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 |
AM260480 |
963,917 |
Δ1 bp |
intergenic (+84/‑3) |
h16_B0849 → / → h16_B0850 |
Acyl‑CoA dehydrogenase/Acyl‑CoA dehydrogenase, short‑chain specific |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260480 | 963,914 | 0 | A | . | 100.0%
| 113.7
/ NA
| 26 | intergenic (+81/‑6) | h16_B0849/h16_B0850 | Acyl‑CoA dehydrogenase/Acyl‑CoA dehydrogenase, short‑chain specific |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base . (13/13); total (13/13) |
CTCCAGCGAGATCCAGCACGAACTGCTGGCCAAGCAGGTGCTGGGCCTGTAGTGGCTCCAATCGTGCCCGCAACCCAGGACAAGGAACTGAACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGGAAAAGCGTGCGGCGCTATGTCGAACGCGGCTACGGCTTCGAGCAGCGCCGCGCGGCGCTGGCCGAGCCCGATGGCTTCTCGCGCAAGCACTGGCAGGCGTTTGCCGAAA > AM260480/963782‑964022
|
cTCCAGCGAGATCCAGCACGAACTGCTGGCCAAGCAGGTGCTGGGCCTGTAGTGGCTCCAATCGTGCCCGCAACCCAGGACAAGGAACTGAACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGGa > 1:88882/1‑133 (MQ=255)
gctgGCCAAGCAGGTGCTGGGCCTGTAGTGGCTCCAATCGTGCCCGCAACCCAGGACAAGGAACTGAACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGTCGAAcgc > 2:326542/1‑134 (MQ=255)
ctgGCCAAGCAGGTGCTGGGCCTGTAGTGGCTCCAATCGTGCCCGCAACCCAGGACAAGGAACTGAACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGTCGAAcgcg > 1:348471/1‑134 (MQ=255)
tcgTGCTGGGCCTGTAGTGGCTCCAATCGTGCCCGCAACCCAGGACAAGGAACTGAACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGt < 2:705725/114‑1 (MQ=255)
tcgTGCTGGGCCTGTAGTGGCTCCAATCGTGCCCGCAACCCAGGACAAGGAACTGAACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGt > 1:705725/3‑116 (MQ=255)
aGGTGCTGGGCCTGTAGTGGCTCCAATCGTGCCCGCAACCCAGGACAAGGAACTGAACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGTCGAACGCGGCTACGGCtt < 1:1008814/134‑1 (MQ=255)
cTGGGCCTGTAGTGGCTCCAATCGTGCCCGCAACCCAGGACAAGGAACTGAACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGTCGAACGCGGCTACGGCTTCGagc < 2:88882/134‑1 (MQ=255)
ccAATCGTGCCCGCAACCCAGGACAAGGAACTGAACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGTCGAACGCGGCTACGGCTTCGAGCAgcgc < 2:88571/122‑1 (MQ=255)
ccAATCGTGCCCGCAACCCAGGACAAGGAACTGAACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGTCGAACGCGGCTACGGCTTCGAGCAgcgc > 1:88571/1‑122 (MQ=255)
cAATCGTGCCCGCAACCCAGGACAAGGAACTGAACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGGaaagcg < 2:662831/80‑4 (MQ=255)
cAATCGTGCCCGCAACCCAGGACAAGGAACTGAACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGGaaagcg > 1:662831/1‑77 (MQ=255)
cAATCGTGCCCGCAACCCAGGACAAGGAACTGAACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGGaaag > 1:884024/1‑77 (MQ=255)
cAATCGTGCCCGCAACCCAGGACAAGGAACTGAACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGGaaag < 2:884024/78‑2 (MQ=255)
gTGCCCGCAACCCAGGACAAGGAACTGAACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGTCGAACGCGGCTACGGCTTCGAGCAGCGCCGCGCGGCGCTGGCCGAg < 2:57943/134‑1 (MQ=255)
cGCAACCCAGGACAAGGAACTGAACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTgc < 1:192805/73‑1 (MQ=255)
cGCAACCCAGGACAAGGAACTGAACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTgc > 2:192805/1‑73 (MQ=255)
cAAGGAACTGAACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGTCGAACGCGGCTACGGCTTCGAGCAGCGCCGCGCGGCGCTGGCCGAGCCCGATGGc > 2:170721/1‑126 (MQ=255)
cAAGGAACTGAACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGTCGAACGCGGCTACGGCTTCGAGCAGCGCCGCGCGGCGCTGGCCGAGCCCGATGGc < 1:170721/126‑1 (MQ=255)
cacaTGAGCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGTCGAACGCGGCTACGGCTTCGAGCAGCGCcgcgc < 1:383304/92‑1 (MQ=255)
cacaTGAGCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGTCGAACGCGGCTACGGCTTCGAGCAGCGCcgcgc > 2:383304/1‑92 (MQ=255)
cacaTGAGCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGTCGAACGCGGCTACGGCTTCGAGCAGCGCCGCGCGGCGCTGGCCGAGCCCGATGGc < 1:905424/114‑1 (MQ=255)
cacaTGAGCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGTCGAACGCGGCTACGGCTTCGAGCAGCGCCGCGCGGCGCTGGCCGAGCCCGATGGc > 2:905424/1‑114 (MQ=255)
cacaTGAGCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGTCGAACGCGGCTACGGCTTCGAGCAGCGCCGCGCGGCGCTGGCCGAGCCCGATGGCTTCTCGCGCAAGCACTGGCa < 2:348471/134‑1 (MQ=255)
gCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTgc > 2:512947/1‑42 (MQ=37)
gCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTgc < 1:512947/42‑1 (MQ=37)
gCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGTCGAACGCGGCTACGGCTTCGAGCAGCGCCGCGCGgcgc > 2:945294/1‑90 (MQ=255)
gCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGTCGAACGCGGCTACGGCTTCGAGCAGCGCCGCGCGgcgc < 1:945294/90‑1 (MQ=255)
aaCGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGTCGAACGCGGCTACGGCTTCGAGCAGCGCCGCGCGGCGCTGGCCGAGCCCGATGGCTTCTCGCGCAAGCACTGGCAGGCGTTTGCCGaaa > 1:754706/1‑134 (MQ=255)
aaCGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGTCGAACGCGGCTACGGCTTCGAGCAGCGCCGCGCGGCGCTGGCCGAGCCCGATGGCTTCTCGCGCAAGCACTGGCAGGCGTTTGCCGaaa > 1:720548/1‑134 (MQ=255)
ggACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGTCGAACGCGGCTAc < 2:5826/55‑1 (MQ=255)
ggACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGTCGAACGCGGCTAc > 1:5826/1‑55 (MQ=255)
|
CTCCAGCGAGATCCAGCACGAACTGCTGGCCAAGCAGGTGCTGGGCCTGTAGTGGCTCCAATCGTGCCCGCAACCCAGGACAAGGAACTGAACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGGAAAAGCGTGCGGCGCTATGTCGAACGCGGCTACGGCTTCGAGCAGCGCCGCGCGGCGCTGGCCGAGCCCGATGGCTTCTCGCGCAAGCACTGGCAGGCGTTTGCCGAAA > AM260480/963782‑964022
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 36 ≤ 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
ATTGCCGGCGGCTCCAGCGAGATCCAGCACGAACTGCTGGCCAAGCAGGTGCTGGGCCTGTAGTGGCTCCAATCGTGCCCGCAACCCAGGACAAGGAACTGAACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGGAAAAGCGTGCGGCGCTATGTCGAACGCGGCTACGGCTTCGAGCAGCGCCGCGCGGCGCTGGCCGAGCCCGATGGCTTCTCGCGCAAGCACTGGCAGGCGTTTGCCGAAATGGGCTGGCTGGCCGTGGGGCTGCCCGAAGCCTGCGG > AM260480/963771‑964059
|
tttttttttttatttttttatttttttttttttttttttttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagCCAACGGACGATCGCCGCATGCTGCAGGAAAG < GWNJ‑0478:712:GW2002102894th:2:2107:17512:86471/32‑1 (MQ=60)
gagctgtagctccgtctcgtgggctcggagatgtgtataagagacagGGCTCCAATCGTGCCCGCAACCCAGGACAAGGAACTGAACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGTCGAAC < GWNJ‑0478:712:GW2002102894th:2:1112:2841:33148/103‑1 (MQ=60)
tttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacAGGAACTGAACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGTCGAAC < GWNJ‑0478:712:GW2002102894th:2:1216:8091:37890/74‑1 (MQ=60)
ATCCAGCACGAACTGCTGGCCAAGCAGGTGCTGGGCCTGTAGTGGCTCCAATCGTGCCCGCAACCCAGGACAAGGAACTGAACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGTCGAACGCGG > GWNJ‑0478:712:GW2002102894th:2:1206:3564:14998/1‑150 (MQ=60)
tgcttggccagcagttcGTGCTGGGCCTGTAGTGGCTCCAATCGTGCCCGCAACCCAGGACAAGGAACTGAACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGTCGAACGCGGCTACGGCTgt > GWNJ‑0478:712:GW2002102894th:2:2113:2008:89733/18‑148 (MQ=60)
CAGGTGCTGGGCCTGTAGTGGCTCCAATCGTGCCCGCAACCCAGGACAAGGAACTGAACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGTCGAACGCGGCTACGGCTTCGAGCAGCGCCGCAC < GWNJ‑0478:712:GW2002102894th:2:2215:13787:26761/150‑1 (MQ=60)
GGGCCTGTAGTGGCTCCAATCGTGCCCGCAACCCAGGACAAGGAACTGAACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGTCGAACGCGGCTACGGCTTCGAGCAGCGCCGCGCGGCGCTGC > GWNJ‑0478:712:GW2002102894th:2:1106:20090:5992/1‑150 (MQ=60)
GGCCTGTAGTGGCTCCAATCGTGCCCGCAACCCAGGACAAGGAACTGAACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGTCtgtctcttatacacatctccgagcccacgagacggagctac > GWNJ‑0478:712:GW2002102894th:2:2207:15888:7974/1‑109 (MQ=60)
GGCCTGTAGTGGCTCCAATCGTGCCCGCAACCCAGGACAAGGAACTGAACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGTCGctgtctcttatacacatctccgagcccacgagacggagct > GWNJ‑0478:712:GW2002102894th:2:2111:13866:41877/1‑110 (MQ=60)
gggctcggagatgtgtataagagacagGGACAAGGAACTGAACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGTCGAACGCGGCTACGGCTTCGAGCAGCGCCGCGCGGCGCTGGCCGAGCC < GWNJ‑0478:712:GW2002102894th:2:1209:9934:31458/122‑1 (MQ=60)
cgtgggctcggagatgtgtataagagacAGGAACTGAACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGTCGAACGCGGCTACGGCTTCGAGCAGCGCCGCGCGGCGCTGGCCGAGCCCGATG < GWNJ‑0478:712:GW2002102894th:2:2210:3723:76558/122‑1 (MQ=60)
agacagGGACAAGGAACTGAACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGTCGAACGCGGCTACGGCTTCGAGCAGCGCCGCGCGGCGCTGGCCGAGCCCGATGGCTTCTCGCGCAAGCAC < GWNJ‑0478:712:GW2002102894th:2:2208:9309:43301/144‑1 (MQ=60)
AACCCAGGACAAGGAACTGAACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGTCGAACGCGGCTACGGCTTCGAGCAGCGCCGCGCGGCGCTGGCCGAGCCCGATGGCTTCTCGCGCAAGCAC < GWNJ‑0478:712:GW2002102894th:2:1113:12418:7683/150‑1 (MQ=60)
ACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGTCGAACGCGGCTACGGCTTCGAGCAGCGCCGCGCGGCGCTGGCCGAGCCCGATGGCTTCTCGCGCAAGCACTGGCAGGCGTTTGCCGAAAT > GWNJ‑0478:712:GW2002102894th:2:2112:19435:75779/1‑150 (MQ=60)
ACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGTCGAACGCGGCTACGGCTTCGAGCAGCGCCGCGCGGCGCTGGCCGAGCCCGATGGCTTCTCGCGCAAGCACTGGCAGGCGTTTGCCGAAAT > GWNJ‑0478:712:GW2002102894th:2:2114:12209:64822/1‑150 (MQ=60)
ACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCT > GWNJ‑0478:712:GW2002102894th:2:1214:17174:98723/1‑56 (MQ=60)
CATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGG‑AAAGCGTGCGGCGCTATGTCGAACGCGGCTACGGCTTCGAGCAGCGCCtgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgctt > GWNJ‑0478:712:GW2002102894th:2:1101:20222:44497/1‑86 (MQ=60)
GCAGG‑AAAGCGTGCGGCGCTATGTCGAACGCGGCTACGGCTTCGAGCAGCGCCGCGCGGCGCTGGCCGAGCCCGATGGCTTCTCGCGCAAGCACTGGCAGGCGTTTGCCGAAATGGGCTGGCTGGCCGTGGGGCTGCCCGAAGCCTGCGG > GWNJ‑0478:712:GW2002102894th:2:1104:14868:100940/1‑150 (MQ=60)
|
ATTGCCGGCGGCTCCAGCGAGATCCAGCACGAACTGCTGGCCAAGCAGGTGCTGGGCCTGTAGTGGCTCCAATCGTGCCCGCAACCCAGGACAAGGAACTGAACACATGAGCGATCCAACGGACGATCGCCGCATGCTGCAGGAAAAGCGTGCGGCGCTATGTCGAACGCGGCTACGGCTTCGAGCAGCGCCGCGCGGCGCTGGCCGAGCCCGATGGCTTCTCGCGCAAGCACTGGCAGGCGTTTGCCGAAATGGGCTGGCTGGCCGTGGGGCTGCCCGAAGCCTGCGG > AM260480/963771‑964059
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
