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 F21 I0 R2
|
308 |
27.9 |
1975068 |
96.7% |
1909890 |
67.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
4,645,120 |
T→C |
24.4% |
S13P (TCC→CCC) |
yjjY → |
hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 4,645,120 | 0 | T | C | 24.4%
| 72.9
/ 24.2
| 41 | S13P (TCC→CCC) | yjjY | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (11/20); new base C (4/6); total (15/26) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.78e-01 |
ATGCATGCTGCAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTCCATCAACGTCAACAACATCATTAGCTTGGTCGTGGGTACTTTCCCTCAGGACCCGACAGTGTCAAA > W3110S.gb/4645051‑4645187
|
atgcatgcTGGAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTc < 1:192545/71‑1 (MQ=255)
atgcatgcTGCAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTc < 1:1913885/71‑1 (MQ=255)
atgcatgcTGCAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTc < 1:884505/71‑1 (MQ=255)
atgcatgcTGCAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTc < 1:810000/71‑1 (MQ=255)
atgcatgcTGCAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTc < 1:1851585/71‑1 (MQ=255)
atgcatgcTGCAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTc < 1:1915121/71‑1 (MQ=255)
atgcatgcTGCAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTc < 1:1376476/71‑1 (MQ=255)
atgcatgcTGCAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTc < 1:1956117/71‑1 (MQ=255)
gcatgcTGCAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTCCa > 1:508828/1‑71 (MQ=255)
gcatgcTGCAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTCCa > 1:1710110/1‑71 (MQ=255)
gcatgcTGCAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTCCa > 1:47593/1‑71 (MQ=255)
gcatgcTGCAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTCCa > 1:543328/1‑71 (MQ=255)
gcatgcTGCAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTCCa > 1:1384891/1‑71 (MQ=255)
gcatgcTGCAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTCCa > 1:689249/1‑71 (MQ=255)
ctgcAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTCCATCAAc > 1:1741490/1‑71 (MQ=255)
ctgcAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTCCATCAAc > 1:694049/1‑71 (MQ=255)
ctgcAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTCCATCAAc > 1:972263/1‑71 (MQ=255)
aTTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTCCATCAACGTcaac < 1:1479006/71‑1 (MQ=255)
aTCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTCCCATCAACGTCAACAAcatcat > 1:974351/1‑70 (MQ=255)
aTCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTCCCATCAACGTCAACAAcatcat > 1:790171/1‑70 (MQ=255)
aTCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTCCCATCAACGTCAACAAcatcat > 1:1074814/1‑70 (MQ=255)
aTCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTCCCATCAACGTCAACAAcatcat > 1:1105286/1‑70 (MQ=255)
aCATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTCCATCAACGTCAACAACATCATTAGCTTGGTc > 1:1262413/1‑71 (MQ=255)
tGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTCCATCAACGTCAACAACATCATTAGCTTGGTCGTg > 1:1703104/1‑71 (MQ=255)
tAATTGCGTTCTTGATGCACTTTCCATCAACGTCAACAACATCATTAGCTTGGTCGTGGGTACTTTCCCTc < 1:1821067/71‑1 (MQ=255)
tAATTGCGTTCTTGATGCACTTTCCATCAACGTCAACAACATCATTAGCTTGGTCGTGGGTACTTTCCCTc < 1:1002040/71‑1 (MQ=255)
tAATTGCGTTCTTGATGCACTTTCCATCAACGTCAACAACATCATTAGCTTGGTCGTGGGTACTTTCCCTc < 1:1225862/71‑1 (MQ=255)
tAATTGCGTTCTTGATGCACTTTCCATCAACGTCAACAACATCATTAGCTTGGTCGTGGGTACTTTCCCTc < 1:1261499/71‑1 (MQ=255)
tAATTGCGTTCTTGATGCACTTTCCATCAACGTCAACAACATCATTAGCTTGGTCGTGGGTACTTTCCCTc < 1:1319600/71‑1 (MQ=255)
tAATTGCGTTCTTGATGCACTTTCCATCAACGTCAACAACATCATTAGCTTGGTCGTGGGTACTTTCCCTc < 1:1415943/71‑1 (MQ=255)
tAATTGCGTTCTTGATGCACTTTCCATCAACGTCAACAACATCATTAGCTTGGTCGTGGGTACTTTCCCTc < 1:449720/71‑1 (MQ=255)
tAATTGCGTTCTTGATGCACTTTCCATCAACGTCAACAACATCATTAGCTTGGTCGTGGGTACTTTCCCTc < 1:313789/71‑1 (MQ=255)
tAATTGCGTTCTTGATGCACTTTCCATCAACGTCAACAACATCATTAGCTTGGTCGTGGGTACTTTCCCTc < 1:1904033/71‑1 (MQ=255)
tAATTGCGTTCTTGATGCACTCTCCATCAACGTCAACAACATCATTAGCTTGGTCGTGGGTACTTTCCCTc < 1:555993/71‑1 (MQ=255)
gATGCACTTTCCATCAACGTCAACAACATCATTAGCTTGGTCGTGGGTACTTTCCCTCAGTACCCGAc < 1:1493768/68‑1 (MQ=255)
cTTCCCATCAACGTCAACAACATCATTAGCTTGGTCGTGGGTACTTTCCCTCAGGACCCGACAGTGTCaaa < 1:1388584/71‑1 (MQ=255)
cTTCCCATCAACGTCAACAACATCATTAGCTTGGTCGTGGGTACTTTCCCTCAGGACCCGACAGTGTCaaa < 1:58423/71‑1 (MQ=255)
cTTCCCATCAACGTCAACAACATCATTAGCTTGGTCGTGGGTACTTTCCCTCAGGACCCGACAGTGTCaaa < 1:529614/71‑1 (MQ=255)
cTTCCCATCAACGTCAACAACATCATTAGCTTGGTCGTGGGTACTTTCCCTCAGGACCCGACAGTGTCaaa < 1:715468/71‑1 (MQ=255)
cTTCCCATCAACGTCAACAACATCATTAGCTTGGTCGTGGGTACTTTCCCTCAGGACCCGACAGTGTCaaa < 1:914052/71‑1 (MQ=255)
cTTCCCATCAACGTCAACAACATCATTAGCTTGGTCGTGGGTACTTTCCCTCAGGACCCGACAGTGTCaaa < 1:1657675/71‑1 (MQ=255)
|
ATGCATGCTGCAAATTAACATGATCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTCCATCAACGTCAACAACATCATTAGCTTGGTCGTGGGTACTTTCCCTCAGGACCCGACAGTGTCAAA > W3110S.gb/4645051‑4645187
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
