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 |
245,288 |
T→G |
L247V (TTG→GTG) |
betA2 → |
choline dehydrogenase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 245,288 | 0 | T | G | 100.0%
| 78.2
/ NA
| 21 | L247V (TTG→GTG) | betA2 | choline dehydrogenase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (15/6); total (15/6) |
TGGCAACAAGCGCGACCGGGCCTGCAATGGCGGCCGCGCGCACCTGCGGGTGCTGACCGATACGCAGGCGCTGCGCATAGTCTTCGAAGGCCGCCATGCGGCCGGGGTGCAGTTGGTGCGCGAGGGCCACCGGCAACTGCTGCGCGCGCGCCGCGACGTGATCGTGTGCGCGGGCACGTTCGGCTCGCCGCAGCTGCTGATGGTGTCGGGCGTCGGCCCCGCCGCGCACTT > AM260479/245176‑245406
|
tGGCAACAAGCGCGACCGGGCCTGCAATGGCGGCCGCGCGCACCTGCGGGTGCTGACCGATACGCAGGCGCTGCGCATAGTCTTCGAAGGCCGCCATGCGGCCGGGGTGCAGGTGGTGCGCGAGGGCCACCgg > 1:814515/1‑133 (MQ=255)
acaaGCGCGACCGGGCCTGCAATGGCGGCCGCGCGCACCTGCGGGTGCTGACCGATACGCAGGCGCTGCGCATAGTCTTCGAAGGCCGCCATGCGGCCGGGGTGCAGGTGGTGCGCGAGGGCCACCGGCAActg > 1:609188/1‑134 (MQ=255)
aCCGGGCCTGCAATGGCGGCCGCGCGCACCTGCGGGTGCTGACCGATACGCAGGCGCTGCGCATAGTCTTCGAAGGCCGCCATGCGGCCGGGGTGCAGGTGGTGCGCGAGGGCCACCGGCAACTGCTgcgcgcg > 2:487089/1‑134 (MQ=255)
aCCGGGCCTGCAATGGCGGCCGCGCGCACCTGCGGGTGCTAACCGATACGCAGGCGCTGCGCATAGTCTTCGAAGGCCGCCATGCGGCCGGTGTGCAGGTGGTGCGCGAGGGCCACCGGCAACTGCTgcgcgcg > 2:752610/1‑134 (MQ=255)
ccGCGCGCACCTGCGGGTGCTGACCGATACGCAGGCGCTGCGCATAGTCTTCGAAGGCCGCCATGCGGCCGGGGTGCAGGTGGTGCGCGAGGGCCACCGGCAACTGCTGCGCGCGCGCCGCGACGTGATCgtgt > 2:609381/1‑134 (MQ=255)
gcgcgcACCTGCGGGTGCTGACCGATACGCAGGCGCTGCGCATAGTCTTCGAAGGCCGCCATGCGGCCGGGGTGCAGGTGGTGCGCGAGGGCCACCGGCAACTGCTGCGCGCGCGCCGCGACGTGATCGTGTgc < 1:361484/134‑1 (MQ=255)
aCCGATACGCAGGCGCTGCGCATAGTCTTCGAAGGCCGCCATGCGGCCGGGGTGCAGGTGGTGCGCGAgg > 1:497480/1‑70 (MQ=255)
aCCGATACGCAGGCGCTGCGCATAGTCTTCGAAGGCCGCCATGCGGCCGGGGTGCAGGTGGTGCGCGAgg < 2:497480/70‑1 (MQ=255)
cgcATAGTCTTCGAAGGCCGCCATGCGGCCGGGGTGCAGGTGGTGCGCGAGGGCCACCGGCAACTGCTGCGCGCGCGCCGCGACGTGATCGTGTGCGCGGGCACGTTCGGCTCGCCGCAGCTGCTGATGGTGTc < 2:609188/134‑1 (MQ=255)
gcATAGTCTTCGAAGGCCGCCATGCGGCCGGGGTGCAGGTGGTGCGCGAGGGCCACCGGCAACTGCTGCGCGCGCGCCGCGACGTGATCGTGTGCGCGGGCACGTTCGGCTCGCCGCAGCTGCTGATGGTGTCg > 1:781344/1‑134 (MQ=255)
gcATAGTCTTCGAAGGCCGCCATGCGGCCGGGGTGCAGGTGGTGCGCGAGGGCCACCGGCAACTGCTGCGCGCGCGCCGCGACGTGATCGTGTGCGCGGGCACGTTCGGCTCGCCGCAGCTGCTGATGGTGTCg > 2:443768/1‑134 (MQ=255)
ttCGAAGGCCGCCATGCGGCCGGGGTGCAGGTGGTGCGCGAGGGCCACCGGCAACTGCTGCGCGCGCGCCGCGACGTGATCGTGTGCGCGGGCACGTTCGGCTCGCCGCAGCTGCTGATGGTGTCGGGCGTCgg > 1:357624/1‑134 (MQ=255)
ttCGAAGGCCGCCATGCGGCCGGGGTGCAGGTGGTGCGCGAGGGCCACCGGCAACTGCTGCGCGCGCGCCGCGACGTGATCGTGTGCGCGGGCACGTTCGGCTCGCCGCAGCTGCTGATGGTGTCGGGCGTCgg > 1:357625/1‑134 (MQ=255)
gccgccATGCGGCCGGGGTGCAGGTGGTGCGCGAGGGCCACCGGCAACTGCTGCGCGCGCGCCGCGACGTGATCGTGTGCGCGGGCACGTTCGGCTCGCCGCAGCTGCTGCTGGTGTCGGGCGTCGGCCccgcc > 1:255068/1‑134 (MQ=255)
gccATGCGGCCGGGGTGCAGGTGGTGCGCGAGGGCCACCGGCAACTGCTGCGCGCGCGCCGCGACGTGATCGTGTGCGCGGGCACGTTCGGCTCGCCGCAGCTGCTGATGGTGTCGGGCGTCGGCCCCGCcgcg > 1:334840/1‑134 (MQ=255)
cATGCGGCCGGGGTGCAGGTGGTGCGCGAGGGCCACCGGCAACTGCTGCGCGCGCGCCGCGACGTGATCGTGTGCGCGGGCACGTTCGGCTcgc < 1:329389/94‑1 (MQ=255)
cATGCGGCCGGGGTGCAGGTGGTGCGCGAGGGCCACCGGCAACTGCTGCGCGCGCGCCGCGACGTGATCGTGTGCGCGGGCACGTTCGGCTcgc > 2:329389/1‑94 (MQ=255)
cATGCGGCCGGGGTGCAGGTGGTGCGCGAGGGCCACCGGCAACTGCTGCGCGCGCGCCGCGACGTGATCGTGTGCGCGGGCACGTTCGGCTCGCCGCAGCTGCTGATGGTGTCGGGCGTCGGCCCCGCCGCGCa > 2:636814/1‑134 (MQ=255)
cGGCCGGGGTGCAGGTGGTGCGCGAGGGCCACCGGCAACTGCTGCGCGCGCGCCGCGACGTGATCGTGTGCGCGGGCACGTTCGGCTCGCCGCAGCTGCTGATGGTGTCGGGCGTCGGCCCCGCCGCGCACtt < 2:334840/133‑1 (MQ=255)
gCAGGTGGTGCGCGAGGGCCACCGGCAACTGCTGCGCGCGCGCCGCGACGTGATCGTGTGCGCGGGCACGTTCGGc < 2:61439/76‑1 (MQ=255)
gCAGGTGGTGCGCGAGGGCCACCGGCAACTGCTGCGCGCGCGCCGCGACGTGATCGTGTGCGCGGGCACGTTCGGc > 1:61439/1‑76 (MQ=255)
|
TGGCAACAAGCGCGACCGGGCCTGCAATGGCGGCCGCGCGCACCTGCGGGTGCTGACCGATACGCAGGCGCTGCGCATAGTCTTCGAAGGCCGCCATGCGGCCGGGGTGCAGTTGGTGCGCGAGGGCCACCGGCAACTGCTGCGCGCGCGCCGCGACGTGATCGTGTGCGCGGGCACGTTCGGCTCGCCGCAGCTGCTGATGGTGTCGGGCGTCGGCCCCGCCGCGCACTT > AM260479/245176‑245406
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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
GCGAGCGCTGGAACGCGGCGCGTGCCTACCTGCACGGTGGCAACAAGCGCGACCGGGCCTGCAATGGCGGCCGCGCGCACCTGCGGGTGCTGACCGATACGCAGGCGCTGCGCATAGTCTTCGAAGGCCGCCATGCGGCCGGGGTGCAGTTGGTGCGCGAGGGCCACCGGCAACTGCTGCGCGCGCGCCGCGACGTGATCGTGTGCGCGGGCACGTTCGGCTCGCCGCAGCTGCTGATGGTGTCGGGCGTCGGCCCCGCCGCGCACTTGCGCGAACATGG > AM260479/245139‑245418
|
GCGAGCGCTGGAACGCGGCGCGTGCCTACCTGCACGGTGGCAACAAGCGCGACCGGGCCTGCAATGGCGGCCGCGCGCACCTGCGGGTGCTGACCGATACGCAGGCGCTGCGCATAGTCTTCGAAGGCCGCCATGCGGCCGGGGTGCAGG < GWNJ‑0478:712:GW2002102894th:2:1110:20424:61783/150‑1 (MQ=60)
TGCCTACCTGCACGGTGGCAACAAGCGCGACCGGGCCTGCAATGGCGGCCGCGCGCACCTGCGGGTGCTGACCGATACGCAGGCGCTGCGCATAGTCTTCGAAGGCCGCCATGCGGCCGGGGTGCAGGTGGTGCGCGAGGGCCACCGGC > GWNJ‑0478:712:GW2002102894th:2:2202:2932:87622/1‑149 (MQ=60)
ACCTGCACGGTGGCAACAAGCGCGACCGGGCCTGCAATGGCGGCCGCGCGCACCTGCGGGTGCTGACCGATACGCAGGCGCTGCGCATAGTCTTCGAAGGCCGCCATGCGGCCGGGGTGCAGGTGGTGCGCGAGGGCCACCGGCAACTGC > GWNJ‑0478:712:GW2002102894th:2:2106:20431:26023/1‑150 (MQ=60)
CGCGCGCACCTGCGGGTGCTGACCGATACGCAGGCGCTGCGCATAGTCTTCGAAGGCCGCCATGCGGCCGGGGTGCAGGTGGTGCGCGAGGGCCACCGGCAACTGCTGCGCGCGCGCCGCGACGTGATCGTGTGCGCGGGCACGTTCGGC < GWNJ‑0478:712:GW2002102894th:2:1208:12828:10917/150‑1 (MQ=60)
CACCTGCGGGTGCTGACCGATACGCAGGCGCTGCGCATAGTCTTCGAAGGCCGCCATGCGGCCGGGGTGCAGGTGGTGCGCGAGGGCCACCGGCAACTGCctgtctcttatacacatctccgagcccacgagacggagctacatctcgt > GWNJ‑0478:712:GW2002102894th:2:1214:15779:80203/1‑100 (MQ=60)
ggctcggagatgtgtataagagacagGTCTTCGAAGGCCGCCATGCGGCCGGGGTGCAGGTGGTGCGCGAGGGCCACCGGCAACTGCTGCGCGCGCGCCGCGACGTGATCGTGTGCGCGGGCACGTTCGGCTCGCCGCAGCTGCTGATGG < GWNJ‑0478:712:GW2002102894th:2:1207:19072:9285/124‑1 (MQ=60)
ATACGCAGGCGCTGCGCATAGTCTTCGAAGGCCGCCATGCGGCCGGGGTGCAGGTGGTGCGCGAGGGCCACCGGCAACTGCTGCGCGCGCGCCGCGACGTGATCGTGTGCGCGGGCACGTTCGGCTCGCCGCAGCTGCTGATGGTGTCGG > GWNJ‑0478:712:GW2002102894th:2:2201:12559:59274/1‑150 (MQ=60)
GTGCTGCGCATAGTCTTCGAAGGCCGCCATGCGGCCGGGGTGCAGGTGGTGCGCGAGGGCCACCGGCAACTGCTGCGCGCGCGCCGCGACGTGATCGTGTGCGCGGGCACGTTCGGCTCGCCGCAGCTGCTGATGGTGTCGGGCGTCGGC > GWNJ‑0478:712:GW2002102894th:2:1206:12868:86351/1‑150 (MQ=60)
GCGCTGCGCATAGTCTTCGAAGGCCGCCATGCGGCCGGGGTGCAGGTGGTGCGCGAGGGCCACCGGCAACTGCTGCGCGCGCGCCGCGACGTGATCGTGTGCGCGGGCACGTTCGGCTCGCCGCAGCTGCTGATGGTGTCGGGCGTCGGC > GWNJ‑0478:712:GW2002102894th:2:1206:12887:86354/1‑150 (MQ=60)
GCATAGTCTTCGAAGGCCGCCATGCGGCCGGGGTGCAGGTGGTGCGCGAGGGCCACCGGCAACTGCTGCGCGCGCGCCGCGACGTGATCGTGTGCGCGGGCACGTTCGGCTCGCCGCCGCTGCTGCTGGTGTCGGGCGTCGGCCCCGCCG > GWNJ‑0478:712:GW2002102894th:2:1116:13181:98674/1‑150 (MQ=60)
TAGTCTTCGAAGGCCGCCATGCGGCCGGGGTGCAGGTGGTGCGCGAGGGCCACCGGCAACTGCTGCGCGCGCGCCGCGACGTGATCGTGTGCGCGGGCACGTTCGGCTCGCCGCAGCTGCTGATGGTGTCGGGCGTCGGCCCCGCCGCGC > GWNJ‑0478:712:GW2002102894th:2:1207:19654:44882/1‑150 (MQ=60)
CCATGCGGCCGGGGTGCAGGTGGTGCGCGAGGGCCACCGGCAACTGCTGCGCGCGCGCCGCGACGTGATCGTGTGCGCGGGCACGTTCGGCTCGCCGCAGCTGCTGctgtctcttatacacatctccgagcccacgagacggagctacat > GWNJ‑0478:712:GW2002102894th:2:1104:14918:25005/1‑106 (MQ=60)
|
GCGAGCGCTGGAACGCGGCGCGTGCCTACCTGCACGGTGGCAACAAGCGCGACCGGGCCTGCAATGGCGGCCGCGCGCACCTGCGGGTGCTGACCGATACGCAGGCGCTGCGCATAGTCTTCGAAGGCCGCCATGCGGCCGGGGTGCAGTTGGTGCGCGAGGGCCACCGGCAACTGCTGCGCGCGCGCCGCGACGTGATCGTGTGCGCGGGCACGTTCGGCTCGCCGCAGCTGCTGATGGTGTCGGGCGTCGGCCCCGCCGCGCACTTGCGCGAACATGG > AM260479/245139‑245418
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
