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 |
|
A3 F1 I1 R1
|
502 |
34.8 |
1912488 |
98.2% |
1878063 |
80.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
4,479,972 |
(T)8→9 |
coding (243/1197 nt) |
yjgN → |
conserved inner membrane protein YjgN |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 4,479,964 | 1 | . | T | 88.2%
| 50.8
/ 0.8
| 17 | coding (235/1197 nt) | yjgN | conserved inner membrane protein YjgN |
| Reads supporting (aligned to +/- strand): ref base . (2/0); new base T (10/5); total (12/5) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.39e-01 |
TCTTTATGCTAATATGGAAGTTAACGGACAACGATTTTCTTATGGAATTACCGGTGGGAATGTTTTTGTTAGTTGTC‑TTTTTTTTGTTTTTTTCTATTTCGCAATCTTAATGACAGTGTCAGCAGATATGCCGCTTGTTGGTTGTG > NC_000913/4479888‑4480033
|
tCTTTATGCTAATATGGAAGTTAACGGACAACGATTTTCTTATGGAATTACCGGTGGGAATGTTTTTGTTAGTTGTC‑ttt < 1:904795/80‑1 (MQ=255)
tATGCTAATATGGAAGTTAACGGACAACGATTTTCTTATGGAATTACCGGTGGGAATGTTTTTGTTAGTTGTC‑tttttt < 2:904796/79‑1 (MQ=255)
aTGCTAATATGGAAGTTAACGGACAACGATTTTCTTATGGAATTACCGGTGGGAATGTTTTTGTTAGTTGTC‑tttttttt < 2:904797/80‑1 (MQ=255)
aaTATGGAAGTTAACGGACAACGATTTTCTTATGGAATTACCGGTGGGAATGTTTTTGTTAGTTGTC‑TTTTTTTTTgtttt > 2:904833/1‑81 (MQ=255)
atatGGAAGTTAACGGACAACGATTTTCTTATGGAATTACCGGTGGGAATGTTTTTGTTAGTTGTC‑TTTTTTTTTgttttt > 1:904818/1‑81 (MQ=255)
atGGAAGTTAACGGACAACGATTTTCTTATGGAATTACCGGTGGGAATGTTTTTGTTAGTTGTCTTTTTTTTTGttttttt > 2:904819/1‑81 (MQ=255)
tGGAAGTTAACGGACAACGATTTTCTTATGGAATTACCGGTGGGAATGTTTTTGTTAGTTGTCTTTTTTTTTGTTTTTTTc > 2:904839/1‑81 (MQ=255)
aCGGACAACGATTTTCTTATGGAATTACCGGTGGGAATGTTTTTGTTAGTTGTCTTTTTTTTTGTTTTTTTCTATTTCGc > 2:904812/1‑80 (MQ=255)
cGGACAACGATTTTCTTATGGAATTACCGGTGGGATTGTTTCTGTTAGTTGTCTTTTTTTTTGTTTTTTTCTATTTCGCaa > 1:904825/1‑81 (MQ=255)
gACAACGATTTTCTTATGGAATTACCGGTGGGAATGTTTTTGTTAGTTGTCTTTTTTTTTGTTTTTTTCTATTTCGCAATc > 2:904823/1‑81 (MQ=255)
cGATTTTCTTATGGAATTACCGGTGGGAATGTTTTTGTTAGTTGTCTTTTTTTTTGTTTTTTTCTATTTCGCAATCTTAAt < 1:904799/81‑1 (MQ=255)
cGATTTTCTTATGGAATTACCGGTGGGAATGTTTTTGTTAGTTGTCTTTTTTTTTGTTTTTTTCTATTTCGCAATCTTAAt < 1:904798/81‑1 (MQ=255)
aTGGAATTACCGGTGGGAATGTTTTTGTTAGTTGTCTTTTTTTTTGTTTTTTTCTATTTCGCAATCTTAATGACAgtgt > 1:904840/1‑79 (MQ=255)
aTGGAATTACCGGTGGGAATGTTTTTGTTAGTTGTCTTTTTTTTTGTTTTTTTCTATTTCGCAATCTTAATGACAgtg < 2:904800/78‑1 (MQ=255)
aaTTACCGGTGGGAATGTTTTTGTTAGTTGTCTTTTTTTTTGTTTTTTTTTATTTCGCAATCTTAATGACAGTGTcag > 2:904827/1‑78 (MQ=255)
aCCGGTGGGAATGTTTTTGTTAGTTGTCTTTTTTTTTGTTTTTTTCTATTTCGCAATCTTAATGACAGTGTCAGCAGatat > 1:904829/1‑81 (MQ=255)
ccGGTGGGAATGTTTTTGTTAGTTGTCTTTTTTTTTGTTTTTTTCTATTTCGCAATCTTAATGACAGTGTCAGCAGatat < 2:904801/80‑1 (MQ=255)
cGGTGGGAATGTTTTTGTTAGTTGTCTTTTTTTTTGTTTTTTTCTATTTCGCAATCTTAATGACAGTGTCAGCAGATATGc > 2:904834/1‑81 (MQ=255)
ggAATGTTTTTGTTAGTTGTCTTTTTTTTTGTTTTTTTCTATTTCGCAATCTTAATGACAGTGTCAGCAGATATGCCGCtt < 1:904802/81‑1 (MQ=255)
tGTTAGTTGTCTTTTTTTTTGTTTTTTTCTATTTCGCAATCTTAATGACAGTGTCAGCAGATATGCCGCTTGTTGGTtgtg > 1:904838/1‑81 (MQ=255)
|
TCTTTATGCTAATATGGAAGTTAACGGACAACGATTTTCTTATGGAATTACCGGTGGGAATGTTTTTGTTAGTTGTC‑TTTTTTTTGTTTTTTTCTATTTCGCAATCTTAATGACAGTGTCAGCAGATATGCCGCTTGTTGGTTGTG > NC_000913/4479888‑4480033
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
