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 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
816,410 |
C→T |
60.6% |
S161S (AGC→AGT) |
hemA → |
glutamyl tRNA reductase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 816,410 | 0 | C | T | 60.6%
| 12.6
/ 23.3
| 38 | S161S (AGC→AGT) | hemA | glutamyl tRNA reductase |
| Reads supporting (aligned to +/- strand): ref base C (4/11); new base T (8/15); total (12/26) |
| Fisher's exact test for biased strand distribution p-value = 7.28e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.72e-01 |
CCAGAAATCTTTCTCTGTCGCGAAACGCGTTCGCACTGAAACAGATATCGGTGCCAGCGCTGTGTCTGTCGCTTTTGCGGCTTGTACGCTGGCGCGGCAGATCTTTGAATCGCTCTCTACGGTCAC > minE/816353‑816478
|
ccAGAAATCTTTCTCTGTCGCGAAACGCGTTCGCACTGAAACAGATATCGGTGCCAGCGCTGtgtctgt > 1:1769583/1‑69 (MQ=255)
ccAGAAATCTTTCTCTGTCGCGAAACGCGTTCGCACTGAAACAGATATCGGTGCCAGCGCTGtgtctgt > 1:2698738/1‑69 (MQ=255)
ccAGAAATCTTTCTCTGTCGCGAAACGCGTTCGCACTGAAACAGATATCGGTGCCAGCGCTGtgtctgt > 1:2994250/1‑69 (MQ=255)
ccAGAAATCTTTCTCTGTCGCGAAACGCGTTCGCACTGAAACAGATATCGGTGCCAGCGCTGtgtctg > 1:3031373/1‑68 (MQ=255)
aTCTTTCTCTGTCGCGAAACGCGTTCGCACTGAAACAGATATCGGTGCCAGCGCTGTGTCTGTCGCttt < 1:935036/69‑1 (MQ=255)
aTCTTTCTCTGTCGCGAAACGCGTTCGCACTGAAACAGATATCGGTGCCAGCGCTGTGTCTGTCGCttt < 1:762103/69‑1 (MQ=255)
aTCTTTCTCTGTCGCGAAACGCGTTCGCACTGAAACAGATATCGGTGCCAGCGCTGTGTCTGTCGCttt < 1:334684/69‑1 (MQ=255)
aTCTTTCTCTGTCGCGAAACGCGTTCGCACTGAAACAGATATCGGTGCCAGCGCTGTGTCTGTCGCttt < 1:2032470/69‑1 (MQ=255)
aTCTTTCTCTGTCGCGAAACGCGTTCGCACTGAAACAGATATCGGTGCCAGCGCTGTGTCTGTCGCttt < 1:1049301/69‑1 (MQ=255)
aTCTTTCTCTGTCGCGAAACGCGTTCGCACTGAAACAGATATCGGTGCCAGCGCTGTGTCTGTCGCttt < 1:974425/69‑1 (MQ=255)
tCTTTCTCTGTCGCGAAACGCGTTCGCACTGAAACAGATATCGGTGCCAGCGCTGTGTCTGTCGCttt < 1:967409/68‑1 (MQ=255)
tCTTTCTCTGTCGCGAAACGCGTTCGCACTGAAACAGATATCGGTGCCAGCGCTGTGTCTGTCGCttt < 1:1088819/68‑1 (MQ=255)
tCTTTCTCTGTCGCGAAACGCGTTCGCACTGAAACAGATATCGGTGCCAGCGCTGTGTCTGTCGCttt < 1:1656302/68‑1 (MQ=255)
tCTTTCTCTGTCGCGAAACGCGTTCGCACTGAAACAGATATCGGTGCCAGCGCTGTGTCTGTCGCttt < 1:3204952/68‑1 (MQ=255)
tctcTGTCGCGAAACGCGTTCGCACTGAAACAGATATCGGTGCCAGTGCTGTGTCTGTCGCTTTTGCgg > 1:513857/1‑69 (MQ=255)
tctcTGTCGCGAAACGCGTTCGCACTGAAACAGATATCGGTGCCAGTGCTGTGTCTGTCGCTTTTGCgg > 1:1027471/1‑69 (MQ=255)
tctcTGTCGCGAAACGCGTTCGCACTGAAACAGATATCGGTGCCAGTGCTGTGTCTGTCGCTTTTGCgg > 1:2926061/1‑69 (MQ=255)
tctcTGTCGCGAAACGCGTTCGCACTGAAACAGATATCGGTGCCAGTGCTGTGTCTGTCGCTTTTGCgg > 1:2720268/1‑69 (MQ=255)
tctcTGTCGCGAAACGCGTTCGCACTGAAACAGATATCGGTGCCAGTGCTGTGTCTGTCGCTTTTGCgg > 1:2590325/1‑69 (MQ=255)
tctcTGTCGCGAAACGCGTTCGCACTGAAACAGATATCGGTGCCAGTGCTGTGTCTGTCGCTTTTGCgg > 1:1012102/1‑69 (MQ=255)
tctcTGTCGCGAAACGCGTTCGCACTGAAACAGATATCGGTGCCAGTGCTGTGTCTGTCGCTTTTGCgg > 1:2031841/1‑69 (MQ=255)
tctcTGTCGCGAAACGCGTTCGCACTGAAACAGATATCGGTGCCAGTGCTGTGTCTGTCGCTTTTGCgg > 1:2586350/1‑69 (MQ=255)
aCGCGTTCGCACTGAAACAGATATCGGTGCCAGCGCTGTGTCTGTCGCttt < 1:1204009/51‑1 (MQ=255)
ggTGCCAGTGCTGTGTCTGTCGCTTTTGCGGCTTGTACGCTGGCGCGGCAGATCTTTGAATCGctctct < 1:3393589/69‑1 (MQ=255)
tGCCAGTGCTGTGTCTGTCGCTTTTGCGGCTTGTACGCTGGCGCGGCAGATCTTTGAATCGCTCTCTa < 1:2662888/68‑1 (MQ=255)
tGCCAGTGCTGTGTCTGTCGCTTTTGCGGCTTGTACGCTGGCGCGGCAGATCTTTGAATCGCTCTCTa < 1:2734877/68‑1 (MQ=255)
tGCCAGTGCTGTGTCTGTCGCTTTTGCGGCTTGTACGCTGGCGCGGCAGATCTTTGAATCGCTCTCTa < 1:1049542/68‑1 (MQ=255)
tGCCAGTGCTGTGTCTGTCGCTTTTGCGGCTTGTACGCTGGCGCGGCAGATCTTTGAATCGCTCTCTa < 1:767955/68‑1 (MQ=255)
tGCCAGTGCTGTGTCTGTCGCTTTTGCGGCTTGTACGCTGGCGCGGCAGATCTTTGAATCGCTCTCTa < 1:1767550/68‑1 (MQ=255)
tGCCAGTGCTGTGTCTGTCGCTTTTGCGGCTTGTACGCTGGCGCGGCAGATCTTTGAATCGCTCTCTa < 1:388771/68‑1 (MQ=255)
tGCCAGTGCTGTGTCTGTCGCTTTTGCGGCTTGTACGCTGGCGCGGCAGATCTTTGAATCGCTCTCTa < 1:3284860/68‑1 (MQ=255)
tGCCAGTGCTGTGTCTGTCGCTTTTGCGGCTTGTACGCTGGCGCGGCAGATCTTTGAATCGCTCTCTa < 1:2044872/68‑1 (MQ=255)
tGCCAGTGCTGTGTCTGTCGCTTTTGCGGCTTGTACGCTGGCGCGGCAGATCTTTGAATCGCTCTCTa < 1:240288/68‑1 (MQ=255)
tGCCAGTGCTGTGTCTGTCGCTTTTGCGGCTTGTACGCTGGCGCGGCAGATCTTTGAATCGCTCTCTa < 1:2944757/68‑1 (MQ=255)
tGCCAGTGCTGTGTCTGTCGCTTTTGCGGCTTGTACGCTGGCGCGGCAGATCTTTGAATCGCTCTCTa < 1:2548076/68‑1 (MQ=255)
tGCCAGTGCTGTGTCTGTCGCTTTTGCGGCTTGTACGCTGGCGCGGCAGATCTTTGAATCGCTCTCTa < 1:2871988/68‑1 (MQ=255)
tGCCAGTGCTGTGTCTGTCGCTTTTGCGGCTTGTACGATGGCGCGGCAGATCTTTGAATCGCTCTCTa < 1:347408/68‑1 (MQ=255)
tGCCAGTGCTGTGTCTGGCGCTTTTGCGGCTTGTACGCTGGCGCGGCAGATCTTTGAATCGCTCTCTa < 1:930722/68‑1 (MQ=255)
cgcTGTGTCTGTCGCTTTTGCGGCTTGTACGCTGGCGCGGCAGATCTTTGAATCGCTCTCTACGGTcac < 1:329934/69‑1 (MQ=255)
cgcTGTGTCTGTCGCTTTTGCGGCTTGTACGCTGGCGCGGCAGATCTTTGAATCGCTCTCTACGGTcac < 1:2032803/69‑1 (MQ=255)
cgcTGTGTCTGTCGCTTTTGCGGCTTGTACGCTGGCGCGGCAGATCTTTGAATCGCTCTCTACGGTcac < 1:3185206/69‑1 (MQ=255)
cgcTGTGTCTGTCGCTTTTGCGGCTTGTACGCTGGCGCGGCAGATCTTTGAATCGCTCTCTACGGTcac < 1:1467564/69‑1 (MQ=255)
cgcTGTGTCTGTCGCTTTTGCGGCTTGTACGCTGGCGCGGCAGATCTTTGAATCGCTCTCTACGGTcac < 1:765769/69‑1 (MQ=255)
cgcTGTGTCTGTCGCTATTGCGGCTTGTACGCTGGCGCGGCAGATCTTTGAATCGCTCTCTACGGTcac < 1:2761382/69‑1 (MQ=255)
|
CCAGAAATCTTTCTCTGTCGCGAAACGCGTTCGCACTGAAACAGATATCGGTGCCAGCGCTGTGTCTGTCGCTTTTGCGGCTTGTACGCTGGCGCGGCAGATCTTTGAATCGCTCTCTACGGTCAC > minE/816353‑816478
|
| 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
