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 |
|
A8 F1 I1 R1
|
82 |
28.6 |
1225488 |
97.4% |
1193625 |
116.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
1,594,132 |
(C)8→10 |
pseudogene (3856/3861 nt) |
yneO ← |
pseudogene, AidA homolog |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,594,124 | 1 | . | C | 100.0%
| 77.7
/ NA
| 22 | pseudogene (2/1461 nt) | yneO | pseudogene, AidA homolog |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (11/11); total (11/11) |
| * | NC_000913 | 1,594,124 | 2 | . | C | 90.9%
| 70.1
/ 1.2
| 22 | pseudogene (2/1461 nt) | yneO | pseudogene, AidA homolog |
| Reads supporting (aligned to +/- strand): ref base . (2/0); new base C (9/11); total (11/11) |
| Fisher's exact test for biased strand distribution p-value = 4.76e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.65e-01 |
GTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑‑‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGA > NC_000913/1593989‑1594234
||
gTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑‑‑ccc < 1:230367/139‑1 (MQ=255)
tcatcaGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑‑‑cccc < 2:455897/139‑1 (MQ=255)
aGGGCATTATGTCGGGTAAAGGTGACGGTAATGGTCTTTACATGCCCCGGTTTCCCCCTTTCGCCAGTCATTTGATCCGTGCCGCCATTTTCCAGGTTGCCGCCGATAGTGGTTTTAGCGAAACGCGGAG‑‑‑ccccacccc < 1:481017/139‑2 (MQ=255)
ccGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑‑CCCCCCCCAGGCATAACGtt > 2:543779/1‑139 (MQ=255)
ataGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCCCCCCCCAGGCATAACGTTCat < 2:213812/139‑1 (MQ=255)
ttGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCC‑CCCCCCCCAGGCATAACGTTCATATCAc > 1:343246/1‑139 (MQ=255)
ccGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCC‑CCCCCCCCAGGCATAACGTTCATATCACCTg < 2:60580/139‑1 (MQ=255)
gTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCa > 2:482315/1‑139 (MQ=255)
gTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGaactt > 1:154493/1‑135 (MQ=255)
tCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGAc > 1:62678/1‑139 (MQ=255)
tCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑‑‑ccccccccccaggcata < 2:66568/104‑10 (MQ=255)
tCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑‑‑ccccccccccaggcata > 1:66568/1‑95 (MQ=255)
ccGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACAt > 1:592611/1‑139 (MQ=255)
ccccccTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCg > 2:54709/1‑139 (MQ=255)
cTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGtt < 2:422231/139‑1 (MQ=255)
tCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTAt < 2:343246/139‑1 (MQ=255)
cGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATg < 2:592611/139‑1 (MQ=255)
tGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGtt < 2:41984/118‑1 (MQ=255)
tGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGtt > 1:41984/1‑118 (MQ=255)
ggTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGc < 1:482315/139‑1 (MQ=255)
tGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTg > 2:330917/1‑98 (MQ=255)
tGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTg < 1:330917/98‑1 (MQ=255)
cgccgATAGTGGTTTTAGCGACACGCAGTGCC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACa > 2:13783/1‑84 (MQ=255)
cgccgATAGTGGTTTTAGCGACACGCAGTGCC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACa < 1:13783/84‑1 (MQ=255)
cgATAGTGGTTTTAGCGACACGCAGTGCC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGa < 1:54709/139‑1 (MQ=255)
aGCGACACGCAGTGCC‑CCCCCCCCAGGCATAACGTTCATATCACCTg < 2:164767/47‑1 (MQ=255)
aGCGACACGCAGTGCC‑CCCCCCCCAGGCATAACGTTCATATCACCTg > 1:164767/1‑47 (MQ=255)
||
GTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑‑‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGA > NC_000913/1593989‑1594234
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
