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 |
|
A3 F2 I1 R1
|
2892 |
75.3 |
5698161 |
66.1% |
3766484 |
59.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
Exported |
756,347 |
T→C |
27.6% |
R158R (CGT→CGC) |
lolD → |
outer membrane‑specific lipoprotein transporter subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | Exported | 756,347 | 0 | T | C | 27.6%
| 68.6
/ 28.9
| 47 | R158R (CGT→CGC) | lolD | outer membrane‑specific lipoprotein transporter subunit |
| Reads supporting (aligned to +/- strand): ref base T (18/16); new base C (2/11); total (20/27) |
| Fisher's exact test for biased strand distribution p-value = 2.45e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.84e-01 |
TCATCGTGCGAATCACCGCCCATCTGAACTTTCTGGCGGCGAACGCCAGCGTGTGGCGATTGCCCGTGCGCTGGTGAATAACCCGCGCCTGGTACTGGCGGATGAACCTACCGGTAACCTCGATGCGCGTAACGCC > Exported/756281‑756416
|
tcatcGTGCGAATCACCGCCCATCTGAACTTTCTGGCGGCGAACGCCAGCGTGTGGCGATTGCCCGTgcgc > 1:4637102/1‑71 (MQ=255)
acGTGCACATCACTACCCTTCCGAACTTTCTGGTGGTCAACAGCAGCGTGTGGCGATTGCCCGCGCGCTgg < 1:1602388/70‑1 (MQ=9)
cGTGCACATCACTACCCTTCCGAACTTTCTGGTGGTCAACAGCAGCGTGTGGCGATTGCCCGCGCGCTggc > 1:4738873/1‑70 (MQ=9)
aaTCACCGCCCATCTGAACTTTCTGGCGGCGAACGCCAGCGTGTGGCGATTGCCCGTGCGCTGGTGAATaa < 1:295227/71‑1 (MQ=255)
aTCACCGCCCATCTGAACTTTCTGGCGGCGAACGCCAGCGTGTGGCGATTGCCCGTGCGCTGGTGAATAAc < 1:2119147/71‑1 (MQ=255)
tCACCGCCCATCTGAACTTTCTGGCGGCGAACGCCAGCGTGTGGCGATTGCCCGTGCGCTGGTGAATAAcc > 1:110642/1‑71 (MQ=255)
aCCGCCCATCTGAACTTTCTGGCGGCGAACGCCAGCGTGTGGCGATTGCCCGTGCGCTGGTGAATAACCcg > 1:2491998/1‑71 (MQ=255)
ccGCCCATCTGAACTTTCTGGCGGCGAACGCCAGCGTGTGGCGATTGCCCGTGCGCTGGTGAATAACCcgc < 1:2408147/71‑1 (MQ=255)
cGCCCATCTGAACTTTCTGGCGGCGAACGCCAGCGTGTGGCGATTGCCCGTGCGCTGGTGAATAACCcgcg > 1:5257174/1‑71 (MQ=255)
cGCCCATCTGAACTTTCTGGCGGCGAACGCCAGCGTGTGGCGATTGCCCGTGCGCTGGTGAATAACCcgc > 1:297353/1‑70 (MQ=255)
cccATCTGAACTTTCTGGCGGCGAACGCCAGCGTGTGGCTATTGCCCGTCCGCTGGTGAATAACCCGCGcc < 1:747219/71‑1 (MQ=255)
cccATCTGAACTTTCTGGCGGCGAACGCCAGCGTGTGGCGATTGCCCGTGCGCTGGTGAATAACCCGCGcc < 1:3835882/71‑1 (MQ=255)
tGAACTTTCTGGCGGCGAACGCCAGCGTGTGGCGATTGCCCGTGCGCTGGt > 1:449435/1‑51 (MQ=255)
tGAACTTTCTGGCGGCGAACGCCAGCGTGTGGCGATTGCCCGTGCGCTGGt > 1:3204423/1‑51 (MQ=255)
tGAACTTTCTGGCGGCGAACGCCAGCGTGTGGCGATTGCCCGTGCGCTGGt > 1:4986793/1‑51 (MQ=255)
gAACTTTCTGGCGGCGAACGCCAGCGTGTGGCGATTGCCCGTGCGCTGGTGAATAACCCGCGCCTgg < 1:2890172/67‑1 (MQ=255)
aaCTTTCTGGCGGCGAACGCCAGCGTGTGGCGATTGCCCGTGCGCTGGTGAATAACCCGCGCCTGGt < 1:5209298/67‑1 (MQ=255)
aaCTTTCTGGCGGCGAACGCCAGCGTGTGGCGATTGCCCGTGCGCTGGTGAATAACCCGCGCCTGGt < 1:5636335/67‑1 (MQ=255)
aaCTTTCTGGCGGCGAACGCCAGCGTGTGGCGATTGCCCGTGCGCTGGTGAATAACCCGCGCCTGGt < 1:4163726/67‑1 (MQ=255)
aaCTTTCTGGCGGCGAACGCCAGCCTGTGGCGATTGCCCGTGCGCTGGTGAATAACCCGCGCCTGGTACTg > 1:1534050/1‑71 (MQ=255)
aCTTTCTGGCGGCGAACGCCAGCGTGTGGCGATTGCCCGTGCGCTGGTGAATAACCCGCGCCTGGTACTgg > 1:4669592/1‑71 (MQ=255)
cTTTCTGGCGGCGAACGCCAGCGTGTGGCGATTGCCCGTGCGCTGGTGAATAACCCGCGCCTGGTAc > 1:1533487/1‑67 (MQ=255)
cTTTCTGGCGGCGAACGCCAGCGTGTGGCGATTGACCGTGCGCTGGTGAATAACCCGCGCCTGGTAc > 1:430245/1‑67 (MQ=255)
tCTGGCGGCGAACGCCAGCGTGTGGCGATTGCCCGTGCGCTGGTGAATAACCCGCGCCTGGTACTGGCgg < 1:5689915/70‑1 (MQ=255)
tCTGGCGGCGAACGCCAGCGTGTGGCGATTGACCGTGCGCTGGTGAATAACCCGCGCCTGGTACTGGCGGa > 1:920414/1‑71 (MQ=255)
gcggcgAACGCCAGCGTGTGGCGATTGCCCGTGCGCTGGTGAATAACCCGCGCCTGGTACTGGCGGATGa < 1:4567061/70‑1 (MQ=255)
aCGCCAGCGTGTGGCGATTGCCCGTGCGCTGGTGAATAACCCGCGCCTGGTACTGGCGGATGAACCTACCg > 1:3649286/1‑71 (MQ=255)
ccAGCGTGTGGCGATTGCCCGTGCGCTGGTGAATAACCCGCGCCTGGTACTGGCGGATGAACCTACCGGTa < 1:3328664/71‑1 (MQ=255)
cAGCGTGTGGCGATTGCCCGTGCGCTGGTGAATAACCCGCGCCTGGTACTGGCGGACGAACCTACCGGTaa > 1:1291907/1‑71 (MQ=255)
cAGCGTGTGGCGATTGCCCGCGCGCTGGcggtgaagccgaaaatgatgctgtttgatgaaccgacttccgc < 1:402484‑M1/71‑44 (MQ=255)
aGCGTGTGGCGATTGCCCGCGCGCTGGcggtgaagccgaaaatgatgctgttt < 1:309163‑M1/53‑27 (MQ=255)
gCGTGTGGCGATTGCCCGTGCGCTGGTGAATAACCCGCGCCTGGTACTGGCGGATGAACCTAc > 1:1204247/1‑63 (MQ=255)
gtgtGGCGATTGCCCGTGCGCTGGTGAATAACCCGCGCCTGGTACTGGCGGATGAACCTACCGGTAACCTc < 1:5540739/71‑1 (MQ=255)
gtgtGGCGATTGCCCGCGCGCTGGcggtgaagccgaaaa < 1:564981‑M1/39‑16 (MQ=255)
tgtgGCGATTGCCCGCGCGCTGGcggtgaagccgaa < 1:1703846‑M1/36‑14 (MQ=255)
tgtgGCGATTGCCCGCGCGCTGGcggtgaagccgaa < 1:1396991‑M1/36‑14 (MQ=255)
tgtgGCGATTGCCCGCGCGCTGGcggtgaagccgaa < 1:82610‑M1/36‑14 (MQ=255)
gtgGCGATTGCCCGTGCGCTGGTGAATAACCCGCGCCTGGTACTGGCGGATGAACCTACCGGTAACCt < 1:4733480/68‑1 (MQ=255)
gtgGCGATTGCCCGTGCGCTGGTGAATAACCCGCGCCTGGTACTGGCGGATGAACCTACCGGTAACCt < 1:1306540/68‑1 (MQ=255)
tgGCGATTGCCCGCGCGCTGGcggtgaagccgaaa < 1:5658675‑M1/35‑15 (MQ=255)
tgGCGATTGCCCGCGCGCTGGcggtgaagccgaaa < 1:4063062‑M1/35‑15 (MQ=255)
gCGATTGCCCGCGCGCTGGcggtgaagccgaaaatgatgctgtttgatgaaccgactt > 1:425317‑M1/1‑19 (MQ=255)
cGATTGCCCGCGCGCTGGcggtgaagccgaaaatgatgctgttt < 1:3063217‑M1/44‑27 (MQ=255)
cGATTGCCCGCGCGCTGGcggtgaagccgaaaatgatgctgttt < 1:739910‑M1/44‑27 (MQ=255)
ttGCCCGTGCGCTGGTGAATAACCCGCGCCTGGTACTGGCGGATGAACCTACCGGTAACCTCGATGCGCGt < 1:1942317/71‑1 (MQ=255)
gTGCGCTGGTGAATAACCCGCGCCTGGTACTGGCGGATGAACCTACCGGTAACCTCGATGCGCGTAACGcc > 1:5064233/1‑71 (MQ=255)
gTGCGCTGGTGAATAACCCGCGCCTGGTACTGGCGGATGAACCTACCGGTAACCTCGATGCGCGTAACGcc > 1:1783349/1‑71 (MQ=255)
|
TCATCGTGCGAATCACCGCCCATCTGAACTTTCTGGCGGCGAACGCCAGCGTGTGGCGATTGCCCGTGCGCTGGTGAATAACCCGCGCCTGGTACTGGCGGATGAACCTACCGGTAACCTCGATGCGCGTAACGCC > Exported/756281‑756416
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
