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 F8 I0 R1
|
311 |
50.1 |
4085234 |
95.9% |
3917739 |
60.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,472,806 |
C→T |
32.1% |
D272D (GAC→GAT) |
intS → |
predicted prophage CPS‑53 integrase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,472,806 | 0 | C | T | 32.1%
| 67.2
/ 43.4
| 53 | D272D (GAC→GAT) | intS | predicted prophage CPS‑53 integrase |
| Reads supporting (aligned to +/- strand): ref base C (9/27); new base T (7/10); total (16/37) |
| Fisher's exact test for biased strand distribution p-value = 3.37e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.62e-01 |
AAATAGGATTATCACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGTAGTTGAACTTCTCACTACGCTAAGCTCCATCACCAAACCAGTCTCAGAGTTTGTTTT > W3110S.gb/2472737‑2472868
|
aaaTAGGATTATCACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGAcc < 1:2566454/71‑1 (MQ=255)
aaTAGGATTATCACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGATCa < 1:2885800/71‑1 (MQ=255)
aaTAGGATTATCACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCa < 1:2997447/71‑1 (MQ=255)
aTAGGATTATCACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGATCa < 1:1806137/70‑1 (MQ=255)
tAGGATTATCACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGATCAgg > 1:1137663/1‑71 (MQ=255)
ggATTATCACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGATCAGGt < 1:2557301/70‑1 (MQ=255)
ggATTATCACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAgg > 1:1481419/1‑69 (MQ=255)
aTCACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGTAGTTg < 1:3007267/70‑1 (MQ=255)
aTCACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGTAGTTg < 1:2139918/70‑1 (MQ=255)
tCACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGTTTCCTATGTCAGACCAGGTAGTTg < 1:2692453/69‑1 (MQ=255)
tCACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGTAGTTg < 1:2785726/69‑1 (MQ=255)
tCACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGTAGTTGaa < 1:3778865/71‑1 (MQ=255)
tCACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGTAGTTGaa < 1:1176660/71‑1 (MQ=255)
tCACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGTAGTTGa < 1:2848447/70‑1 (MQ=255)
cATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGATCAGGTAGTTGAACTtc > 1:573103/1‑71 (MQ=255)
cATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGATCAGGTAGTTGAACTtc > 1:1666432/1‑71 (MQ=255)
aTCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGATCAGGTAGTTGAACTtct < 1:410467/71‑1 (MQ=255)
aTCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGTAGTTGAACTtct < 1:1002339/71‑1 (MQ=255)
tctaCGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGTAGTTGAAc < 1:530688/63‑1 (MQ=255)
tCGACGCCAGTTTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCa < 1:806874/55‑1 (MQ=255)
tCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGATCAGGTAGTTGAACtt < 1:1359632/68‑1 (MQ=255)
tCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGATCAGGTAGTTGAACtt < 1:1668640/68‑1 (MQ=255)
tCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAgg < 1:1771446/57‑1 (MQ=255)
tCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAgg < 1:3120568/57‑1 (MQ=255)
tCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAgg < 1:2643583/57‑1 (MQ=255)
tCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGTAGTTGAAc < 1:1508289/66‑1 (MQ=255)
cGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAgg < 1:1255360/56‑1 (MQ=255)
gACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGATCAGGTAg > 1:3648230/1‑58 (MQ=255)
gACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGATCAGGTAGTTGAACTtct > 1:1143749/1‑68 (MQ=255)
gACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGTAGTTGAACTTCTCAc < 1:1516916/71‑1 (MQ=255)
gACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGTAGTTGAACTTCTCAc < 1:1496742/71‑1 (MQ=255)
cAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGTAGTTGAACTTCTCACTACGc > 1:3206084/1‑71 (MQ=255)
cAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGTAGTTGAACTTCTCACTACGc > 1:1390398/1‑71 (MQ=255)
gtgATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAg > 1:3627158/1‑45 (MQ=255)
gtgATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAg > 1:3870644/1‑45 (MQ=255)
atgaAATGACGCAAAATTCATGTGGTTCCTATGTCAGACCAg > 1:688075/1‑42 (MQ=255)
tgaAAGGACGCAAAATTCATGTGGTTCCTATGTCAGATCAGGTAGTTGAACTtct < 1:143979/55‑1 (MQ=255)
aaGGACGCAAAATTCATGTGGTTCCTATGTCAGATCAGGTAGTTg < 1:1758985/45‑1 (MQ=255)
aaaaTTCATGTGGTTCCTATGTCAGACCAGGTAGTTGAACTTCTCACTACGCTAAGCTCCATCACCAAAcc < 1:801636/71‑1 (MQ=255)
aaaaTTCATGTGGTTCATATGTCAGACCAGGTAGTTGAACTTCTCACTACGCTAAGCTCCATCACCAAAcc < 1:1728478/71‑1 (MQ=255)
aaTTCATGTGGTTCCTATGTCAGACCAGGTAGTTGAACTTCTCACTACGCTAAGCTCCATCACCaaagc < 1:3045271/69‑3 (MQ=255)
aTTCATGTGGTTCCTATGTCAGACCAGGTAGTTGAACTTCTCACTACGCTa < 1:1421856/51‑1 (MQ=255)
ttCATGTGGTTCCTATGTCAGACCAGGTAGTTGAACTTCTCACTACGCTa < 1:1995610/50‑1 (MQ=255)
aTGTGGTTCCTATGTCAGACCAGGTAGTTGAACTTCTCACTACGCTAAGCTCCATCACCAAACCAGTCTCa < 1:2985130/71‑1 (MQ=255)
tgGTTCCTATGTCAGATCAGGTAGTTGAACTTCTCACTACGCTAAGCTCCATCACCAAACCAGTCTCaga < 1:3698524/70‑1 (MQ=255)
gTTCCTATGTCAGACCAGGTAGTTGAACTTCTCACTACGCTAAGCTCCATCACCAAACCAGTCTCagaggc > 1:1141504/1‑69 (MQ=255)
gTTCCTATGTCAGACCAGGTAGTTGAACTTCTCACTACGCTAAGCTCCATCACCAAACCAGTCTCagaggc > 1:2398231/1‑69 (MQ=255)
ccTATGTCAGACCAGGTAGTTGAACTTCTCACTACGCTAAGCTCCATCACCAAACCAGTCTCAGAgtttgt > 1:3749273/1‑71 (MQ=255)
tGTCAGACCAGGTAGTTGAACTTCTCACTACGCTAAGCTCCATCACCAAACCAGTCTCAGAGTTTGtttt < 1:613589/70‑1 (MQ=255)
tGTCAGACCAGGTAGTTGAACTTCTCACTACGCTAAGCTCCATCACCAAACCAGTCTCAGAGTTTGtttt < 1:3299068/70‑1 (MQ=255)
gTCAGATCAGGTAGTTGAACTTCTCACTACGCTAAGCTCCa > 1:3528381/1‑41 (MQ=255)
tCAGATCAGGTAGTTGAACTTCTCACTACGCTAAGCTc < 1:1400207/38‑1 (MQ=255)
tCAGACCAGGTAGTTGAACTTCTCACTACGCTAAGCTCCATCACCAAACCAGTCTCAGAgtttgtt < 1:1722196/66‑1 (MQ=255)
aGATCAGGTAGTTGAACTTCTCACTACGCTAAGCTCCATCACCaaa > 1:2380253/1‑46 (MQ=255)
|
AAATAGGATTATCACCATCGACGCCAGTGTGATGAAAGGACGCAAAATTCATGTGGTTCCTATGTCAGACCAGGTAGTTGAACTTCTCACTACGCTAAGCTCCATCACCAAACCAGTCTCAGAGTTTGTTTT > W3110S.gb/2472737‑2472868
|
| 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
