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
|
152 |
24.9 |
2083062 |
91.6% |
1908084 |
109.2 |
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%
| 39.7
/ NA
| 10 | 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 . (4/6); total (4/6) |
CGTCGAGGCCGAGCGCGCCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTACCCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCCGGCGGACTAGTGCGATAAC > AM260479/2955075‑2955290
|
cgtcgAGGCCGAGCGCGCCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATg > 2:434498/1‑133 (MQ=255)
cgtcgAGGCCGAGCGCGCCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATg > 2:613914/1‑133 (MQ=255)
aGCGCGCCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATg < 1:185172/134‑1 (MQ=255)
ccgccTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCAt < 1:633123/134‑1 (MQ=255)
cgccTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCAtt < 1:434498/134‑1 (MQ=255)
cGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCcgcg > 2:401476/1‑134 (MQ=255)
gAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGaa < 1:533720/96‑1 (MQ=255)
gAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGaa > 2:533720/1‑96 (MQ=255)
acgaGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTAccag > 1:220650/1‑75 (MQ=255)
acgaGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTAccag < 2:220650/77‑3 (MQ=255)
gcTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTAcc > 1:79529/1‑44 (MQ=255)
gcTGGCGCGGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTAcc < 2:79529/44‑1 (MQ=255)
gcgcTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCCGGCGGACTAGTGCGATAAc < 1:186936/133‑1 (MQ=255)
gcgcTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCAGCGCCATGGCTTACGCCGGCTAGTCCGGCGGACTAGTGCGATaa < 1:401476/132‑1 (MQ=255)
|
CGTCGAGGCCGAGCGCGCCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTACCCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCCGGCGGACTAGTGCGATAAC > AM260479/2955075‑2955290
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ 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
TCGTCGAGGCCGAGCGCGCCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTACCCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCCGGCGGACTAGTGCGATAACCGCACAACGCACGCAAGAACGGACCGCCCCTGGCGGTCCGTTTTC > AM260479/2955074‑2955335
|
agattatattgtcgttttttatttttttttttttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacaGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAG < GWNJ‑0478:712:GW2002102894th:2:1114:7347:21997/42‑1 (MQ=60)
cggagatgtgtataagagacagATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCAT < GWNJ‑0478:712:GW2002102894th:2:2101:10332:76013/126‑1 (MQ=60)
gtgtataagagacagGCCTACATGTAAACCTTCATCGAGGCCGACGGGATCGCCGTACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGTGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTC < GWNJ‑0478:712:GW2002102894th:2:1203:5772:100427/135‑1 (MQ=60)
GAGCGCGCCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAG < GWNJ‑0478:712:GW2002102894th:2:1113:17160:88635/150‑1 (MQ=60)
GCCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTAT < GWNJ‑0478:712:GW2002102894th:2:2108:16418:58877/150‑1 (MQ=60)
CCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATC < GWNJ‑0478:712:GW2002102894th:2:1213:10608:22583/150‑1 (MQ=60)
CCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACctgtctcttatacacatctccgagcccacgagacggagctac > GWNJ‑0478:712:GW2002102894th:2:1115:7237:85925/1‑107 (MQ=60)
CATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgtaaaaaaaa > GWNJ‑0478:712:GW2002102894th:2:1107:20395:48046/1‑74 (MQ=60)
gtagctccgtctcgtgggctcggagatgtgtataagagacaGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCCGGCGGACTAGTGCGATAAC < GWNJ‑0478:712:GW2002102894th:2:2211:7279:7259/109‑1 (MQ=60)
GGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCCGGCGGACTAGTGCGATAACCGCACAACGCACGCA < GWNJ‑0478:712:GW2002102894th:2:1113:14309:98586/149‑1 (MQ=60)
GGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCAGCGCCATGGCTTACGCCGGCTAGTCCGGCGGACTAGTGCGATAACCGCACAACGCACGC < GWNJ‑0478:712:GW2002102894th:2:1211:19926:36126/148‑1 (MQ=60)
AGTCGGGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCCGGCGGACTAGTGCGATAACCGCACAACGCACGCActgtctcttatacacatctccgagccc > GWNJ‑0478:712:GW2002102894th:2:2203:9931:96820/1‑122 (MQ=60)
GGCCGTA‑CCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCCGGCGGACTAGTGCGATAACCGCACAACGCACGCActgtctcttatacacatctccgagcccacg > GWNJ‑0478:712:GW2002102894th:2:1208:7721:20607/1‑117 (MQ=60)
|
TCGTCGAGGCCGAGCGCGCCGCCTACATGGAAACCTGCATCGAGGACGACGAGATCGCCGAACGCATGGATGCCGGCCGGCTGGCGCTGCTCAAGCGCGGCACCAGCGAAGTCGGGCCGTACCCAGTCGCCGATGGAAGACGGCATGCAGCATTTCCATGAGTGGTATCGCCGCGCCATGGCTTACGCCGGCTAGTCCGGCGGACTAGTGCGATAACCGCACAACGCACGCAAGAACGGACCGCCCCTGGCGGTCCGTTTTC > AM260479/2955074‑2955335
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
