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 |
1,892,351 |
G→A |
100% |
L177L (CTG→TTG) |
ygdL ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,892,351 | 0 | G | A | 78.4%
| 58.9
/ 10.7
| 46 | L177L (CTG→TTG) | ygdL | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (1/9); new base A (36/0); total (37/9) |
| Fisher's exact test for biased strand distribution p-value = 9.08e-09 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.76e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
TACCTTTACTGTTTTTCACTACGCCAAAATCGCTTTTCAGGCGCTCGCGCAACTTCGCCGCCAGCGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGATCAATCTGCCCACCCG > minE/1892288‑1892416
|
tACCTTTACTGTTTTTCACTACGCCAAAATCGCTTTTCAGGCGCTCGCGCAACTTCGCCGCCAGCggg > 1:3332968/1‑68 (MQ=255)
tttCACTACGCCAAAATCGCTTTTCAGGCGCTCGCGCAACTTCGCCGCCAACGGGTCCTGAATCGtttt > 1:2852620/1‑69 (MQ=255)
tttCACTACGCCAAAATCGCTTTTCAGGCGCTCGCGCAACTTCGCCGCCAACGGGTCCTGAATCGtttt > 1:3236225/1‑69 (MQ=255)
tttCACTACGCCAAAATCGCTTTTCAGGCGCTCGCGCAACTTCGCCGCCAACGGGTCCTGAATCGtttt > 1:505096/1‑69 (MQ=255)
tttCACTACGCCAAAATCGCTTTTCAGGCGCTCGCGCAACTTCGCCGCCAACGGGTCCTGAATCGtttt > 1:1494110/1‑69 (MQ=255)
tttCACTACGCCAAAATCGCTTTTCAGGCGCTCGCGCAACTTCGCCGCCAACGGGTCCTGAATCGtttt > 1:1452006/1‑69 (MQ=255)
tttCACTACGCCAAAATCGCTTTTCAGGCGCTCGCGCAACTTCGCCGCCAACGGGTCCTGAATCGtttt > 1:3004654/1‑69 (MQ=255)
tttCACTACGCCAAAATCGCTTTTCAGGCGCTCGCGCAACTTCGCCGCCAACGGGTCCTGAATCGtttt > 1:141790/1‑69 (MQ=255)
tttCACTACGCCAAAATCGCTTTTCAGGCGCTCGCGCAACTTCGCCGCCAACGGGTCCTGAATCGtttt > 1:2129357/1‑69 (MQ=255)
tttCACTACGCCAAAATCGCTTTTCAGGCGCTCGCGCAACTTCGCCGCCAACGGGTCCTGAATCGtttt > 1:2154329/1‑69 (MQ=255)
tttCACTACGCCAAAATCGCTTTTCAGGCGCTCGCGCAACTTCGCCGCCAACGGGTCCTGAATCGtttt > 1:2889976/1‑69 (MQ=255)
tttCACTACGCCAAAATCGCTTTTCAGGCGCTCGCGCAACTTCGCCGCCAACGGGTCCTGAATCGtttt > 1:1158958/1‑69 (MQ=255)
tttCACTACGCCAAAATCGCTTTTCAGGCGCTCGCGCAACTTCGCCGCCAACGGGTCCTGAATCGtttt > 1:2461515/1‑69 (MQ=255)
tttCACTACGCCAAAATCGCTTTTCAGGCGCTCGCGCAACTTCGCCGCCAACGGGTCCTGAATCGtttt > 1:60178/1‑69 (MQ=255)
gCTTTTCAGGCGCTCGCGCAACTTCGCCGCCAGCGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTg < 1:2254567/69‑1 (MQ=255)
gCTTTTCAGGCGCTCGCGCAACTTCGCCGCCAGCGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTg < 1:100372/69‑1 (MQ=255)
gCTTTTCAGGCGCTCGCGCAACTTCGCCGCCAGCGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTg < 1:2021241/69‑1 (MQ=255)
gCTTTTCAGGCGCTCGCGCAACTTCGCCGCCAGCGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTg < 1:1421303/69‑1 (MQ=255)
gCTTTTCAGGCGCTCGCGCAACTTCGCCGCCAGCGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTg < 1:1346434/69‑1 (MQ=255)
gCTTTTCAGGCGCTCGCGCAACTTCGCCGCCAGCGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTg < 1:380259/69‑1 (MQ=255)
gCTTTTCAGGCGCTCGCGCAACTTCGCCGCCAGCGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTg < 1:1096766/69‑1 (MQ=255)
cgccAGCGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGATCAATCTGCCCAcc < 1:700683/69‑1 (MQ=255)
ccAACGGGTCCTGCATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAc > 1:1362180/1‑66 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTa > 1:111127/1‑35 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:3305128/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:3278129/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:3277311/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:3348225/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:407750/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:2837152/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:2615714/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:2175618/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:2094078/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:208525/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:2055500/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:2032930/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:1921358/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:1906537/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:1888725/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:1524470/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:1097778/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAcca > 1:1061644/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAcca > 1:1347491/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATAGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:2552799/1‑67 (MQ=255)
ccAACGGGTCCTGAATAGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCggg > 1:762246/1‑52 (MQ=38)
cAGCGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTg < 1:3385249/39‑1 (MQ=255)
|
TACCTTTACTGTTTTTCACTACGCCAAAATCGCTTTTCAGGCGCTCGCGCAACTTCGCCGCCAGCGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGATCAATCTGCCCACCCG > minE/1892288‑1892416
|
| 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
