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 |
|
A1 F21 I0 R1
|
476 |
35.3 |
2812105 |
96.7% |
2719305 |
61.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,427,990 |
G→A |
9.1% |
intergenic (+296/‑178) |
ydaY → / → ynaA |
hypothetical protein/predicted tail protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,427,990 | 0 | G | A | 9.1%
| 164.4
/ 6.4
| 55 | intergenic (+296/‑178) | ydaY/ynaA | hypothetical protein/predicted tail protein |
| Reads supporting (aligned to +/- strand): ref base G (16/34); new base A (3/2); total (19/36) |
| Fisher's exact test for biased strand distribution p-value = 3.27e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.68e-01 |
CGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGAT > W3110S.gb/1427923‑1428059
|
cGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAg > 1:1634547/1‑71 (MQ=255)
gTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAgtg < 1:1699330/71‑1 (MQ=255)
attgattgAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAgtgtg > 1:1233062/1‑71 (MQ=255)
ttgattgaGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAgtgtgt > 1:814128/1‑71 (MQ=255)
gattgaGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAgtgtgtg > 1:1716959/1‑70 (MQ=255)
attgaGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATTACCAGTATTTTCAGGAGCAgtgtgtgt < 1:1013611/70‑1 (MQ=255)
attgaGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAgtgtgtgt < 1:692907/70‑1 (MQ=255)
attgaGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAgtgtgtgt < 1:2180866/70‑1 (MQ=255)
cgcgATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAgttgtt < 1:873191/71‑1 (MQ=255)
gATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAgttgtt < 1:58262/68‑1 (MQ=255)
gATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAAt < 1:1201244/71‑1 (MQ=255)
gATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAAt < 1:847351/71‑1 (MQ=255)
aTGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAAt < 1:660724/70‑1 (MQ=255)
aaTTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACg < 1:1189954/71‑1 (MQ=255)
aaTTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACg < 1:142768/71‑1 (MQ=255)
tGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTaca > 1:952171/1‑71 (MQ=255)
tGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTaca > 1:1959901/1‑71 (MQ=255)
tGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTac < 1:2629274/70‑1 (MQ=255)
tGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAACAGTGTGTGTAGTTGTTAATTACGTaca > 1:1617711/1‑71 (MQ=255)
tGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAACAGTGTGTGTAGTTGTTAATTACGTaca > 1:1411052/1‑71 (MQ=255)
gTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAgttgtt < 1:1272944/53‑1 (MQ=255)
tGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAgtgtgtgt < 1:319612/45‑1 (MQ=255)
tGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAAtt < 1:1544323/56‑1 (MQ=255)
tGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAAtt < 1:1468611/56‑1 (MQ=255)
gATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTa > 1:1087364/1‑70 (MQ=255)
aTCTTTTCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAgtt > 1:2573/1‑47 (MQ=255)
aTCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTATTTGTTAATTACGTa > 1:733887/1‑59 (MQ=255)
aTCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTacac > 1:2127013/1‑62 (MQ=255)
aTCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTa > 1:2223438/1‑59 (MQ=255)
aTCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTa < 1:1120645/59‑1 (MQ=255)
aTCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTa > 1:1871206/1‑69 (MQ=255)
aTCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTa > 1:251094/1‑69 (MQ=255)
cTTTGCACTGGATGACCAGTATTTTCAGGAACAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACa > 1:873770/1‑69 (MQ=255)
tttGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAAt < 1:509341/50‑1 (MQ=255)
tGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACaga < 1:401271/68‑1 (MQ=255)
tGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACaga < 1:404504/68‑1 (MQ=255)
tGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACaga < 1:497422/68‑1 (MQ=255)
tGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAgaga < 1:418004/70‑1 (MQ=255)
tGGATGACCAGTATTTTCAGGAACAGTGTGTGTAgttgtt < 1:1980161/40‑1 (MQ=255)
aCCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGATGgtgt < 1:2562998/70‑1 (MQ=255)
aGTATTTTCAGGAACAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCttt < 1:1096652/71‑1 (MQ=255)
tATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACActct < 1:118959/44‑1 (MQ=255)
tATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACActct < 1:2807191/44‑1 (MQ=255)
tATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACaga < 1:575470/52‑1 (MQ=255)
tATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACaga < 1:2229694/52‑1 (MQ=255)
tATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGAtgt < 1:2345233/57‑1 (MQ=255)
tATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGAtgt < 1:116116/57‑1 (MQ=255)
ttttCAGGAGCAGTGTGTGTAGTTGTTAATTACGTa > 1:973230/1‑36 (MQ=255)
ttttCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGa > 1:1024960/1‑57 (MQ=255)
ttttCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTttaatt < 1:1027950/71‑1 (MQ=255)
ttttCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTttaat > 1:2638652/1‑70 (MQ=255)
ttCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTttaatta < 1:1268433/70‑1 (MQ=255)
aGCAGTGTGTGTAGTTGTTTATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCgat < 1:517478/71‑1 (MQ=255)
aGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCgat < 1:1662029/71‑1 (MQ=255)
aGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCgat < 1:1059292/71‑1 (MQ=255)
|
CGGTATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATCGAT > W3110S.gb/1427923‑1428059
|
| 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
