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 |
4,501,500 |
A→G |
35.1% |
Q23Q (CAA→CAG) |
intB → |
predicted integrase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 4,501,500 | 0 | A | G | 35.1%
| 35.2
/ 34.8
| 37 | Q23Q (CAA→CAG) | intB | predicted integrase |
| Reads supporting (aligned to +/- strand): ref base A (17/7); new base G (4/9); total (21/16) |
| Fisher's exact test for biased strand distribution p-value = 3.57e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01 |
TGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAG > W3110S.gb/4501439‑4501552
|
tGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTg > 1:1903472/1‑71 (MQ=255)
tGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTg > 1:1938347/1‑71 (MQ=255)
caAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTgg > 1:1681022/1‑60 (MQ=255)
caAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGtt > 1:490557/1‑71 (MQ=255)
caAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGtt > 1:232197/1‑71 (MQ=255)
caAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGtt > 1:1842379/1‑71 (MQ=255)
cTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGa < 1:911365/70‑1 (MQ=255)
cTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGa < 1:454726/70‑1 (MQ=255)
cTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGa < 1:294403/70‑1 (MQ=255)
tAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGa < 1:724263/69‑1 (MQ=255)
aGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGaa < 1:451596/68‑1 (MQ=255)
aGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGaa < 1:1412944/68‑1 (MQ=255)
aGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGaa < 1:1628814/68‑1 (MQ=255)
aGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAAt < 1:1069769/70‑1 (MQ=255)
aGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAAt < 1:304501/70‑1 (MQ=255)
aGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAAt < 1:1631427/70‑1 (MQ=255)
aGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAAt < 1:1629285/70‑1 (MQ=255)
aGTACTGCCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGaa < 1:96936/68‑1 (MQ=255)
gTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCg < 1:1732554/71‑1 (MQ=255)
gTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCg < 1:320443/71‑1 (MQ=255)
gTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCg < 1:1088092/71‑1 (MQ=255)
aCCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGa < 1:1501284/49‑1 (MQ=255)
ccGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCagag > 1:974629/1‑71 (MQ=255)
ccGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCagag > 1:905772/1‑71 (MQ=255)
ccGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCagag > 1:1735961/1‑71 (MQ=255)
ccGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCagag > 1:984116/1‑71 (MQ=255)
ccGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCagag > 1:941265/1‑71 (MQ=255)
ccGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCagag > 1:403932/1‑71 (MQ=255)
ccGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCagag > 1:1648620/1‑71 (MQ=255)
ccGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCaga > 1:1262263/1‑70 (MQ=255)
aTGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATcaca > 1:1210563/1‑50 (MQ=255)
aTGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATcaca > 1:1279248/1‑50 (MQ=255)
aTGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATcaca > 1:842172/1‑50 (MQ=255)
aTGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATcaca > 1:1006365/1‑50 (MQ=255)
aTGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATcaca > 1:1506542/1‑50 (MQ=255)
aTGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATcaca > 1:1516885/1‑50 (MQ=255)
aTGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATcaca > 1:1769114/1‑50 (MQ=255)
|
TGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAG > W3110S.gb/4501439‑4501552
|
| 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
