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 |
|
A0 F0 I1 R1
|
155 |
25.8 |
2285122 |
88.0% |
2010907 |
104.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AM260479 |
2,955,197 |
Δ1 bp |
coding (1034/1071 nt) |
h16_A2735 → |
phenylpropionate dioxygenase or related ring‑hydroxylating dioxygenase, large terminal subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 2,955,195 | 0 | C | . | 100.0%
| 68.4
/ NA
| 16 | coding (1032/1071 nt) | h16_A2735 | phenylpropionate dioxygenase or related ring‑hydroxylating dioxygenase, large terminal subunit |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base . (9/7); total (9/7) |
AGCGCGAGTTCGTCGAGGCCGAGCGCGCCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTACCCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCCGGCGGACTAGTGCGATAACCGCACAACGCACGCAAGAACGGACCGC > AM260479/2955065‑2955317
|
aGCGCGAGTTCGTCGAGGCCGAGCGCGCCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTAccag < 1:877166/134‑3 (MQ=255)
cgtcgAGGCCGAGCGCGCCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATg > 1:13619/1‑133 (MQ=255)
aGCGCGCCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATg < 2:13619/134‑1 (MQ=255)
tCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATcgccgc < 2:527508/134‑1 (MQ=255)
tCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATcgccgc > 2:1128241/1‑134 (MQ=255)
gATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCcggcg > 2:730836/1‑133 (MQ=255)
gcgcTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATcgccg < 1:87879/89‑1 (MQ=255)
gcgcTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATcgccg > 2:87879/1‑89 (MQ=255)
gcgcTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGc > 2:25812/1‑104 (MQ=255)
gcgcTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGc < 1:25812/104‑1 (MQ=255)
gcgcTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCCGGCGGACTAGTGCGATAAcc > 1:516781/1‑134 (MQ=255)
ctCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCCGGCGGACTAGTGCGATAACCGcac < 1:730836/132‑1 (MQ=255)
aGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTa > 2:360388/1‑73 (MQ=255)
aGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTa < 1:360388/73‑1 (MQ=255)
aGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCCGGCGGACTAGTGCGATAACCGCACAacgca > 1:788356/1‑134 (MQ=255)
aCCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCCGGCGGACTAGTGCGATAACCGCACAACGCACGCAAGaa < 2:516781/134‑1 (MQ=255)
aGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCCGGCGGACTAGTGCGATAACCGCACAACGCACGCAAGAACGGACCGc > 1:166647/1‑134 (MQ=255)
|
AGCGCGAGTTCGTCGAGGCCGAGCGCGCCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTACCCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCCGGCGGACTAGTGCGATAACCGCACAACGCACGCAAGAACGGACCGC > AM260479/2955065‑2955317
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 35 ≤ 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
GTTCGAGCGCGAGTTCGTCGAGGCCGAGCGCGCCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTACCCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCCGGCGGACTAGTGCGATAACCGCACAACGCACGCAAGAACGGACCGCC > AM260479/2955060‑2955318
|
GTTCGAGCGCGAGTTCGTCGAGGCCGAGCGCGCCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGG > GWNJ‑0478:712:GW2002102894th:2:1101:16469:89035/1‑149 (MQ=60)
GAGCGCGAGTTCGTCGAGGCCGAGCGCGCCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGAC < GWNJ‑0478:712:GW2002102894th:2:2203:13081:43925/150‑1 (MQ=60)
gagattagcgagtgtctcgtgggctcggagatgtgtataagagacagGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGC < GWNJ‑0478:712:GW2002102894th:2:1204:4963:86019/103‑1 (MQ=60)
cgtgggctcggagatgtgtataagagacaGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGC < GWNJ‑0478:712:GW2002102894th:2:1107:15773:48910/120‑1 (MQ=60)
gtgtataagagacaGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCCGGCGG < GWNJ‑0478:712:GW2002102894th:2:1103:14417:66711/135‑1 (MQ=60)
GATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCCGGCGGACTAGTGCGATAACCG > GWNJ‑0478:712:GW2002102894th:2:1215:9042:18153/1‑150 (MQ=60)
GGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCCGGCGGACTAGTGCGATAACCGCACAACGCAC > GWNJ‑0478:712:GW2002102894th:2:2112:10852:63126/1‑150 (MQ=60)
GCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCCGGCGGACTAGTGCGATAACCGCACAACGCACGCAAGAAC < GWNJ‑0478:712:GW2002102894th:2:2111:11522:55675/148‑1 (MQ=60)
GCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCCGGCGGACTAGTGCGATAACCGCACAACGCACGCAAGAACGGACCGCC > GWNJ‑0478:712:GW2002102894th:2:1111:12708:93427/1‑150 (MQ=60)
|
GTTCGAGCGCGAGTTCGTCGAGGCCGAGCGCGCCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTACCCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCCGGCGGACTAGTGCGATAACCGCACAACGCACGCAAGAACGGACCGCC > AM260479/2955060‑2955318
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
