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 |
|
A4 F21 I0 R1
|
1009 |
73.8 |
4146436 |
87.4% |
3623985 |
60.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,474,821 |
T→G |
20.0% |
intergenic (+119/‑115) |
nrdA → / → nrdB |
ribonucleoside diphosphate reductase 1, alpha subunit/ribonucleoside diphosphate reductase 1, beta subunit, ferritin‑like |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,474,821 | 0 | T | G | 20.0%
| 41.4
/ 8.7
| 20 | intergenic (+119/‑115) | nrdA/nrdB | ribonucleoside diphosphate reductase 1, alpha subunit/ribonucleoside diphosphate reductase 1, beta subunit, ferritin‑like |
| Reads supporting (aligned to +/- strand): ref base T (7/9); new base G (2/2); total (9/11) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.35e-01 |
CTGATAAGACGCGCCAGCGTCGCATCAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAGGATGCGGC > minE/1474762‑1474891
|
cTGATAAGACGCGCCAGCGTCGCATCAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTAc > 1:3132577/1‑71 (MQ=255)
tAAGACGCGCCAGCGTCGCATCAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTACGGCt < 1:3644908/71‑1 (MQ=255)
aGACGCGCCAGCGTCGCATCAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTACGGCTCg < 1:3323169/71‑1 (MQ=255)
cgcgCCAGCGTCGCATCAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑t > 1:2683499/1‑71 (MQ=255)
cgcCAGCGTCGCATCAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑ttt < 1:1382229/71‑1 (MQ=255)
gcCAGCGTCGCATCAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑TTTg < 1:2149011/71‑1 (MQ=255)
gcCAGCGTCGCATCAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑TTTg < 1:2094629/71‑1 (MQ=255)
aGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAg < 1:778086/70‑1 (MQ=255)
ccGGATGCAGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTc > 1:2642924/1‑71 (MQ=255)
gATGCAGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCa < 1:1285296/71‑1 (MQ=255)
gATGCAGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCa < 1:1280417/71‑1 (MQ=255)
gATGCAGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCa > 1:3807445/1‑71 (MQ=255)
cgtaGCGTAAACGCCTGATCCGTCCAACGGTTCGGATTTTGTAGGCCTGATAAGACGCGGTAGCGTCGCAt > 1:1274066/4‑71 (MQ=2)
gtaaaCGCCTGATCCGTCCAACGGTTCGGATTTTGTAGGCCTGATAAGACGCGGTAGCGTCGCATCAGGca < 1:3461498/68‑1 (MQ=2)
taaaCGCCTGATCCGTCCAACGGTTCGGATTTTGTAGGCCTGATAAGAcg < 1:4043089/48‑1 (MQ=2)
gAACGCCTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCAt < 1:1152260/62‑1 (MQ=255)
aaCGCCTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAg > 1:3381782/1‑70 (MQ=255)
aaCGCCTGATCCGTCCAACGGTTCGGATTTTGTAGGCCTGATAAGACGCGGTAGCGTCGCATCAGGcatct > 1:1589145/1‑68 (MQ=2)
ccTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAGGATgc > 1:3008940/1‑71 (MQ=255)
cTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAGGATgcg > 1:930117/1‑71 (MQ=255)
tATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAGGATgcggc > 1:968122/1‑71 (MQ=255)
tATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAGGATgcggc > 1:2947588/1‑71 (MQ=255)
tATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAGGATgcggc > 1:1572154/1‑71 (MQ=255)
|
CTGATAAGACGCGCCAGCGTCGCATCAGGCTCCGGGTGCCGGATGCAGCGTGAACGCCTTATCCGGCCTACGGCTCGGA‑TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCACAGGATGCGGC > minE/1474762‑1474891
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
