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 |
2,548,716:1 |
+T |
100% |
intergenic (+67/‑208) |
htrL → / → kbl |
hypothetical protein/glycine C‑acetyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,548,716 | 1 | . | T | 95.2%
| 66.6
/ ‑2.3
| 21 | intergenic (+67/‑208) | htrL/kbl | hypothetical protein/glycine C‑acetyltransferase |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base T (0/20); total (0/21) |
| 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. |
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. |
GGGTAGCGTTTTGATACCAACTGAGATAGGAAAAATGATGCTTTGGCATCA‑TTTTTTCTTTTTATATCAATGCAGTAAAATCAATCATC > minE/2548666‑2548754
|
gggTAGCGTTTTGATACCAACTGAGATAGGAAAAATGATGCTTTGGCATCA‑TTTTTTCTTTTtata < 1:1272946/66‑1 (MQ=255)
aTAGGATAAATGATGCTTTGGCATCATTTTTTTCTTTTTATATCAATGCAGTAAAATCAatcatc < 1:1154451/65‑1 (MQ=255)
aTAGGAAAAATGATGCTTTGGCATCATTTTTTTCTTTTTATATCAATGCAGTAAAATCAatcatc < 1:1804698/65‑1 (MQ=255)
aTAGGAAAAATGATGCTTTGGCATCATTTTTTTCTTTTTATATCAATGCAGTAAAATCAatcatc < 1:776803/65‑1 (MQ=255)
aTAGGAAAAATGATGCTTTGGCATCATTTTTTTCTTTTTATATCAATGCAGTAAAATCAatcatc < 1:638438/65‑1 (MQ=255)
aTAGGAAAAATGATGCTTTGGCATCATTTTTTTCTTTTTATATCAATGCAGTAAAATCAatcatc < 1:62454/65‑1 (MQ=255)
aTAGGAAAAATGATGCTTTGGCATCATTTTTTTCTTTTTATATCAATGCAGTAAAATCAatcatc < 1:466383/65‑1 (MQ=255)
aTAGGAAAAATGATGCTTTGGCATCATTTTTTTCTTTTTATATCAATGCAGTAAAATCAatcatc < 1:450275/65‑1 (MQ=255)
aTAGGAAAAATGATGCTTTGGCATCATTTTTTTCTTTTTATATCAATGCAGTAAAATCAatcatc < 1:315538/65‑1 (MQ=255)
aTAGGAAAAATGATGCTTTGGCATCATTTTTTTCTTTTTATATCAATGCAGTAAAATCAatcatc < 1:2150513/65‑1 (MQ=255)
aTAGGAAAAATGATGCTTTGGCATCATTTTTTTCTTTTTATATCAATGCAGTAAAATCAatcatc < 1:1982715/65‑1 (MQ=255)
aTAGGAAAAATGATGCTTTGGCATCATTTTTTTCTTTTTATATCAATGCAGTAAAATCAatcatc < 1:1873808/65‑1 (MQ=255)
aTAGGAAAAATGATGCTTTGGCATCATTTTTTTCTTTTTATATCAATGCAGTAAAATCAatcatc < 1:1113877/65‑1 (MQ=255)
aTAGGAAAAATGATGCTTTGGCATCATTTTTTTCTTTTTATATCAATGCAGTAAAATCAatcatc < 1:1769138/65‑1 (MQ=255)
aTAGGAAAAATGATGCTTTGGCATCATTTTTTTCTTTTTATATCAATGCAGTAAAATCAatcatc < 1:171715/65‑1 (MQ=255)
aTAGGAAAAATGATGCTTTGGCATCATTTTTTTCTTTTTATATCAATGCAGTAAAATCAatcatc < 1:1507319/65‑1 (MQ=255)
aTAGGAAAAATGATGCTTTGGCATCATTTTTTTCTTTTTATATCAATGCAGTAAAATCAatcatc < 1:1477271/65‑1 (MQ=255)
aTAGGAAAAATGATGCTTTGGCATCATTTTTTTCTTTTTATATCAATGCAGTAAAATCAatcatc < 1:1342618/65‑1 (MQ=255)
aTAGGAAAAATGATGCTTTGGCATCATTTTTTTCTTTTTATATCAATGCAGTAAAATCAatcatc < 1:1236767/65‑1 (MQ=255)
aTAGGAAAAATGATGCTTTGGCATCATTTTTTTCTTTTTATATCAATGCAGTAAAATCAatcatc < 1:1214722/65‑1 (MQ=255)
tAGGAAAAATGATGCTTTGGCATCATTTTTTTCTTTTTATATCAATGCAGTAAAATCAatcatc < 1:823664/64‑1 (MQ=255)
|
GGGTAGCGTTTTGATACCAACTGAGATAGGAAAAATGATGCTTTGGCATCA‑TTTTTTCTTTTTATATCAATGCAGTAAAATCAATCATC > minE/2548666‑2548754
|
| 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
