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 |
|
A83 F1 I1 R1
|
17 |
39.7 |
2446701 |
98.6% |
2412447 |
76.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
1,454,614 |
T→G |
D722E (GAT→GAG) |
hrpA → |
ATP‑dependent helicase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 1,454,614 | 0 | T | G | 97.4%
| 149.5
/ ‑3.2
| 39 | D722E (GAT→GAG) | hrpA | ATP‑dependent helicase |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base G (12/26); total (12/27) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.74e-01 |
AACGGAAAAAGTCACTGTTTATGGTTTGCCGATTGTTGCCGCGCGCAAGGTCAACTACAGCCAGATCGATCCGGCGTTATGTCGTGAACTCTTTATTCGCCATGCGCTGGTGGAAGGTGACTGGCAGACGCGTCACGCATT > REL606/1454545‑1454685
|
aaCGGAAAAAGTCACTGTTTATGGTTTGCCGATTGTTGCCGCGCGCAAGGTCAACTACAGCCAGATCGAGCCGGCg < 1:1182307/76‑1 (MQ=255)
aaCGGAAAAAGTCACTGTTTATGGTTTGCCGATTGTTGCCGCGCGCAAGGTCAACTACAGCCAGATCGAGCCGGCg < 1:1182310/76‑1 (MQ=255)
aaCGGAAAAAGTCACTGTTTATGGTTTGCCGATTGTTGCCGCGCGCAAGGTCAACTACAGCCAGATCGAGCCGGCg > 2:793300/1‑76 (MQ=255)
aaCGGAAAAAGTCACTGTTTATGGTTTGCCGATTGTTGCCGCGCGCAAGGTCAACTACAGCCAGATCGAGCCGGCg < 2:481342/76‑1 (MQ=255)
aaGTCACTGTTTATGGTTTGCCGATTGTTGCCGCGCGCAAGGTCAACTACAGCCAGATCGAGCCGGCGTTATGTCg < 2:126788/76‑1 (MQ=255)
gTCACTGTTTATGGTTTGCCGATTGTTGCCGCGCGCAAGGTCAACTACAGCCAGATCGAGCCGGCGTTATGTCGTg < 2:808798/76‑1 (MQ=255)
gTCACTGTTTATGGTTTGCCGATTGTTGCCGCGCGCAAGGTCAACTACAGCCAGATCGAGCCGGCGTTATGTCGTg < 1:289871/76‑1 (MQ=255)
tCACTGTTTATGGTTTGCCGATTGTTGCCGCGCGCAAGGTCAACTACAGCCAGATCGAGCCGGCGTTATGTCGTGa > 1:698287/1‑76 (MQ=255)
cACTGTTTATGGTTTGCCGATTGTTGCCGCGCGCAAGGTCAACTACAGCCAGATCGAGCCGGCGTTATGTCGTGaa > 2:273581/1‑76 (MQ=255)
tATGTTTTGCCGATTGTTGCCGCGCGCAAGGTCAACTACAGCCAGATCGAGCCGGCGTTATGTCGTGAACTCTTTa < 1:1076805/76‑1 (MQ=255)
tATGGTTTGCCGATTGTTGCCGCGCGCAAGGTCAACTACAGCCAGATCGAGCCGGCGTTATGTCGTGAACTCTTTa < 2:388356/76‑1 (MQ=255)
tATGGTTTGCCGATTGTTGCCGCGCGCAAGGTCAACTACAGCCAGATCGAGCCGGCGTTATGTCGTGAACTCTTTa < 1:904445/76‑1 (MQ=255)
aTGGTTTGCCGATTGTTGCCGCGCGCAAGGTCAACTACAGCCAGATCGAGCCGGCGTTATGTCGTGAACTCTTTAt < 1:1192983/76‑1 (MQ=255)
tgttttGCCGATTGTTGCCGCGCGCAAGGTCAACTACAGCCAGATCGAGCCGGCGTTATGTCGTGAACTCTTTAtt < 1:172672/73‑1 (MQ=255)
tGGTTTGCCGATTGTTGCCGCGCGCAAGGTCAACTACAGCCAGATCGAGCCGGCGTTATGTCGTGAACTCTTTAtt < 1:1041340/76‑1 (MQ=255)
tGGTTTGCCGATTGTTGCCGCGCGCAAGGTCAACTACAGCCAGATCGAGCCGGCGTTATGTCGTGAACTCTTTAtt > 1:897655/1‑76 (MQ=255)
ttGCCGATTGTTGCCGCGCGCAAGGTCAACTACAGCCAGATCGAGCCGGCGTTATGTCGTGAACTCTTTATTCGcc < 1:1005406/76‑1 (MQ=255)
ttGCCGATTGTTGCCGCGCGCAAGGTCAACTACAGCCAGATCGAGCCGGCGTTATGTCGTGAACTCTTTATTCGcc < 1:1084684/76‑1 (MQ=255)
tGCCGATTGTTGCCGCGCGCAAGGTCAACTACAGCCAGATCGAGCCGGCGTTATGTCGTGAACTCTTTATTCGCCa > 1:529712/1‑76 (MQ=255)
gCCGATTGTTGCCGCGCGCAAGGTCAACTACAGCCAGATCGAGCCGGCGTTATGTCGTGAACTCTTTATTCGCCAt > 1:432794/1‑76 (MQ=255)
gCCGATTGTTGCCGCGCGCAAGGTCAACTACAGCCAGATCGAGCCGGCGTTATGTCGTGAACTCTTTATTCGCCAt < 2:492726/76‑1 (MQ=255)
ttgCCGCGCGCAAGGTCAACTACAGCCAGATCGAGCCGGCGTTATGTCGTGAACTCTTTATTCGCCATGCGCtggt < 1:1039784/76‑1 (MQ=255)
tgCCGCGCGCAAGGTCAACTACAGCCAGATCGAGCCGGCGTTATGTCGTGAACTCTTTATTCGCCATGCGCtggtg > 2:107868/1‑76 (MQ=255)
gcgcgcAAGGTCAACTACAGCCAGATCGAGCCGGCGTTATGTCGTGAACTCTTTATTCGCCATGCGCTGGTGGAAg < 2:268441/76‑1 (MQ=255)
gcgcAAGGTCAACTACAGCCAGATCGAGCCGGCGTTATGTCGTGAACTCTTTATTCGCCATGCGCTGGTGGAAGGt < 1:949149/76‑1 (MQ=255)
aaGGTCAACTACAGCCAGATCGAGCCGGCGTTATGTCGTGAACTCTTTATTCGCCATGCGCTGGTGGAAGGTGACt < 2:592985/76‑1 (MQ=255)
aaGGTCAACTACAGCCAGATCGAGCCGGCGTTATGTCGTGAACTCTTTATTCGCCATGCGCTGGTGGAAGGTGACt > 2:861293/1‑76 (MQ=255)
aaGGTCAACTACAGCCAGATCGAGCCGGCGTTATGTCGTGAACTCTTTATTCGCCATGCGCTGGTGGAAGGTGACt > 1:1149829/1‑76 (MQ=255)
aGGTCAACTACAGCCAGATCGAGCCGGCGTTATGTCGTGAACTCTTTATTCGCCATGCGCTGGTGGAAGGTGACTg < 1:490447/76‑1 (MQ=255)
ggTCAACTACAGCCAGATCGATCCGGCGTTATGTCGTGAACTCTTTATTCGCCATGCGCTGGTGGAAGGTGACTgg < 1:1118506/76‑1 (MQ=255)
gTCAACTACAGCCAGATCGAGCCGGCGTTATGTCGTGAACTCTTTATTCGCCATGCGCTGGTGGAAGGTGACTGGc < 1:874242/76‑1 (MQ=255)
cAACTACAGCCAGATCGAGCCGGCGTTATGTCGTGAACTCTTTATTCGCCATGCGCTGGTGGAAGGTGACTGGCAg > 2:1043517/1‑76 (MQ=255)
cAACTACAGCCAGATCGAGCCGGCGTTATGTCGTGAACTCTTTATTCGCCATGCGCTGGTGGAAGGTGACTGGCAg < 1:576332/76‑1 (MQ=255)
cAACTACAGCCAGATCGAGCCGGCGTTATGTCGTGAACTCTTTATTCGCCATGCGCTGGTGGAAGGTGACTGGCAg > 2:542329/1‑76 (MQ=255)
aCTACAGCCAGATCGAGCCGGCGTTATGTCGTGAACTCTTTATTCGCCATGCGCTGGTGGAAGGTGACTGGCAGAc < 2:537172/76‑1 (MQ=255)
tACAGCCAGATCGAGCCGGCGTTATGTCGTGAACTCTTTATTCGCCATGCGCTGGTGGAAGGTGACTGGCAGAcgc > 2:165572/1‑76 (MQ=255)
aGCCAGATCGAGCCGGCGTTATGTCGTGAACTCTTTATTCGCCATGCGCTGGTGGAAGGTGACTGGCAGACGCGTc > 1:1219914/1‑76 (MQ=255)
gCCAGATGGAGCCGGCGTTATGTCGTGAACTCTTTATTCGCCATGCGCTGGTGGAAGGTGACTGGCAGACGCGTCa < 1:624432/76‑1 (MQ=255)
gCCAGATCGAGCCGGCGTTATGTCGTGAACTCTTTATTCGCCATGCGCTGGTGGAAGGTGACTGGCAGACGCGTCa < 1:624414/76‑1 (MQ=255)
cAGATCGAGCCGGCGTTATGTCGTGAACTCTTTATTCGCCATGCGCTGGTGGAAGGTGACTGGCAGACGCGTCACg > 1:981106/1‑76 (MQ=255)
aGATCGAGCCGGCGTTATGTCGTGAACTCTTTATTCGCCATGCGCTGGTGGAAGGTGACTGGCAGACGCGTCACGc < 1:306546/76‑1 (MQ=255)
tcgagcCGGCGTTATGTCGTGAACTCTTTATTCGCCATGCGCTGGTGGAAGGTGACTGGCAGACGCGTCACGCAtt < 2:125510/76‑1 (MQ=255)
tcgagcCGGCGTTATGTCGTGAACTCTTTATTCGCCATGCGCTGGTGGAAGGTGACTGGCAGACGCGTCACGCAtt > 1:711033/1‑76 (MQ=255)
|
AACGGAAAAAGTCACTGTTTATGGTTTGCCGATTGTTGCCGCGCGCAAGGTCAACTACAGCCAGATCGATCCGGCGTTATGTCGTGAACTCTTTATTCGCCATGCGCTGGTGGAAGGTGACTGGCAGACGCGTCACGCATT > REL606/1454545‑1454685
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
