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 F8 I0 R1
|
82 |
77.9 |
2158605 |
86.8% |
1873669 |
62.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
813,910 |
A→G |
100% |
C60C (TGT→TGC) |
prsA ← |
phosphoribosylpyrophosphate synthase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 813,910 | 0 | A | G | 99.4%
| 172.7
/ ‑6.6
| 46 | C60C (TGT→TGC) | prsA | phosphoribosylpyrophosphate synthase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); major base G (0/45); minor base T (0/1); total (0/46) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
GAAGCACGACGCAGGGCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGACTGGATGATGAAAAT > minE/813848‑813933
|
gAAGCTCGACGCAGGGCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCGCAAg < 1:682979/67‑1 (MQ=255)
gAAGCACGACGCAGGGCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCGCAAg < 1:1949412/67‑1 (MQ=255)
gAAGCACGACGCAGGGCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCGCAAg < 1:657152/67‑1 (MQ=255)
gAAGCACGACGCAGGGCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCGCAAg < 1:591787/67‑1 (MQ=255)
gAAGCACGACGCAGGGCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCGCAAg < 1:514266/67‑1 (MQ=255)
gAAGCACGACGCAGGGCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCGCAAg < 1:498454/67‑1 (MQ=255)
gAAGCACGACGCAGGGCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCGCAAg < 1:462458/67‑1 (MQ=255)
gAAGCACGACGCAGGGCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCGCAAg < 1:364234/67‑1 (MQ=255)
gAAGCACGACGCAGGGCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCGCAAg < 1:806731/67‑1 (MQ=255)
gAAGCACGACGCAGGGCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCGCAAg < 1:2085171/67‑1 (MQ=255)
gAAGCACGACGCAGGGCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCGCAAg < 1:1934003/67‑1 (MQ=255)
gAAGCACGACGCAGGGCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCGCAAg < 1:1876943/67‑1 (MQ=255)
gAAGCACGACGCAGGGCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCGCAAg < 1:1790200/67‑1 (MQ=255)
gAAGCACGACGCAGGGCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCGCAAg < 1:1021379/67‑1 (MQ=255)
gAAGCACGACGCAGGGCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCGCAAg < 1:1745216/67‑1 (MQ=255)
gAAGCACGACGCAGGGCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCGCAAg < 1:971444/67‑1 (MQ=255)
gAAGCACGACGCAGGGCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCGCAAg < 1:884991/67‑1 (MQ=255)
gAAGCACGACGCAGGGCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCGCAAg < 1:1473774/67‑1 (MQ=255)
gAAGCACGACGCAGGGCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCGCAAg < 1:1733796/67‑1 (MQ=255)
gAAGCACGACGCAGGGCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCGCAAg < 1:893519/67‑1 (MQ=255)
aaGCACGACGCAGGGCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCGCAAg < 1:880308/66‑1 (MQ=255)
aaGCACGACGCAGGGCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCGCAAg < 1:150486/66‑1 (MQ=255)
aaGCACGACGCAGGGCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCGCAAg < 1:762882/66‑1 (MQ=255)
cAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCGCAAg < 1:406285/48‑1 (MQ=255)
aCTAATTCCATCAGGTTGTCGTTAGTAGGGGCTCAAg < 1:954085/37‑1 (MQ=255)
tGTCGTTAGTAGTGGCGCAAGTGGACTGGATGATGAAAat < 1:1746590/40‑1 (MQ=38)
tGTCGTTAGTAGGGGCGCAAGTGGACTGGATGATGTAAat < 1:1406/40‑1 (MQ=255)
tGTCGTTAGTAGGGGCGCAAGTGGACTGGATGATGAAAat < 1:759238/40‑1 (MQ=255)
tGTCGTTAGTAGGGGCGCAAGTGGACTGGATGATGAAAat < 1:698451/40‑1 (MQ=255)
tGTCGTTAGTAGGGGCGCAAGTGGACTGGATGATGAAAat < 1:821294/40‑1 (MQ=255)
tGTCGTTAGTAGGGGCGCAAGTGGACTGGATGATGAAAat < 1:687855/40‑1 (MQ=255)
tGTCGTTAGTAGGGGCGCAAGTGGACTGGATGATGAAAat < 1:992384/40‑1 (MQ=255)
tGTCGTTAGTAGGGGCGCAAGTGGACTGGATGATGAAAat < 1:666163/40‑1 (MQ=255)
tGTCGTTAGTAGGGGCGCAAGTGGACTGGATGATGAAAat < 1:603367/40‑1 (MQ=255)
tGTCGTTAGTAGGGGCGCAAGTGGACTGGATGATGAAAat < 1:472326/40‑1 (MQ=255)
tGTCGTTAGTAGGGGCGCAAGTGGACTGGATGATGAAAat < 1:367788/40‑1 (MQ=255)
tGTCGTTAGTAGGGGCGCAAGTGGACTGGATGATGAAAat < 1:352121/40‑1 (MQ=255)
tGTCGTTAGTAGGGGCGCAAGTGGACTGGATGATGAAAat < 1:2157316/40‑1 (MQ=255)
tGTCGTTAGTAGGGGCGCAAGTGGACTGGATGATGAAAat < 1:1867768/40‑1 (MQ=255)
tGTCGTTAGTAGGGGCGCAAGTGGACTGGATGATGAAAat < 1:173819/40‑1 (MQ=255)
tGTCGTTAGTAGGGGCGCAAGTGGACTGGATGATGAAAat < 1:1610701/40‑1 (MQ=255)
tGTCGTTAGTAGGGGCGCAAGTGGACTGGATGATGAAAat < 1:1582985/40‑1 (MQ=255)
tGTCGTTAGTAGGGGCGCAAGTGGACTGGATGATGAAAat < 1:1277859/40‑1 (MQ=255)
tGTCGTTAGTAGGGGCGCAAGTGGACTGGATGATGAAAat < 1:1163012/40‑1 (MQ=255)
tGTCGGTAGTAGGGGCGCAAGTGGACTGGATGATGAAAat < 1:536871/40‑1 (MQ=38)
gTCGTTAGTAGGGGCGCAAGTGGACTGGATGATGAAAat < 1:360351/39‑1 (MQ=255)
|
GAAGCACGACGCAGGGCATCAACCATAACGACTAATTCCATCAGGTTGTCGTTAGTAGGGGCACAAGTGGACTGGATGATGAAAAT > minE/813848‑813933
|
| 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
