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 |
380,351 |
C→T |
54.2% |
V190V (GTC→GTT) |
entC → |
isochorismate synthase 1 |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 380,351 | 0 | C | T | 54.2%
| 2.2
/ 38.3
| 48 | V190V (GTC→GTT) | entC | isochorismate synthase 1 |
| Reads supporting (aligned to +/- strand): ref base C (13/9); new base T (16/10); total (29/19) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.86e-01 |
GGAACGGTTGATTGCGCAAAACCCGGTTAGTTACAACTTCCATGTTCCGCTGGCTGATGGTGGCGTCCTGCTGGGGGCCAGCCCGGAACTGCTGCTACGTAAAGACGGCGAGCGTTTTAGCTCCATTCC > minE/380285‑380413
|
ggAACGGTTGATTGCGCAAAACCCGGTTAGTTACAACTTCCATGTTCCGCTGGCTGATGGTGGCGTCct > 1:775522/1‑69 (MQ=255)
gttagttaCAACTTCCATGTTCCGTTGGCTGATGGTGGCGTTCTGCTGGGGGCCAGCCCGGAActgct > 1:2294182/1‑68 (MQ=255)
gttagttaCAACTTCCATGTTCCGTTGGCTGATGGTGGCGTTCTGCTGGGGGCCAGCCCGGAActgct > 1:3017357/1‑68 (MQ=255)
gttagttaCAACTTCCATGTTCCGTTGGCTGATGGTGGCGTTCTGCTGGGGGCCAGCCCGGAActgct > 1:2952684/1‑68 (MQ=255)
gttagttaCAACTTCCATGTTCCGTTGGCTGATGGTGGCGTTCTGCTGGGGGCCAGCCCGGAActgct > 1:308700/1‑68 (MQ=255)
gttagttaCAACTTCCATGTTCCGTTGGCTGATGGTGGCGTTCTGCTGGGGGCCAGCCCGGAActgct > 1:3316456/1‑68 (MQ=255)
gttagttaCAACTTCCATGTTCCGTTGGCTGATGGTGGCGTTCTGCTGGGGGCCAGCCCGGAActgct > 1:2694179/1‑68 (MQ=255)
gttagttaCAACTTCCATGTTCCGTTGGCTGATGGTGGCGTTCTGCTGGGGGCCAGCCCGGAActgct > 1:2690356/1‑68 (MQ=255)
gttagttaCAACTTCCATGTTCCGTTGGCTGATGGTGGCGTTCTGCTGGGGGCCAGCCCGGAActgct > 1:2654608/1‑68 (MQ=255)
gttagttaCAACTTCCATGTTCCGTTGGCTGATGGTGGCGTTCTGCTGGGGGCCAGCCCGGAActgct > 1:373662/1‑68 (MQ=255)
gttagttaCAACTTCCATGTTCCGTTGGCTGATGGTGGCGTTCTGCTGGGGGCCAGCCCGGAActgct > 1:2544565/1‑68 (MQ=255)
gttagttaCAACTTCCATGTTCCGTTGGCTGATGGTGGCGTTCTGCTGGGGGCCAGCCCGGAActgct > 1:2391792/1‑68 (MQ=255)
gttagttaCAACTTCCATGTTCCGTTGGCTGATGGTGGCGTTCTGCTGGGGGCCAGCCCGGAActgct > 1:1360165/1‑68 (MQ=255)
gttagttaCAACTTCCATGTTCCGTTGGCTGATGGTGGCGTTCTGCTGGGGGCCAGCCCGGAActgct > 1:1609150/1‑68 (MQ=255)
gttagttaCAACTTCCATGTTCCGTTGGCTGATGGTGGCGTTCTGCTGGGGGCCAGCCCGGAActgct > 1:809736/1‑68 (MQ=255)
gttagttaCAACTTCCATGTTCCGTTGGCTGATGGTGGCGTTCTGCTGGGGGCCAGCCCGGAActgct > 1:19977/1‑68 (MQ=255)
gttagttaCAACTTCCATGTTCCGTTGGCTGATGGTGGCGTTCTGCTGGGGGCCACCCCGGaa > 1:2346145/1‑63 (MQ=255)
ttagttaCAACTTCCATGTTCCGCTGGCTGATGGTGGCGTCCTGCTGGGGGCCAGCCCGGAACtgctgc < 1:1799698/69‑1 (MQ=255)
cTTCCATGTTCCGTTGGCTGATGGTGGCGTTCTGCTGGGGGCCAGCCCGGAACTGCTGCTACGTAAAGa < 1:2598085/69‑1 (MQ=255)
cTTCCATGTTCCGTTGGCTGATGGTGGCGTTCTGCTGGGGGCCAGCCCGGAACTGCTGCTACGTAAAGa < 1:863971/69‑1 (MQ=255)
cTTCCATGTTCCGTTGGCTGATGGTGGCGTTCTGCTGGGGGCCAGCCCGGAACTGCTGCTACGTAAAGa < 1:1837581/69‑1 (MQ=255)
cTTCCATGTTCCGTTGGCTGATGGTGGCGTTCTGCTGGGGGCCAGCCCGGAACTGCTGCTACGTAAAGa < 1:1925579/69‑1 (MQ=255)
cTTCCATGTTCCGTTGGCTGATGGTGGCGTTCTGCTGGGGGCCAGCCCGGAACTGCTGCTACGTAAAGa < 1:1928352/69‑1 (MQ=255)
cTTCCATGTTCCGTTGGCTGATGGTGGCGTTCTGCTGGGGGCCAGCCCGGAACTGCTGCTACGTAAAGa < 1:1962026/69‑1 (MQ=255)
cTTCCATGTTCCGTTGGCTGATGGTGGCGTTCTGCTGGGGGCCAGCCCGGAACTGCTGCTACGTAAAGa < 1:2451748/69‑1 (MQ=255)
cTTCCATGTTCCGTTGGCTGATGGTGGCGTTCTGCTGGGGGCCAGCCCGGAACTGCTGCTACGTAAAGa < 1:489950/69‑1 (MQ=255)
cTTCCATGTTCCGTTGGCTGATGGTGGCGTTCTGCTGGGGGCCAGCCCGGAACTGCTGCTACGTAAAGa < 1:2129327/69‑1 (MQ=255)
gTTCCGCTGGCTGATGGTGGCGTCCTGCTGGGGGCCAGCCCGGAACTGCTGCTACGTAAAGACGGCTAg < 1:696172/69‑1 (MQ=255)
gTTCCGCTGGCTGATGGTGGCGTCCTGCTGGGGGCCAGCCCGGAACTGCTGCTACGTAAAGACGGCGAg < 1:827103/69‑1 (MQ=255)
gTTCCGCTGGCTGATGGTGGCGTCCTGCTGGGGGCCAGCCCGGAACTGCTGCTACGTAAAGACGGCGAg < 1:928779/69‑1 (MQ=255)
gTTCCGCTGGCTGATGGTGGCGTCCTGCTGGGGGCCAGCCCGGAACTGCTGCTACGTAAAGACGGCGAg < 1:2899052/69‑1 (MQ=255)
gTTCCGCTGGCTGATGGTGGCGTCCTGCTGGGGGCCAGCCCGGAACTGCTGCTACGTAAAGACGGCGAg < 1:1966478/69‑1 (MQ=255)
gTTCCGCTGGCTGATGGTGGCGTCCTGCTGGGGGCCAGCCCGGAACTGCTGCTACGTAAAGACGGCGAg < 1:2282236/69‑1 (MQ=255)
ttCCGCTGGCTGATGGTGGCGTCCTGCTGGGGGCCAGCCCGGAACTGCTGCTACGTAAAGACGGCGAg < 1:1727306/68‑1 (MQ=255)
ctggctgATGGTGGCGTCCTGCTGGGGGCCAGCCCGGAACtgctgc < 1:90223/46‑1 (MQ=255)
tggctgATGGTGGCGTTCTGCTGGGGGCCAGCCCGGAACTGCTGCTACGTAAAGa < 1:2413371/55‑1 (MQ=255)
ttggCGTCCTGTTGGGGGCCAGCCCGGAACTGCTGCTACGTAAAGACGGCGAGCGtttt > 1:52650/2‑59 (MQ=255)
gtggCGTCCTGTTGGGGGCCAGCCCGGAACTGCTGCTACGTAAAGACGGCGAGCGtttt > 1:1348089/1‑59 (MQ=255)
gtggCGTCCTGTTGGGGGCCAGCCCGGAACTGCTGCTACGTAAAGACGGCGAGCGtttt > 1:1351692/1‑59 (MQ=255)
gtggCGTCCTGTTGGGGGCCAGCCCGGAACTGCTGCTACGTAAAGACGGCGAGCGtttt > 1:2019442/1‑59 (MQ=255)
gtggCGTCCTGTTGGGGGCCAGCCCGGAACTGCTGCTACGTAAAGACGGCGAGCGtttt > 1:626571/1‑59 (MQ=255)
gtggCGTCCTGTTGGGGGCCAGCCCGGAACTGCTGCTACGTAAAGACGGCGAGCGtttt > 1:44064/1‑59 (MQ=255)
gtggCGTCCTGTTGGGGGCCAGCCCGGAACTGCTGCTACGTAAAGACGGCGAGCGtttt > 1:2629315/1‑59 (MQ=255)
gtggCGTCCTGTTGGGGGCCAGCCCGGAACTGCTGCTACGTAAAGACGGCGAGCGtttt > 1:3171882/1‑59 (MQ=255)
gtggCGTCCTGTTGGGGGCCAGCCCGGAACTGCTGCTACGTAAAGACGGCGAGCGtttt > 1:3106476/1‑59 (MQ=255)
gtggCGTCCTGTTGGGGGCCAGCCCGGAACTGCTGCTACGTAAAGACGGCGAGCGtttt > 1:2922216/1‑59 (MQ=255)
gtggCGACCTGTTGGGGGCCAGCCCGGAACTGCTGCTACGTAAAGACGGCGAGCGtttt > 1:4115/1‑59 (MQ=255)
tggCGTCCTGCTGGGGGCCAGCCCGGAACTGCTGCTACGTAAAGACGGCGAGCGTTTTAGCTCCATTcc > 1:299616/1‑69 (MQ=255)
|
GGAACGGTTGATTGCGCAAAACCCGGTTAGTTACAACTTCCATGTTCCGCTGGCTGATGGTGGCGTCCTGCTGGGGGCCAGCCCGGAACTGCTGCTACGTAAAGACGGCGAGCGTTTTAGCTCCATTCC > minE/380285‑380413
|
| 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
