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 |
|
A2 F999 I1 R1
|
226 |
132.7 |
9745491 |
85.7% |
8351885 |
75.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
3,957,548 |
1 bp→GG |
intergenic (‑117/‑744) |
ppiC ← / → rep |
peptidyl‑prolyl cis‑trans isomerase C/rep helicase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 3,957,547 | 1 | . | G | 95.7%
| 114.2
/ ‑0.7
| 46 | intergenic (‑116/‑745) | ppiC/rep | peptidyl‑prolyl cis‑trans isomerase C/rep helicase |
| Reads supporting (aligned to +/- strand): ref base . (1/1); new base G (18/26); total (19/27) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01 |
| * | NC_000913 | 3,957,548 | 0 | T | G | 97.8%
| 116.6
/ NA
| 46 | intergenic (‑117/‑744) | ppiC/rep | peptidyl‑prolyl cis‑trans isomerase C/rep helicase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); major base G (18/27); minor base C (1/0); total (19/27) |
| Fisher's exact test for biased strand distribution p-value = 4.13e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AATTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCC‑T‑GC‑TCGCAGGT‑CCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGG > NC_000913/3957495‑3957610
|||
aaTTGTCAGTCAGGGAGTGGCTGGGACATATATGGCAAAAGCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAggg > 1:2373864/1‑76 (MQ=255)
ttGTCAGTCAGGGAGTGGCTGGTAGATATATGGCAAAAGCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGga < 2:3321418/76‑1 (MQ=255)
tGTCAGTCAGGGAGTGGCTGGGACATATTAGGCAAAAGCCCGGAAAATCCGG‑GCTTCGCAGGTACCTCCAGGGgag > 1:4168813/1‑76 (MQ=255)
cagtcagGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGaaa < 1:4356466/76‑1 (MQ=255)
tcagGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACt < 1:3855424/76‑1 (MQ=255)
agGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAAccta < 1:4707900/76‑4 (MQ=255)
gAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTTAggg < 2:4554110/76‑1 (MQ=255)
gAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTTAggg > 1:3794618/1‑76 (MQ=255)
aGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTTAGGGc < 2:2121655/76‑1 (MQ=255)
aGTGGCTGGGACATATATGGCAAAAACCCGGAAAAACC‑CGGCTTCGCAGGTCCCTCCAGGGGAGAAAAATTAGGGc > 1:3217191/1‑76 (MQ=255)
gTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTTAGGGcc < 1:3110394/76‑1 (MQ=255)
gTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTTAGGGcc > 1:2666640/1‑76 (MQ=255)
tGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTTAg > 1:3946159/1‑71 (MQ=255)
tGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTTAg < 2:3946159/71‑1 (MQ=255)
tGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTTAGGGCct > 2:3268205/1‑76 (MQ=255)
tGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTTAGGGCct < 2:2843061/76‑1 (MQ=255)
tGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTTAGGGCct < 2:1905488/76‑1 (MQ=255)
ggCTGGTACATATATGGCAAAAGCCCGGAAAATCC‑GGGCTTCGCAGGTCCCTCAAGGGGAGAAAACTTAGGGCctc < 1:744419/76‑1 (MQ=255)
gCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTTAGGGCctct < 2:3803222/76‑1 (MQ=255)
tGGTACATATATGGCAAGAGCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTTAGGGCCTCTAt < 2:3761809/76‑1 (MQ=255)
gctACATATATGGCAAAAGCACGGAAAATCCGG‑GCGTCGCAGGTCCCTCAAGGGGAGAAAACTTAGGGCCTCTATg > 2:2490405/3‑76 (MQ=255)
gTACATATATGGCAAAAGCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTTAGGGCCTCTATgg < 2:704951/76‑1 (MQ=255)
gTACATATATGGCAAAAGCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTTAGGGCCTCTATgg > 2:1560184/1‑76 (MQ=255)
gTACATATATGGCAAAAGCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTTAGGGCCTCTATgg > 1:4823847/1‑76 (MQ=255)
tACATATATGGCAAAAGCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTTAGGGCCTCTATggg > 2:4790288/1‑76 (MQ=255)
tACATATATGGCAAAAGCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTTAGGGCCTCTATggg > 1:4058316/1‑76 (MQ=255)
atatctGGCAAAAGCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTGAGGGCCTCTATGGGCTa > 2:3075676/1‑76 (MQ=255)
atatatGGCAAAAGCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTa < 1:1969954/76‑1 (MQ=255)
tatatGGCAAAAGCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTTACGGCCTCTATGGGCTAc > 2:2405603/1‑76 (MQ=255)
atatGGCAAAAGCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACa < 1:3861387/76‑1 (MQ=255)
atGGCAAAAGCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACaaa < 1:2297354/76‑1 (MQ=255)
tGGCAAAAGCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACaacg > 2:4538089/1‑74 (MQ=255)
ggCAAAAGCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGt < 1:17239/76‑1 (MQ=255)
gCAAAAGCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTc < 2:3031416/76‑1 (MQ=255)
gCAAAAGCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTc < 2:61027/76‑1 (MQ=255)
aaaaGCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCAt < 2:270808/76‑1 (MQ=255)
aaaaGCCCGGAAAATCCGG‑GCTTCGCAGGGCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTGAt < 2:279557/76‑1 (MQ=255)
aaGCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTa > 2:4742274/1‑76 (MQ=255)
aaGCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTa < 2:1049561/76‑1 (MQ=255)
aGCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTAt < 2:666846/76‑1 (MQ=255)
gCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATc < 2:3719838/76‑1 (MQ=255)
gCCCGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATc < 2:2373863/76‑1 (MQ=255)
cccGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCg > 1:181306/1‑76 (MQ=255)
cccGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCg > 2:4770214/1‑76 (MQ=255)
cccGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCg > 1:3479906/1‑76 (MQ=255)
cGGAAAATCCGG‑GCTTCGCAGGTCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCggg < 1:3236507/76‑1 (MQ=255)
|||
AATTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCC‑T‑GC‑TCGCAGGT‑CCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGG > NC_000913/3957495‑3957610
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
