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 |
3,247,992 |
Δ1 bp |
coding (756/813 nt) |
h16_A3001 → |
transcriptional regulator, LysR‑family |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 3,247,991 | 0 | C | . | 100.0%
| 59.6
/ NA
| 16 | coding (755/813 nt) | h16_A3001 | transcriptional regulator, LysR‑family |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base . (10/6); total (10/6) |
CTGCGCCACCTGGAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGATTCGTCGCCGGCGTCGCCTATGATGCCCGAGCCGCGACCCGCAACCTTGCCCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAACCGTGACGCACCTGGCCGTC‑AGCAGGGTGCCTACCTGCGCAGCTTTGTGTACACCTTCATCGAGCTG > AM260479/3247873‑3248110
|
cTGCGCCACCTGGAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACCtgcg > 2:778139/1‑131 (MQ=255)
cACCTGGAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCAt > 2:81929/1‑134 (MQ=255)
ggACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTcggccggc > 2:1048414/1‑133 (MQ=255)
gTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGtt < 1:675195/134‑1 (MQ=255)
gAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGgca < 1:81929/133‑1 (MQ=255)
aCGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACg > 2:603967/1‑134 (MQ=255)
cgGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCAc < 1:603967/134‑1 (MQ=255)
gTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGc < 1:1048414/134‑1 (MQ=255)
aGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTc‑aag > 1:933379/1‑132 (MQ=255)
tacgtGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAggg > 1:764413/1‑134 (MQ=255)
tacgtGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAggg > 2:898450/1‑134 (MQ=255)
tcgtcgCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTTGTCTACAcc > 1:171229/1‑134 (MQ=255)
tcgtcgCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTTGTCTACAcc > 1:32789/1‑134 (MQ=255)
tCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTTGTCTACACCTTCATCGAGCTg < 2:933379/134‑1 (MQ=255)
gccGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTcggccggc < 1:451203/38‑1 (MQ=0)
gccGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTcggccggc > 2:451203/2‑39 (MQ=2)
|
CTGCGCCACCTGGAGCCGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGATTCGTCGCCGGCGTCGCCTATGATGCCCGAGCCGCGACCCGCAACCTTGCCCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAACCGTGACGCACCTGGCCGTC‑AGCAGGGTGCCTACCTGCGCAGCTTTGTGTACACCTTCATCGAGCTG > AM260479/3247873‑3248110
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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
CGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGATTCGTCGCCGGCGTCGCCTATGATGCCCGAGCCGCGACCCGCAACCTTGCCCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAACCGTGACGCACCTGGCCGTC‑AGCAGGGTGCCTACCTGCGCAGCTTTGTGTACACCTTCATCGAGCTGTTCTCGCCGACGCTCAACCG > AM260479/3247889‑3248130
|
ttttttttttttttcaagcagaagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacagGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGC < GWNJ‑0478:712:GW2002102894th:2:1211:14908:87341/69‑1 (MQ=33)
CGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGAC < GWNJ‑0478:712:GW2002102894th:2:2106:15649:40341/150‑1 (MQ=60)
GGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACC < GWNJ‑0478:712:GW2002102894th:2:1107:4475:14537/149‑1 (MQ=60)
ACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTC‑Aagc > GWNJ‑0478:712:GW2002102894th:2:2205:6679:92045/1‑147 (MQ=60)
GCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAG < GWNJ‑0478:712:GW2002102894th:2:2103:13143:94250/150‑1 (MQ=60)
GACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGT > GWNJ‑0478:712:GW2002102894th:2:2113:1970:35871/1‑150 (MQ=60)
CGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGC < GWNJ‑0478:712:GW2002102894th:2:2212:15077:35016/150‑1 (MQ=60)
GGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTTGTCTACACCT > GWNJ‑0478:712:GW2002102894th:2:1105:19728:10574/1‑150 (MQ=60)
GGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTTGTCTACACCT > GWNJ‑0478:712:GW2002102894th:2:1110:4049:19519/1‑150 (MQ=60)
CCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTTGTCTACACCTTCATCGAGCTGTTCTCGCCGACGCTCAACC > GWNJ‑0478:712:GW2002102894th:2:1211:13093:43027/1‑150 (MQ=60)
CTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatg > GWNJ‑0478:712:GW2002102894th:2:2106:3937:70733/1‑98 (MQ=57)
CTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTTGTCTACACCTTCATCGAGCctgtctcttatacacatctccg > GWNJ‑0478:712:GW2002102894th:2:1208:2588:27774/1‑128 (MQ=60)
|
CGGACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGATTCGTCGCCGGCGTCGCCTATGATGCCCGAGCCGCGACCCGCAACCTTGCCCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAACCGTGACGCACCTGGCCGTC‑AGCAGGGTGCCTACCTGCGCAGCTTTGTGTACACCTTCATCGAGCTGTTCTCGCCGACGCTCAACCG > AM260479/3247889‑3248130
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
