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 |
1,345,070 |
C→A |
100% |
M260I (ATG→ATT) |
wza ← |
lipoprotein required for capsular polysaccharide translocation through the outer membrane |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,345,070 | 0 | C | A | 80.8%
| 107.7
/ 31.3
| 52 | M260I (ATG→ATT) | wza | lipoprotein required for capsular polysaccharide translocation through the outer membrane |
| Reads supporting (aligned to +/- strand): ref base C (10/0); new base A (0/42); total (10/42) |
| Fisher's exact test for biased strand distribution p-value = 6.32e-11 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
GTCAGGGTCATGCCGCTAAAGTCCATTTTCAGGGTGCTCTGTTTCTTCACTTCACCCATCACAAATACTTTCAGATCATCATTACGTGGCA > minE/1345014‑1345104
|
gtcagGGTCATGCCGCTAAAGTCCATTTTCAGGGTGCTCTGTTTCTTCACTTCACCCATCACAAATa > 1:364100/1‑67 (MQ=255)
gtcagGGTCATGCCGCTAAAGTCCATTTTCAGGGTGCTCTGTTTCTTCACTTCACCCATCACAAATa > 1:1722873/1‑67 (MQ=255)
gtcagGGTCATGCCGCTAAAGTCCATTTTCAGGGTGCTCTGTTTCTTCACTTCACCCATCACAAATa > 1:1128926/1‑67 (MQ=255)
gtcagGGTCATGCCGCTAAAGTCCATTTTCAGGGTGCTCTGTTTCTTCACTTCACCCATCACAAATa > 1:237074/1‑67 (MQ=255)
gtcagGGTCATGCCGCTAAAGTCCATTTTCAGGGTGCTCTGTTTCTTCACTTCACCCATCACAAATa > 1:1692789/1‑67 (MQ=255)
gtcagGGTCATGCCGCTAAAGTCCATTTTCAGGGTGCTCTGTTTCTTCACTTCACCCATCACAAATa > 1:1272420/1‑67 (MQ=255)
gtcagGGTCATGCCGCTAAAGTCCATTTTCAGGGTGCTCTGTTTCTTCACTTCACCCATCACAAATa > 1:593034/1‑67 (MQ=255)
gtcagGGTCATGCCGCTAAAGTCCATTTTCAGGGTGCTCTGTTTCTTCACTTCACCCATCACAAATa > 1:1312995/1‑67 (MQ=255)
gtcagGGTCATGCCGCTAAAGTCCATTTTCAGGGTGCTCTGTTTCTTCACTTCACCCATCACAAATa > 1:425017/1‑67 (MQ=255)
gtcagGGTCATGCCGCTAAAGTCCATTTTCAGGGTGCTCTGTTTCTTCACTTCACCCATCACAAATa > 1:303518/1‑67 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATTATTACGTGGCa < 1:563537/66‑1 (MQ=25)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:29947/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:388433/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:310501/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:330826/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:237757/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:2145958/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:351958/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:2118835/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:3704/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:1941973/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:424526/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:476907/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:488662/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:710952/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:714709/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:796611/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:90134/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:1676021/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:1047726/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:106970/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:1149254/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:1207309/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:1290774/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:1506480/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:1508125/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:1543967/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:1658382/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:1680331/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:1739787/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:1767852/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:1810595/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:1830790/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:1830927/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:183155/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:1844520/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:1855655/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:191445/66‑1 (MQ=255)
ttttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:1035780/66‑1 (MQ=255)
tttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:2049979/65‑1 (MQ=255)
tttCAGGGTGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:809364/65‑1 (MQ=255)
tGCTCTGTTTCTTCACTTCACCAATCACAAATACTTTCAGATCATCATTACGTGGCa < 1:437476/57‑1 (MQ=255)
|
GTCAGGGTCATGCCGCTAAAGTCCATTTTCAGGGTGCTCTGTTTCTTCACTTCACCCATCACAAATACTTTCAGATCATCATTACGTGGCA > minE/1345014‑1345104
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
