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 F28 I1 R2
|
328 |
63.0 |
4687567 |
98.0% |
4593815 |
65.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,051,238 |
T→C |
intergenic (+286/+147) |
insB → / ← cspH |
IS1 transposase InsAB'/stress protein, member of the CspA‑family |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,051,238 | 0 | T | C | 95.0%
| 132.5
/ ‑4.2
| 40 | intergenic (+286/+147) | insB/cspH | IS1 transposase InsAB'/stress protein, member of the CspA‑family |
| Reads supporting (aligned to +/- strand): ref base T (0/0); major base C (24/14); minor base A (2/0); total (26/14) |
| Fisher's exact test for biased strand distribution p-value = 5.33e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01 |
GTTACGAAAGCTATTAATTATTGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTTAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCTTAAATGGATTAGTTTCTTTGTGGAA > W3110S.gb/1051177‑1051302
|
gTTACGAAAGCTATTAATTATTGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTCAAATGGCa < 1:3535891/70‑1 (MQ=255)
aaGCTATTAATTATTGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTCAAATGGCATTTATAAc < 1:1899251/71‑1 (MQ=255)
ttaattaTTGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTCAAATGGCATTTATAACTATTa < 1:1174859/70‑1 (MQ=255)
taattaTTGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTCAAATGGCATTTATAACTATTAgg > 1:872954/1‑71 (MQ=255)
aattaTTGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTCAAATGGCATTTATAACTATTAGGt > 1:1956949/1‑71 (MQ=255)
aattaTTGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTCAAATGGCATTTATAACTATTAGGt > 1:1922753/1‑71 (MQ=255)
attattGTTGGTAATATAGTTTCAAGAGGTACTATAACTGGCTGTCAAATGGCATTTATAACTATTAgg > 1:726690/1‑69 (MQ=255)
ttattGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTCAAATGGCATTTATAACt < 1:1958209/62‑1 (MQ=255)
attGTTGGTAATATAGTTTCCAGTGGTACTATAACTGGCTGTCAAATGGCATTTATAACTATTAggag > 1:2389057/1‑66 (MQ=255)
ggTAATATAGTTTCAAGTGGTACTATAACTGGCTGTCAAATGGCATTTATAACTa > 1:3635207/1‑55 (MQ=255)
ataGTTTCAAGTGGTACTATAACTGGCTGTCAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCt > 1:55096/1‑70 (MQ=255)
ataGTTTCAAGTGGTACTATAACTGGCTGTCAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCt > 1:651967/1‑70 (MQ=255)
taGTTTCAAGTGGTACTATAACTGGCTGTCAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCtt > 1:3976064/1‑70 (MQ=255)
taGTTTCAAGTGGTACTATAACTGGCTGTCAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCtt > 1:3825586/1‑70 (MQ=255)
taGTTTCAAGTGGTACTATAACTGGCTGTCAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCtt > 1:3774090/1‑70 (MQ=255)
taGTTTCAAGTGGTACTATAACTGGCTGTCAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCtt > 1:2538976/1‑70 (MQ=255)
taGTTTCAAGTGGTACTATAACTGGCTGTCAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCTTa < 1:65516/71‑1 (MQ=255)
taGTTTCAAGTGGTACTATAACTGGCTGTCAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCTTa < 1:123508/71‑1 (MQ=255)
taGTTTCAAGTGGTACTATAACTGGCTGTCAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCTTa < 1:1477620/71‑1 (MQ=255)
taGTTTCAAGTGGTACTATAACTGGCTGTCAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCTTa < 1:1957472/71‑1 (MQ=255)
cAAGTGGTACTATAACTGGCTGTCAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCTTAAATgg < 1:2280040/70‑1 (MQ=255)
cAAGTGGTACTATAACTGGCTGTCAAATGGCATTTATAACTATTACGTGCAGAGATATTCGCTTAAATgg < 1:2529465/70‑1 (MQ=255)
tGGTACTATAACTGGCTGTCAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCTTAAATGGATTAg > 1:3982243/1‑71 (MQ=255)
ggTACTATAACTGGCTGTCAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCTTAAATGGATTAGt > 1:242015/1‑71 (MQ=255)
gTACTATAACTGGCTGTCAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCTTAAATGGATTAGtt > 1:4016753/1‑71 (MQ=255)
tACTATAACTGGCTGTCAAATGGCATTTATAACTAtt < 1:1448360/37‑1 (MQ=255)
tACTATAACTGGCTGTCAAATGGCATTTATAACTAtt < 1:3113113/37‑1 (MQ=255)
cTATAACTGGCTGTCAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCTTAAATGGATTAGTTTCt < 1:3458076/71‑1 (MQ=255)
tataACTGGCTGTCAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCTTAAATGGATTAGTTTCtt > 1:4166505/1‑71 (MQ=255)
ataACTGGCTGTCAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCTTAAATGGATTAGTTTCttt > 1:3717265/1‑71 (MQ=255)
ataACTGGCTGTCAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCTTAAATGGATTAGTTTCttt > 1:3547448/1‑71 (MQ=255)
ataACTGGCTGTCAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCTTAAATGGATTAGTTTCttt > 1:546357/1‑71 (MQ=255)
taACTGGCTGTCAAATGGCATTTATAACTATTAGGTGCAgaga > 1:2478168/1‑43 (MQ=255)
taACTGGCTGTCAAATGGCATTTATAACTATTAGGTGCAGAGata > 1:1527017/1‑45 (MQ=255)
taACTGGCTGTCAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCTTAAATGGATTAGTTTCttt > 1:248152/1‑70 (MQ=255)
taACTGGCTGTCAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCTTAAATGGATTAGTTTCTTtg > 1:1883251/1‑71 (MQ=255)
taACTGGCTGTCAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCTTAAATGGATTAGTTTCTTtg > 1:1692839/1‑71 (MQ=255)
taACTGGCTGTAAAATGGCATTTATAACTATTAGGTGCAGAGata > 1:2721584/1‑45 (MQ=255)
taACTGGCTGTAAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCTTAAATGGATTAGTTTCTTtg > 1:2538718/1‑71 (MQ=255)
gCTGTCAAATGTCATTTATAACTATTAGGTGCAGAGATATTCGCTTAAATGGATTAGTTTCTTTGTGGaa < 1:678392/70‑1 (MQ=255)
|
GTTACGAAAGCTATTAATTATTGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTTAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCTTAAATGGATTAGTTTCTTTGTGGAA > W3110S.gb/1051177‑1051302
|
| 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
