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 |
|
A6 F1 I0 R2
|
251 |
90.0 |
5200563 |
86.9% |
4519289 |
59.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,266,192 |
C→G |
22.2% |
G84G (GGG→GGC) |
tufB ← |
protein chain elongation factor EF‑Tu |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,266,192 | 0 | C | G | 22.2%
| 101.0
/ 21.8
| 45 | G84G (GGG→GGC) | tufB | protein chain elongation factor EF‑Tu |
| Reads supporting (aligned to +/- strand): ref base C (9/26); new base G (4/6); total (13/32) |
| Fisher's exact test for biased strand distribution p-value = 4.41e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AGGATCGCGCCGTCCATCTGCGCAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCGGGCAGTCTACGTGTGCGTAGTGACGG > minE/2266133‑2266222
|
aGGATCGCGCCGTCCATCTGCGCAGCACCGGTAATCATGTTCTTGATGTAGTCGGCGTGGCCTGGGCAGt > 1:1879085/1‑70 (MQ=11)
aGGATCGCGCCGTCCATCTGCGCAGCACCGGTAATCATGTTCTTGATGTAGTCGGCGTGGCCTGGGCAGTc < 1:712045/71‑1 (MQ=11)
aGGATCGCGCCGTCCATCTGCGCAGCACCGGTAATCATGTTCTTGATGTAGTCGGCGTGGCCTGGGCAGTc < 1:4985370/71‑1 (MQ=11)
aGGATCGCGCCGTCCATCTGCGCAGCACCGGTAATCATGTTCTTGATGTAGTCGGCGTGGCCTGGGCAGTc < 1:268631/71‑1 (MQ=11)
aGGATCGCGCCGTCCATCTGCGCAGCACCGGTAATCATGTTCTTGATGTAGTCGGCGTGGCCTGGGCAGTc < 1:297206/71‑1 (MQ=11)
gATCGCGCCGTCCATCTGCGCAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCggg < 1:801683/64‑1 (MQ=35)
gATCGCGCCGTCCATCTGCGCAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCggg < 1:2438177/64‑1 (MQ=35)
gATCGCGCCGTCCATCTGCGCAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCggg < 1:2677146/64‑1 (MQ=35)
gATCGCGCCGTCCATCTGCGCAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCggg < 1:3995979/64‑1 (MQ=35)
tCGCGCCGTCCATCTGCGCAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGcc > 1:3194415/1‑57 (MQ=35)
tCGCGCCGTCCATCTGCGCAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCGGGCAGTCTAc > 1:1514593/1‑70 (MQ=35)
tCGCGCCGTCCATCTGCGCAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCGGGCAGTCTACg > 1:3369030/1‑71 (MQ=34)
tCGCGCCGTCCATCTGCGCAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCGGGCAGTCTACg > 1:4584516/1‑71 (MQ=34)
tCGCGCCGTCCATCTGCGCAGCACAGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCGGGCAGTCTACg > 1:2615751/1‑71 (MQ=21)
ccGTCCATCTGCGCAGCACCGGTGATCATGTTTTCAACATAGTCGGCGTGCCCCGGGCAGTCTACGTGTGc > 1:2021762/1‑71 (MQ=21)
cggccATCTGCGCAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCGGGCAGTCTACGTGTGCg < 1:1234672/68‑1 (MQ=21)
cGTCCATCTGCGCAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCGGGCAGTCTACGTGTGCg < 1:3536838/71‑1 (MQ=34)
cGTCCATCTGCGCAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCGGGCAGTCTACGTGTGCg < 1:5083395/71‑1 (MQ=34)
cGTCCATCTGCGCAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCGGGCAGTCTACGTGTGCg < 1:1024165/71‑1 (MQ=34)
cGTCCATCTGCGCAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCGGGCAGTCTACGTGTGCg < 1:2576480/71‑1 (MQ=34)
gTCCATCTGCGCAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTTCCCCGGGCAGTCTACGTGTGCGt < 1:116911/71‑1 (MQ=21)
gTCCATCTGCGCAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCGGGCAGTCTACGTGTGCGt < 1:1005779/71‑1 (MQ=34)
gTCCATCTGCGCAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCGGGCAGTCTACGTGTGCGt < 1:758690/71‑1 (MQ=34)
tCCATCTGCGCAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCGGGCAGTCTACGTGTGCGTa < 1:4593377/71‑1 (MQ=34)
ccATCTGCGCAGCACCGGTAATCATGTTCTTGATGTAGTCGGCGTGGCCTGGGCAGTCAACGTGCGCGTa > 1:2374542/1‑70 (MQ=2)
ccATCTGCGCAGCACCGGTAATCATGTTCTTGATGTAGTCGGCGTGGCCTGGGCAGTCAACGTGCGCGTa > 1:2323996/1‑70 (MQ=2)
ccATCTGCGCAGCACCGGTAATCATGTTCTTGATGTAGTCGGCGTGGCCTGGGCAGTCAACGTGCGCGTAg > 1:4104371/1‑71 (MQ=2)
cATCTGCGCAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCGGGCAGTCTACGTGTGCGTAg < 1:2274659/70‑1 (MQ=35)
cATCTGCGCAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCGGGCAGTCTACGTGTGCGTAg < 1:1112507/70‑1 (MQ=35)
cATCTGCGCAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCGGGCAGTCTACGTGTGCGTAGt > 1:2603834/1‑71 (MQ=34)
cATCTGCGCAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCGGGCAGTCTACGTGTGCGTAGt > 1:4327106/1‑71 (MQ=34)
cATCTGCGCAGCACCGGTAATCATGTTCTTGATGTAGTCGGCGTGGCCTGGGCAGTCAACGTGAGCGTAGt < 1:4400135/71‑1 (MQ=2)
cATCTGCGCAGCACCGGTAATCATGTTCTTGATGTAGTCGGCGTGGCCTGGGCAGTCAACGTGAGCGTAGt < 1:1730082/71‑1 (MQ=2)
tCTGCGCAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCGGGCAGTCTACGTGTGCGTAGt < 1:1465794/69‑1 (MQ=35)
tCTGCGCAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCGGGCAGTCTACGTGTGCGTAGt < 1:4568808/69‑1 (MQ=35)
tCTGCGCAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCGGGCAGTCTACGTGTGCGTAGt < 1:1075632/69‑1 (MQ=35)
tCTGCGCAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCGGGCAGTCTACGTGTGCGTAGt < 1:2374937/69‑1 (MQ=35)
tCTGCGCAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCGGGCAGTCTACGTGTGCGTAGt < 1:770768/69‑1 (MQ=35)
tCTGCGCAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCGGGCAGTCTACGTGTGCGTAGt < 1:88499/69‑1 (MQ=35)
tCTGCGCAGCACCGGTGATCATGTGTTTAACATAGTCGGCGTGCCCCGGGCAGTCTACGTGTGCGTAGt < 1:738858/69‑1 (MQ=25)
cTGCGCAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCGGGCAGTCTACGTGTGCGTAGt < 1:3748934/68‑1 (MQ=35)
tGCGCAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCGGGCAGTGTACGTGTGCGTAGTGACg > 1:2382090/1‑71 (MQ=21)
tGCGCAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCGGGCAGTCTACGTGTGCGTAGTGACg > 1:2796724/1‑71 (MQ=34)
cgcAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCGGGCAGTCTACGTGTGCGTAGTGACgg < 1:3849002/70‑1 (MQ=31)
cgcAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCGGGCAGTCTACGTGTGCGTAGTGACgg < 1:1102974/70‑1 (MQ=31)
cgcAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCGGGCAGTCTACGTGTGCGTAGTGACgg < 1:1077606/70‑1 (MQ=31)
|
AGGATCGCGCCGTCCATCTGCGCAGCACCGGTGATCATGTTTTTAACATAGTCGGCGTGCCCCGGGCAGTCTACGTGTGCGTAGTGACGG > minE/2266133‑2266222
|
| 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
