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 |
|
A1 F1 I1 R1
|
154 |
26.6 |
2069536 |
90.2% |
1866721 |
108.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AM260479 |
3,301,576 |
+G |
intergenic (+45/‑146) |
lspA → / → dfp |
lipoprotein signal peptidase II/phosphopantothenoylcysteine synthetase/decarboxylase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 3,301,574 | 1 | . | G | 100.0%
| 46.0
/ NA
| 13 | intergenic (+43/‑148) | lspA/dfp | lipoprotein signal peptidase II/phosphopantothenoylcysteine synthetase/decarboxylase |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (5/8); total (5/8) |
GGCCTTCAACGTGGCCGACTGCGCGATCACGGTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCA‑GGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAACCGCCCGCCCTCACCCCCGGCCCCACTCCCGCCGTGCGGGAGTGGGG > AM260479/3301447‑3301659
|
ggccTTCAACGTGGCCGACTGCGCGATCACGGTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCA‑gggtga < 2:685650/134‑5 (MQ=255)
ggccTTCAACGTGGCCGACTGCGCGATCACGGTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCA‑gggt > 2:462553/1‑130 (MQ=255)
cTTCAACGTGGCCGACTGCGCGATCACGGTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAggg < 1:462553/134‑1 (MQ=255)
ggCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGaa < 1:647155/133‑1 (MQ=255)
gTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAAc < 1:637416/128‑1 (MQ=255)
gTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAAc > 2:637416/1‑128 (MQ=255)
cggcgCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAACCGCCCGCCCTCACCCCCGGCCCCACTCCCGCCGTGCgg < 2:1000863/133‑1 (MQ=255)
ggcgCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTc < 1:8874/70‑1 (MQ=255)
ggcgCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTc > 2:8874/1‑70 (MQ=255)
ccACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGca < 1:110356/75‑1 (MQ=255)
ccACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGca > 2:110356/1‑75 (MQ=255)
gcgcCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAACCGCCCGCCCTCACCCCCGGCCCCACTCCCGCCGTGCGGGAGTgggg < 1:163770/129‑1 (MQ=255)
gcgcCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAACCGCCCGCCCTCACCCCCGGCCCCACTCCCGCCGTGCGGGAGTgggg > 2:163770/1‑129 (MQ=255)
gCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGCACCACGccac < 1:606341/59‑1 (MQ=255)
gCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGCACCACGccac > 2:606341/1‑59 (MQ=255)
|
GGCCTTCAACGTGGCCGACTGCGCGATCACGGTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCA‑GGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAACCGCCCGCCCTCACCCCCGGCCCCACTCCCGCCGTGCGGGAGTGGGG > AM260479/3301447‑3301659
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GGCCTTCAACGTGGCCGACTGCGCGATCACGGTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCA‑GGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAACCGCCCGCCCTCACCCCCGGCCCCACTCCCGCCGTGCGGGAGTGGGGAGCCAACCCTCAGCCGGCTTC > AM260479/3301447‑3301680
|
ttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacaGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAA < GWNJ‑0478:712:GW2002102894th:2:2205:14314:98262/80‑1 (MQ=60)
CCTTCAACGTGGCCGACTGCGCGATCACGGTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCA‑GGgtgagggcgggcggttctggtg < GWNJ‑0478:712:GW2002102894th:2:1212:4162:95536/150‑23 (MQ=60)
acgagatgtagctccgtctcgtgggctcggagatgtgtataagagacaGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGCACCACGC < GWNJ‑0478:712:GW2002102894th:2:1101:18941:65743/101‑1 (MQ=60)
gatgtagctccgtctcgtgggctcggagatgtgtataagagacagGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAAC < GWNJ‑0478:712:GW2002102894th:2:1108:12808:44221/105‑1 (MQ=60)
agaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacaGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAACCGCCCGCCC < GWNJ‑0478:712:GW2002102894th:2:2106:14731:7760/90‑1 (MQ=60)
CGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAACCGCCCGCCCTCACCC < GWNJ‑0478:712:GW2002102894th:2:2109:16164:10943/150‑1 (MQ=60)
CGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAACCGCCCGCCCTCACC < GWNJ‑0478:712:GW2002102894th:2:2109:7236:70511/149‑1 (MQ=60)
GCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCA‑GGgctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaaaaaaaaaaaaaa > GWNJ‑0478:712:GW2002102894th:2:1113:19321:5374/1‑67 (MQ=60)
CACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAACCGCCCGCCCTCACCCCCGGCCCCACTCCCGCCGTGCGGGAGTGGGGAGCCAACCCTCAGCC < GWNJ‑0478:712:GW2002102894th:2:1110:14605:67464/150‑1 (MQ=60)
CCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAActgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaaaaaaaaaaaaaaaaaag > GWNJ‑0478:712:GW2002102894th:2:2113:20429:50121/1‑61 (MQ=60)
|
GGCCTTCAACGTGGCCGACTGCGCGATCACGGTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCA‑GGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAACCGCCCGCCCTCACCCCCGGCCCCACTCCCGCCGTGCGGGAGTGGGGAGCCAACCCTCAGCCGGCTTC > AM260479/3301447‑3301680
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
