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 |
|
A10 F1 I2 R1
|
67 |
36.0 |
1614110 |
95.1% |
1535018 |
114.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
1,594,132 |
(C)8→9 |
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 | 96.2%
| 88.1
/ ‑2.8
| 26 | pseudogene (2/1461 nt) | yneO | pseudogene, AidA homolog |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base C (12/13); total (13/13) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.11e-01 |
AACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCC‑TTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCC > NC_000913/1593986‑1594255
|
aaCGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCC‑TTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTg > 2:388607/1‑139 (MQ=255)
cGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCC‑TTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTGTTAGCGACACGCAGTG‑‑cc < 2:447321/139‑1 (MQ=255)
caGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCC‑TTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑‑cccccccc < 1:191696/139‑1 (MQ=255)
caGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCC‑TTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑‑cccccccc < 1:378686/139‑1 (MQ=255)
caGGCCATTGTCTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCC‑TTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑‑cccccccc < 1:526139/139‑1 (MQ=255)
ttGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCC‑TTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCAcc > 1:741579/1‑139 (MQ=255)
ccGTTAACGGTCAGTACATTCCCCGGTTTCCCCCC‑TTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGc < 1:766031/139‑1 (MQ=255)
gTTAACGGTCAGTACATTCCCCGGTTTCCCCCC‑TTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAg > 1:431991/1‑139 (MQ=255)
aCATTCCCCGGTTTCCCCCC‑TTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTcc < 2:316626/139‑1 (MQ=255)
tttCCCCCCTTTCCCTTTTCATTTGACCCGGCCCCCCATTCCCAAGGTGGCCCCGGAAATGGTTTTTACCGACACGCGGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATcaca < 1:773683/139‑1 (MQ=255)
tttCCCCCC‑TTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCCGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCacac < 1:388607/139‑1 (MQ=255)
tttCCCCCC‑TTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCacac < 2:431991/139‑1 (MQ=255)
tCCCCCC‑TTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCg < 2:468229/139‑1 (MQ=255)
tCCCCCC‑TTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCCCCGCTAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCg < 2:127807/139‑1 (MQ=255)
ttCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTAt > 1:442400/1‑139 (MQ=255)
cATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTaa > 1:619158/1‑139 (MQ=255)
ttGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAAtgt > 1:600824/1‑139 (MQ=255)
aaCCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACAt > 1:240988/1‑110 (MQ=255)
aaCCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACAt < 2:240988/110‑1 (MQ=255)
aaCCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGtt > 1:178897/1‑139 (MQ=255)
aaCCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGtt > 2:234033/1‑139 (MQ=255)
cGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGAc < 2:280192/139‑1 (MQ=255)
tGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGa < 1:186540/136‑1 (MQ=255)
tGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGa > 2:186540/1‑136 (MQ=255)
cgccATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGcc < 2:600824/139‑1 (MQ=255)
ggTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGtt < 2:247381/103‑1 (MQ=255)
ggTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGtt > 1:247381/1‑103 (MQ=255)
ccgccgATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCAt > 1:557799/1‑46 (MQ=255)
ccgccgATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCAt < 2:557799/46‑1 (MQ=255)
aGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAAttt > 2:452446/1‑139 (MQ=255)
cacGCAGTG‑‑‑CCCCCCCAGGCATAACGCTCATATCACCGGCAGTAGTGACACTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTTACTTGCCATATTAATGGCAGAGTCGCAACCGAAAGCAATTTtcccccc > 1:539196/1‑139 (MQ=255)
|
AACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCC‑TTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCC > NC_000913/1593986‑1594255
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
