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 |
|
A6 F21 I0 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
425,152 |
C→T |
27.0% |
D301N (GAT→AAT) |
nagA ← |
N‑acetylglucosamine‑6‑phosphate deacetylase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 425,152 | 0 | C | T | 27.0%
| 115.7
/ 48.2
| 74 | D301N (GAT→AAT) | nagA | N‑acetylglucosamine‑6‑phosphate deacetylase |
| Reads supporting (aligned to +/- strand): ref base C (21/33); new base T (7/13); total (28/46) |
| Fisher's exact test for biased strand distribution p-value = 7.95e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.79e-01 |
CAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTCAATGTTGGCACCTG > minE/425082‑425220
|
cAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATc > 1:1862216/1‑71 (MQ=255)
cAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATTCACACAAAGTc < 1:3922405/71‑1 (MQ=255)
aGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATTCACACAAAGTcc < 1:1903632/71‑1 (MQ=255)
aTTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGt < 1:655560/71‑1 (MQ=255)
ttACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTTATCCACACAAAGTCCGt < 1:288176/70‑1 (MQ=255)
ttACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGt > 1:2158650/1‑70 (MQ=255)
cgcacgcCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTAc < 1:86993/70‑1 (MQ=255)
cgcacgcCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTAc < 1:126793/70‑1 (MQ=255)
gcacgcCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATTCACACAAAGTCCGTTACgg < 1:2752018/71‑1 (MQ=255)
gcacgcCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATTCACACAAAGTCCGTTACgg < 1:69855/71‑1 (MQ=255)
acgcCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTc > 1:3012552/1‑61 (MQ=255)
acgcCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGgta < 1:1064065/71‑1 (MQ=255)
acgcCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGgta < 1:405375/71‑1 (MQ=255)
cgcCTTCTATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGgta < 1:2869552/70‑1 (MQ=255)
cgcCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAg < 1:1432254/58‑1 (MQ=255)
gcCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGgtag > 1:1989292/1‑70 (MQ=255)
cTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGgtagta > 1:583595/1‑70 (MQ=255)
tCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATTCACACAAAGTCCGTTACGgta > 1:3802358/1‑65 (MQ=255)
aaTCATGGTTAAGGATGAACCGCTTAACGTACTGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTg < 1:2092180/71‑1 (MQ=255)
aaTCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTg < 1:221455/71‑1 (MQ=255)
aTCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTg < 1:1778322/70‑1 (MQ=255)
aTCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGt < 1:3478509/71‑1 (MQ=255)
cATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATTCACACAAAGTCCGTTACGGTAGTATATTGttt > 1:2903815/1‑71 (MQ=255)
aTGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATTCACACAAAGTCCGTTACGGTAGTATATTGtttt < 1:581633/71‑1 (MQ=255)
aTGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTc > 1:738713/1‑49 (MQ=255)
aTGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGtttt < 1:1549037/71‑1 (MQ=255)
aTGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGtttt < 1:1730783/71‑1 (MQ=255)
aTGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGtttt < 1:1612156/71‑1 (MQ=255)
gTTAAGGATGAACCGCTTAACGTACCGTTCTCATc > 1:3207996/1‑35 (MQ=255)
gTTAAGGATGAACCGCTTAACGTACCGTTCTCATTCACACAAAGTCCGTTa > 1:27953/1‑51 (MQ=255)
ttAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTa < 1:1997892/68‑1 (MQ=255)
aGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGtt < 1:1286553/62‑1 (MQ=255)
aGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGc > 1:56251/1‑70 (MQ=255)
aGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGc > 1:2998155/1‑70 (MQ=255)
ggATGAACCGCTTAACGTACCGTTCTCATTCACACAAAGTCCGTTACGgta < 1:2579933/51‑1 (MQ=255)
ggATGAACCGCTTAACGTACCGTTCTCATTCACACAAAGTCCGTTACGgta < 1:928696/51‑1 (MQ=255)
ggATGAACCGCTTAACGTACCGTTCTCATTCACACAAAGTCCGTTACGgta < 1:1042416/51‑1 (MQ=255)
ggATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGtttt < 1:3456404/63‑1 (MQ=255)
ggATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGtttt < 1:1626983/63‑1 (MQ=255)
ggATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCa > 1:1073497/1‑70 (MQ=255)
aTGAACCGCTTAACGTACCGTTCTCATTCACACAAAGTCCGTTACGgta < 1:2555447/49‑1 (MQ=255)
aTGAACCGCTTAACGTACCGTTCTCATTCACACAAAGTCCGTTACGgta < 1:892325/49‑1 (MQ=255)
aTGAACCGCTTAACGTACCGTTCTCATCCACACaaa > 1:639036/1‑36 (MQ=255)
aTGAACCGCTTAACGTACCGTTCTCATCCACACaa > 1:2832508/1‑35 (MQ=255)
aTGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGttt > 1:2977845/1‑60 (MQ=255)
aTGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGttt > 1:2624275/1‑60 (MQ=255)
aTGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCaaaa < 1:2082678/71‑1 (MQ=255)
aTGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCaaaa < 1:1306900/71‑1 (MQ=255)
gAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAAt > 1:1127309/1‑71 (MQ=255)
aaCCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATg < 1:3885590/71‑1 (MQ=255)
aCCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATg < 1:2929655/70‑1 (MQ=255)
cTTAACGTACCGTTCTCATTCACACAAAGTCCGTTACGGTAGTATATTGTTTTa > 1:138988/1‑54 (MQ=255)
cTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACg < 1:626918/38‑1 (MQ=255)
cTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTatat > 1:1456824/1‑47 (MQ=255)
tAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCaaaa > 1:3295265/1‑61 (MQ=255)
tAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGtt > 1:1153002/1‑71 (MQ=255)
aaCGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGtt < 1:1360069/70‑1 (MQ=255)
aCGTACCGTTCTCATTCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTc < 1:3703845/70‑1 (MQ=255)
cGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCaaaa < 1:1437566/58‑1 (MQ=255)
cGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCa > 1:2860562/1‑55 (MQ=255)
cGTACCCTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCa > 1:510316/1‑55 (MQ=255)
gTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTg < 1:958847/43‑1 (MQ=255)
gTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATg < 1:1468536/60‑1 (MQ=255)
gTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATg < 1:3816860/60‑1 (MQ=255)
tACCGTTCTCATTCACACAAAGTCCGTTACGGTAGTATATTGTTTTAccc < 1:126074/50‑1 (MQ=255)
tACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTCAATg < 1:555778/71‑1 (MQ=255)
aCCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGaa > 1:2287031/1‑60 (MQ=255)
ccGTTCTCATTCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGc > 1:3465072/1‑50 (MQ=255)
ccGTTCTCATTCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTCAATGt < 1:123639/70‑1 (MQ=255)
cGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTCAATGTTg > 1:3003326/1‑71 (MQ=255)
ttCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATg < 1:2930526/54‑1 (MQ=255)
ttCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTCAATGTTGGc < 1:3406714/71‑1 (MQ=255)
ctcATTCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTCAATGTTGGCAc > 1:2183575/1‑71 (MQ=255)
ctcATTCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTCAATGTTGGCAc > 1:2670158/1‑71 (MQ=255)
tcATCCACACAAAGTCCGTTACGGTAGTATATTGtttt < 1:2835507/38‑1 (MQ=255)
aTCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTCAATGTTGGCACctg > 1:2018064/1‑71 (MQ=255)
|
CAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTCAATGTTGGCACCTG > minE/425082‑425220
|
| 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
