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 F17 I0 R2
|
278 |
43.2 |
2215644 |
94.6% |
2095999 |
61.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,485,005 |
C→T |
13.1% |
D279N (GAT→AAT) |
menF ← |
isochorismate synthase 2 |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,485,005 | 0 | C | T | 13.1%
| 100.7
/ 7.2
| 38 | D279N (GAT→AAT) | menF | isochorismate synthase 2 |
| Reads supporting (aligned to +/- strand): ref base C (13/20); new base T (3/2); total (16/22) |
| Fisher's exact test for biased strand distribution p-value = 6.32e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.92e-01 |
GGTATCGGCCTGTAATCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGATTATTTGCTACTGTTCCCGC > minE/1484940‑1485074
|
ggTATCGGCCTGTAATCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTtattat < 1:1351407/68‑1 (MQ=255)
cTGTAATCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGc > 1:820413/1‑70 (MQ=255)
tAATCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATTCGCCAt < 1:1045172/63‑1 (MQ=255)
tAATCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCa > 1:2045107/1‑69 (MQ=255)
tAATCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCa < 1:1474725/69‑1 (MQ=255)
tAATCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCAct > 1:992015/1‑71 (MQ=255)
tAATCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCAc < 1:666113/70‑1 (MQ=255)
aaTCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCActc > 1:457612/1‑71 (MQ=255)
aTCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATTATCCGCCATCAGCCActc < 1:1764704/70‑1 (MQ=255)
aTCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCActct > 1:1038624/1‑71 (MQ=255)
gTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCAt > 1:526381/1‑58 (MQ=255)
gTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCa > 1:322922/1‑64 (MQ=255)
gTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTcc > 1:1032334/1‑70 (MQ=255)
gATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAActgct < 1:295885/71‑1 (MQ=255)
atatCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATTATCCGCCATCAGCCACTCTCCTAActgct > 1:1397018/1‑70 (MQ=255)
cTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCActc < 1:2032708/55‑1 (MQ=255)
ttCCACCACCAGCATGTTCTCGCGCTGGTTTTTATTATCCGCCATCAGCCACTCTCCTAACTGCTgcgc > 1:256430/1‑69 (MQ=255)
ttCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCa < 1:867868/47‑1 (MQ=255)
ttCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCa < 1:2128701/47‑1 (MQ=255)
caccaccaGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCt < 1:1437190/71‑1 (MQ=255)
accaccaGCATGTTCTCGCGCTGGTTTTTATTATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTg < 1:188863/68‑1 (MQ=255)
accaccaGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCtt < 1:1701656/71‑1 (MQ=255)
ccaccaGCATGTTCTCGCGCTGGTTTTTATTATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTa > 1:834201/1‑71 (MQ=255)
accaGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTatc < 1:1439075/71‑1 (MQ=255)
ccaGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCtt < 1:674696/67‑1 (MQ=255)
ccaGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCtt < 1:552990/67‑1 (MQ=255)
gCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCa > 1:2180111/1‑40 (MQ=255)
gCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCa > 1:821661/1‑40 (MQ=255)
gCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTatcat > 1:2141890/1‑69 (MQ=255)
gcgcTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGATTAttt > 1:2204261/1‑70 (MQ=255)
cgcTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGATTATTTGc < 1:37341/71‑1 (MQ=255)
cgcTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGATTATTTGc < 1:1356296/71‑1 (MQ=255)
gcTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGATTATTTGc < 1:1398842/70‑1 (MQ=255)
gTTTTTATCATCCGCCATCATCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGATTATTTGCTa < 1:1604728/68‑1 (MQ=255)
gTTTTTATCATCCGCCATCAGCCACTCTCCTAActgctg > 1:666334/1‑39 (MQ=255)
gTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGATTATTTGCTa < 1:1602269/68‑1 (MQ=255)
gTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGATTATTTGCTACTg < 1:1339384/71‑1 (MQ=255)
gTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGATTATTTGCTACTg < 1:1269959/71‑1 (MQ=255)
gTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGATTATTTGCTACTg < 1:1464918/71‑1 (MQ=255)
atcatcCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGATTATTTGCTACTGTTccc > 1:783844/1‑70 (MQ=255)
atcatcCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGATTATTTGCTACTGTTCCCg > 1:225522/1‑71 (MQ=255)
tcatcCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGATTATTTGCTACTGTTCCCGc < 1:59986/71‑1 (MQ=255)
|
GGTATCGGCCTGTAATCGTTGACAGATATCTTCCACCACCAGCATGTTCTCGCGCTGGTTTTTATCATCCGCCATCAGCCACTCTCCTAACTGCTGCGCCTGCTTATCATCAGGATTATTTGCTACTGTTCCCGC > minE/1484940‑1485074
|
| 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
