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 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,258,470 |
A→G |
50.9% |
G891G (GGT→GGC) |
rpoB ← |
RNA polymerase, beta subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,258,470 | 0 | A | G | 50.9%
| ‑1.8
/ 47.2
| 55 | G891G (GGT→GGC) | rpoB | RNA polymerase, beta subunit |
| Reads supporting (aligned to +/- strand): ref base A (10/17); new base G (12/16); total (22/33) |
| Fisher's exact test for biased strand distribution p-value = 7.85e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.68e-01 |
GGCTTTCTCACCGAAGATCGCACGCAGCAGTTTTTCTTCTGGGGTCAGCTGAGTTTCACCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCACTTCCGCACCAATGTAAAC > minE/2258413‑2258532
|
ggCTTTCTCACCGAAGATCGCACGCAGCAGTTTTTCTTCTGGGGTCAGCTGAGTTTCACCTTTCGGCGt < 1:2030158/69‑1 (MQ=255)
ttttCTTCTGGGGTCAGCTGAGTTTCGCCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTc > 1:791475/1‑69 (MQ=255)
ttttCTTCTGGGGTCAGCTGAGTTTCGCCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTc > 1:730928/1‑69 (MQ=255)
ttttCTTCTGGGGTCAGCTGAGTTTCGCCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTc > 1:1864962/1‑69 (MQ=255)
ttttCTTCTGGGGTCAGCTGAGTTTCGCCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTc > 1:1546987/1‑69 (MQ=255)
ttttCTTCTGGGGTCAGCTGAGTTTCGCCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTc > 1:1394935/1‑69 (MQ=255)
ttttCTTCTGGGGTCAGCTGAGTTTCGCCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTc > 1:2972147/1‑69 (MQ=255)
ttttCTTCTGGGGTCAGCTGAGTTTCGCCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTc > 1:636142/1‑69 (MQ=255)
ttttCTTCTGGGGTCAGCTGAGTTTCGCCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTc > 1:1189553/1‑69 (MQ=255)
ttttCTTCTGGGGTCAGCTGAGTTTCGCCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTc > 1:1169690/1‑69 (MQ=255)
ttttCTTCTGGGGTCAGCTGAGTTTCGCCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTc > 1:3400202/1‑69 (MQ=255)
ttttCTTCTGGGGTCAGCTGAGTTTCGCCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTc > 1:952607/1‑69 (MQ=255)
ttttCTTCTGGGGTCAGCTGAGTTTCGCCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTc > 1:367644/1‑69 (MQ=255)
tttCTTCTGGGGTCAGCTGAGTTTCACCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCa > 1:946257/1‑69 (MQ=255)
tttCTTCTGGGGTCAGCTGAGTTTCACCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCa > 1:2944380/1‑69 (MQ=255)
tttCTTCTGGGGTCAGCTGAGTTTCACCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCa > 1:2765451/1‑69 (MQ=255)
tttCTTCTGGGGTCAGCTGAGTTTCACCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCa > 1:589535/1‑69 (MQ=255)
ctGGGGTCAGCTGAGTTTCACCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGt < 1:250389/61‑1 (MQ=255)
ctGGGGTCAGCTGAGTTTCACCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGt < 1:2456291/61‑1 (MQ=255)
ctGGGGTCAGCTGAGTTTCACCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGt < 1:2406835/61‑1 (MQ=255)
gTCAGCTGAGTTTCACCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGt < 1:1008825/56‑1 (MQ=255)
gTCAGCTGAGTTTCACCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCACTTCCGCAcc > 1:3114299/1‑68 (MQ=255)
gTCAGCTGAGTTTCACCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCACTTCCGCAcc > 1:1554200/1‑68 (MQ=255)
gTCAGCTGAGTTTCACCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCACTTCCGCACCa > 1:1924240/1‑69 (MQ=255)
gTCAGCTGAGTTTCACCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCACTTCCGCACCa < 1:1056600/69‑1 (MQ=255)
gTCAGCTGAGTTTCACCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCACTTCCGCACCa < 1:1226641/69‑1 (MQ=255)
gTCAGCTGAGTTTCACCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCACTTCCGCACCa < 1:3206734/69‑1 (MQ=255)
gTCAGCTGAGTTTCACCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCACTTCCGCACCa > 1:1723185/1‑69 (MQ=255)
gTCAGCTGAGTTTCACCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCACTTCCGCACCa < 1:1861327/69‑1 (MQ=255)
tCAGCTGAGTTTCACCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCACTTCCGCACCaa > 1:358460/1‑69 (MQ=255)
tCAGCTGAGTTTCACCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCACTTCCGCACCaa > 1:2804611/1‑69 (MQ=255)
gAGTTTCGCCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCACTTcc < 1:2682396/56‑1 (MQ=255)
gAGTTTCGCCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCACTTcc < 1:1040196/56‑1 (MQ=255)
gAGTTTCGCCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCACTTcc < 1:1974317/56‑1 (MQ=255)
gAGTTTCGCCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCACTTcc < 1:3386714/56‑1 (MQ=255)
gAGTTTCGCCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCACTTcc < 1:2098898/56‑1 (MQ=255)
gAGTTTCGCCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCACTTcc < 1:3239640/56‑1 (MQ=255)
gAGTTTCGCCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCACTTcc < 1:1843980/56‑1 (MQ=255)
gAGTTTCGCCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCACTTcc < 1:3056986/56‑1 (MQ=255)
gAGTTTCGCCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCACTTcc < 1:3038398/56‑1 (MQ=255)
gAGTTTCGCCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCACTTcc < 1:1233057/56‑1 (MQ=255)
gAGTTTCGCCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCACTTcc < 1:69106/56‑1 (MQ=255)
gAGTTTCGCCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCACTTcc < 1:730169/56‑1 (MQ=255)
gAGTTTCGCCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCACTTcc < 1:1573066/56‑1 (MQ=255)
gAGTTTCGCCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCACTTcc < 1:2600320/56‑1 (MQ=255)
gAGTTTCGCCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTAACTTcc < 1:1026688/56‑1 (MQ=39)
gAGTATCGCCATTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCACTTcc < 1:998646/56‑1 (MQ=255)
gTTTCACCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCACTTCCGCACCa < 1:2831531/60‑1 (MQ=255)
tttCACCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCACTTCCGCACCAATGTAAAc < 1:331264/67‑1 (MQ=255)
tttCACCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCACTTCCGCACCAATGTAAAc < 1:2887901/67‑1 (MQ=255)
tttCACCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCACTTCCGCACCAATGTAAAc < 1:2045209/67‑1 (MQ=255)
tttCACCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCACTTCCGCACCAATGTAAAc < 1:754996/67‑1 (MQ=255)
tttCACCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCACTTCCGCACCAATGTAAAc < 1:1394130/67‑1 (MQ=255)
tttCACCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCACTTCCGCACCAATGTAAAc < 1:118263/67‑1 (MQ=255)
tttCACCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCACTTCCGCACCAATGTAAAc < 1:1045080/67‑1 (MQ=255)
|
GGCTTTCTCACCGAAGATCGCACGCAGCAGTTTTTCTTCTGGGGTCAGCTGAGTTTCACCTTTCGGCGTTACCTTACCAACCAGAATGTCGCCACCGGTCACTTCCGCACCAATGTAAAC > minE/2258413‑2258532
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
