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 F3 I0 R1
|
328 |
90.1 |
2317887 |
85.2% |
1974839 |
62.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,345,150 |
C→A |
100% |
D234Y (GAC→TAC) |
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 | 1,345,150 | 0 | C | A | 83.8%
| 79.2
/ 14.4
| 37 | D234Y (GAC→TAC) | wza | lipoprotein required for capsular polysaccharide translocation through the outer membrane |
| Reads supporting (aligned to +/- strand): ref base C (2/4); new base A (0/31); total (2/35) |
| Fisher's exact test for biased strand distribution p-value = 2.25e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.90e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
ATCATTACGTGGCACGTAGAGAATATCGCCGGGGTAAAGCAGGCGATTCTGGTTGAGGTCGCCGTTTTGCATCAGCGCCTGCAAAGAAATGCGCTCTTCACGACC > minE/1345091‑1345195
|
atcatTACGTGGCACGTAGAGAATATCGCCGGGGTCAAGCAGGCGATTCTGGTTGAGGTAGCCGttt < 1:874284/67‑1 (MQ=255)
atcatTACGTGGCACGTAGAGAATATCGCCGGGGTAAAGCAGGCGTTTCTGGTTGAGGTAGCCGttt < 1:506680/67‑1 (MQ=255)
atcatTACGTGGCACGTAGAGAATATCGCCGGGGTAAAGCAGGCGATTCTGGTTGAGGTAGCCGttt < 1:1090453/67‑1 (MQ=255)
atcatTACGTGGCACGTAGAGAATATCGCCGGGGTAAAGCAGGCGATTCTGGTTGAGGTAGCCGttt < 1:593677/67‑1 (MQ=255)
atcatTACGTGGCACGTAGAGAATATCGCCGGGGTAAAGCAGGCGATTCTGGTTGAGGTAGCCGttt < 1:495308/67‑1 (MQ=255)
atcatTACGTGGCACGTAGAGAATATCGCCGGGGTAAAGCAGGCGATTCTGGTTGAGGTAGCCGttt < 1:481132/67‑1 (MQ=255)
atcatTACGTGGCACGTAGAGAATATCGCCGGGGTAAAGCAGGCGATTCTGGTTGAGGTAGCCGttt < 1:476623/67‑1 (MQ=255)
atcatTACGTGGCACGTAGAGAATATCGCCGGGGTAAAGCAGGCGATTCTGGTTGAGGTAGCCGttt < 1:441089/67‑1 (MQ=255)
atcatTACGTGGCACGTAGAGAATATCGCCGGGGTAAAGCAGGCGATTCTGGTTGAGGTAGCCGttt < 1:393848/67‑1 (MQ=255)
atcatTACGTGGCACGTAGAGAATATCGCCGGGGTAAAGCAGGCGATTCTGGTTGAGGTAGCCGttt < 1:320363/67‑1 (MQ=255)
atcatTACGTGGCACGTAGAGAATATCGCCGGGGTAAAGCAGGCGATTCTGGTTGAGGTAGCCGttt < 1:66381/67‑1 (MQ=255)
atcatTACGTGGCACGTAGAGAATATCGCCGGGGTAAAGCAGGCGATTCTGGTTGAGGTAGCCGttt < 1:2135058/67‑1 (MQ=255)
atcatTACGTGGCACGTAGAGAATATCGCCGGGGTAAAGCAGGCGATTCTGGTTGAGGTAGCCGttt < 1:1045402/67‑1 (MQ=255)
atcatTACGTGGCACGTAGAGAATATCGCCGGGGTAAAGCAGGCGATTCTGGTTGAGGTAGCCGttt < 1:843117/67‑1 (MQ=255)
atcatTACGTGGCACGTAGAGAATATCGCCGGGGTAAAGCAGGCGATTCTGGTTGAGGTAGCCGttt < 1:1786517/67‑1 (MQ=255)
atcatTACGTGGCACGTAGAGAATATCGCCGGGGTAAAGCAGGCGATTCTGGTTGAGGTAGCCGttt < 1:1639750/67‑1 (MQ=255)
atcatTACGTGGCACGTAGAGAATATCGCCGGGGTAAAGCAGGCGATTCTGGTTGAGGTAGCCGttt < 1:1553787/67‑1 (MQ=255)
atcatTACGTGGCACGTAGAGAATATCGCCGGGGTAAAGCAGGCGATTCTGGTTGAGGTAGCCGttt < 1:1425174/67‑1 (MQ=255)
atcatTACGTGGCACGTAGAGAATATCGCCGGGGTAAAGCAGGCGATTCTGGTTGAGGTAGCCGttt < 1:878464/67‑1 (MQ=255)
atcatTACGTGGCACGTAGAGAATATCGCCGGGGTAAAGCAGGCGATTCTGGTTGAGGTAGCCGttt < 1:1283260/67‑1 (MQ=255)
atcatTACGTGGCACGTAGAGAATATCGCCGGGGTAAAGCAGGCGATTCTGGTTGAGGTAGCCGttt < 1:1252410/67‑1 (MQ=255)
atcatTACGTGGCACGTAGAGAATATCGCCGGGGTAAAGCAGGCGATTCTGGTTGAGGTAGCCGttt < 1:1232529/67‑1 (MQ=255)
atcatTACGTGGCACGTAGAGAATATCGCCGGGGTAAAGCAGGCGATTCTGGTTGAGGTAGCCGttt < 1:1186807/67‑1 (MQ=255)
atcatTACGTGGCACGTAGAGAATATCGCCGGGGTAAAGCAGGCGATTCTGGTTGAGGTAGCCGttt < 1:932212/67‑1 (MQ=255)
atcatTACGTGGCACGTAGAGAATATCGCCGGGGTAAAGCAGGCGATTCTGGTTGAGGTAGCCGttt < 1:111755/67‑1 (MQ=255)
tcatTACGTGGCACGTAGAGAATATCGCCGGGGTAAAGCAGGCGATTCTGGTTGAGGTAGCGGttt < 1:157/66‑1 (MQ=255)
tcatTACGTGGCACGTAGAGAATATCGCCGGGGTAAAGCAGGCGATTCTGGTTGAGGTAGCCGttt < 1:1740340/66‑1 (MQ=255)
tcatTACGTGGCACGTAGAGAATATCGCCGGGGTAAAGCAGGCGATTCTGGTTGAGGTAGCCGttt < 1:854334/66‑1 (MQ=255)
tACGTGGCACGTAGAGAATATCGCCGGGGTAAAGCAGGCGATTCTGGTTGAGGTAGCCGttt < 1:2114644/62‑1 (MQ=255)
aCGTGGCACGTAGAGAATATCGCCGGGGTAAAGCAGGCGATTCTGGTTGAGGTAGCCGttt < 1:948318/61‑1 (MQ=255)
aCGTAGAGAATATCGCCGGGGTAAAGCAGGCGATTCTGGTTGAGGTCGCCGTTTTGCATCAGCGcc > 1:2206504/1‑66 (MQ=255)
aCGTAGAGAATATCGCCGGGGTAAAGCAGGCGATTCTGGTTGAGGTCGCCGTTTTGCATCAGCGcc > 1:1178246/1‑66 (MQ=255)
cGCCGGGGTAAAGCAGGCGATTCTGGTTGAGGTAGCCGttt < 1:1315687/41‑1 (MQ=255)
cTGGTTGAGGTCGCCGTTTTGCATCAGCGCCTGCAAAGAAATGCGCTCTTc < 1:2014943/51‑1 (MQ=255)
cTGGTTGAGGTCGCCGTTTTGCATCAGCGCCTGCAAAGAAATGCGCTCTTc < 1:1855199/51‑1 (MQ=255)
cTGGTTGAGGTCGCCGTTTTGCATCAGCGCCTGCAAAGAAATGCGCTCTTc < 1:1291421/51‑1 (MQ=255)
tGAGGTCGCCGTTTTGCATCAGCGCCTGCAAAGAAATGCGCTCTTCACGAcc < 1:514516/52‑1 (MQ=255)
|
ATCATTACGTGGCACGTAGAGAATATCGCCGGGGTAAAGCAGGCGATTCTGGTTGAGGTCGCCGTTTTGCATCAGCGCCTGCAAAGAAATGCGCTCTTCACGACC > minE/1345091‑1345195
|
| 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
