATCGCCTTCTCGCCCCCTTTCACGGCAACg < 1:2327798/70‑1 (MQ=255)
gCCTCGGCGTCGGCTCTCTTGCAGGGCGTGGGCGGCGTCGATCGCCATCTCGCCCCCTTTCACGGCAACg > 1:918411/1‑70 (MQ=255)
gCCTCGGCGTCGGCTCTCTTGCAGGGCGTGGGCGGCGTCGATCGCCATCTCGCCCCCTTTCACGGCAACg > 1:3311513/1‑70 (MQ=255)
gCCTCGGCGTCGGCTCTCTTGCAGGGCGTGGGCGGCGTCGATCGCCATCTCGCCCCCTTTCACGGCAACg > 1:3729334/1‑70 (MQ=255)
gCCTCGGCGTCGGCTCTCTTGCAGGGCGTGGGCGGCGTCGATCGCCATCTCGCCCCCTTTCACGGCAACg > 1:454136/1‑70 (MQ=255)
gtcGTCGGCTCTCTTGCAGGGCGTGGGCGGCGTCGATCGCCATCTCGCCCCCTTTCACGGCAACGTACATc < 1:1723946/69‑1 (MQ=255)
ggCGTCGGCTCTCTTGCAGGGCGTGGGCGGCGTCGATCGCCTTCTCGCCCCCTTTCACGGCaa > 1:2878693/1‑63 (MQ=255)
ggCGTCGGCTCTCTTGCAGGGCGTGGGCGGCGTCGATCGCCTTCTCGCCCCCTTTCACGGCAACGTACa < 1:2063943/69‑1 (MQ=255)
ggCGTCGGCTCTCTTGCAGGGCGTGGGCGGCGTCGATCGCCTTCTCGCCCCCTTTCACGGCAACGTACAt > 1:719392/1‑70 (MQ=255)
gCGTCGGCTCTCTTGCAGGGCGTGGGCGGCGTCGATCGCCTtc < 1:2295842/43‑1 (MQ=255)
gCGTCGGCTCTCTTGCAGGGCGTGGGCGGCGTCGATCGCCATCTCGCCCCCTTTCACGGCAACg < 1:789512/64‑1 (MQ=255)
ggCTCTCTTGCAGGGCGTGGGCGGCGTCGATCGCCATCTCGCCCCCTTTCa > 1:2767341/1‑51 (MQ=255)
ctctTGCAGGGCGTGGGCGGCGTCGATCGCCTTCTCGCCCCCTTTCACGGCAACGTACATCAGCACACCTc > 1:3872363/1‑71 (MQ=255)
ctctTGCAGGGCGTGGGCGGCGTCGATCGCCATCTCGCCCCCTTTCACGGCAACGTACATCAGCacac > 1:1720023/1‑68 (MQ=255)
tctTGCAGGGCGTGGGCGGCGTCGATCGCCTTCTCGCCCCCTTTCACGGCAACGTACAt < 1:488318/59‑1 (MQ=255)
tGCAGGGCGTGGGCGGCGTCGATCGCCTTCTCGCCCCCTTTCACGGCAACGTACATCAGCACACCTCcaca > 1:194357/1‑71 (MQ=255)
gCAGGGCGT‑GGCGGCGTCGATCGCCTTCTCGCCCCCTTTCACGGCAACGTACATCAGCACACCTCCACAt < 1:13305/70‑1 (MQ=255)
cAGGGCGTGGGCGGCGTCGATCGCCTTCTCGCCCCCTTTCACGGCAACGTACATCAGCACACCTCCACAt < 1:1156602/70‑1 (MQ=255)
cAGGGCGTGGGCGGCGTCGATCGCCTTCTCGCCCCCTTTCACGGCAACGTACATCAGCACACCTCCACAt < 1:3331064/70‑1 (MQ=255)
cGTGGGCGGCGTCGATCGCCTTCTCGCCCCCTTTCACGGCAACGTACATCAGCACACCTCCACATGAGTgg > 1:2619957/1‑71 (MQ=255)
tGGGCGGCGTCGATCGCCATCTCGCCCCCTTTCACGGCAACGTACATCAGCACACCTCCACATGa > 1:336271/1‑65 (MQ=255)
gcggcgTCGATCGCCTTCTCGCCCCCTTTCACGGCAACGTACATCAGCACACCTCCACATGAGTGGTTcgc > 1:3863592/1‑71 (MQ=255)
gcgTCGATCGCCTTCTCGCCCCCTTTCACGGCAACGTACa < 1:1859509/40‑1 (MQ=255)
gcgTCGATCGCCTTCTCGCCCCCTTTCACGGCAACGTACATCAGCACACCTCCACATGAGTGGTTCGCGGa < 1:4272843/71‑1 (MQ=255)
gTCGATCGCCTTCTCGCCCCCTTTCACGGCAACGTACa < 1:3018253/38‑1 (MQ=255)
gTCGATCGCCTTCTCGCCCCCTTTCACGGCAACGTACATCAGCACACCTCCACATGAGTGGTTCGCGGaa > 1:2485667/1‑70 (MQ=255)
gTCGATCGCCTTCTCGCCCCCTTTCACGGCAACGTACATAAGCACACCTCcaca > 1:3343624/1‑54 (MQ=255)
tCGATCGCCTTCTCGCCCCCTTTCACGGCAACGTACATCAGCACACCTCCACATGAGTGGTTCGCGGAAt < 1:2967684/70‑1 (MQ=255)
tCGATCGCCATCTCGCCCCCTTTCACGGCAACGTACATCAGCACACCTCCACATGAGTGGTTCGCGGAATa < 1:2874653/71‑1 (MQ=255)
gATCGCCTTCTCGCCCCCTTTCACGGCAACGTACATCAGCacac > 1:3988494/1‑44 (MQ=255)
gATCGCCTTCTCGCCCCCTTTCAAGGCAACGTACATCAGCACACCTCCACATGAGTGGTTCGCGGAATAGc > 1:1861687/1‑71 (MQ=255)
gATCGCCATCTCGCCCCCTTTCACGGCAACGTACATCAGCACACCTCCACATGAGTGGTTCGCGGAATAGc > 1:1882686/1‑71 (MQ=255)
cGCCTTCTCGCCCCCTTTCACGGCAACGTACATCAGCACACCTCCACATGAGTGGTTCGCGGAATAGCcag > 1:272140/1‑71 (MQ=255)
ttCTCGCCCCCTTTCACGGCAACGTACATCAGCACACCTCCACATGAGTGGTTCGCGGAATAGCCAGCAgg > 1:2568424/1‑71 (MQ=255)
|
AGTTCGGGCAAATCGGTATCGCCTCGGCGTCGGCTCTCTTGCAGGGCGTGGGCGGCGTCGATCGCCTTCTCGCCCCCTTTCACGGCAACGTACATCAGCACACCTCCACATGAGTGGTTCGCGGAATAGCCAGCAGG > W3110S.gb/4325249‑4325385
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
