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 |
3,248,045 |
Δ1 bp |
coding (809/813 nt) |
h16_A3001 → |
transcriptional regulator, LysR‑family |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 3,248,044 | 0 | C | . | 100.0%
| 115.9
/ NA
| 26 | coding (808/813 nt) | h16_A3001 | transcriptional regulator, LysR‑family |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base . (11/15); total (11/15) |
CCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGATTCGTCGCCGGCGTCGCCTATGATGCCCGAGCCGCGACCCGCAACCTTGCCCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAACCGTGACGCACCTGGCCGTC‑AGCAGGGTGCCTACCTGCGCAGCTTTGTGTACACCTTCATCGAGCTGTTCTCGCCGACGCTCAACCGCAAGCTGGTTGAGCAGGCCATGTCCGGCGAACACGAAGCCT > AM260479/3247907‑3248171
|
ccATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAAc > 1:842525/1‑134 (MQ=255)
tCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAAcgt > 1:360318/1‑131 (MQ=255)
gACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGAc > 1:1025731/1‑134 (MQ=255)
cgGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCAc < 1:977130/134‑1 (MQ=255)
ggAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGcc > 2:489611/1‑133 (MQ=255)
gagaTCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTc > 1:247771/1‑120 (MQ=255)
gagaTCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTc < 2:247771/120‑1 (MQ=255)
gagaTCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTa > 1:962653/1‑134 (MQ=255)
cTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTc‑aagcag < 2:674110/117‑6 (MQ=255)
cTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTc‑aagcag > 1:674110/1‑112 (MQ=255)
cTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTAcc < 1:292652/127‑1 (MQ=255)
cTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTAcc > 2:292652/1‑127 (MQ=255)
cTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAg > 2:142426/1‑134 (MQ=255)
ggcatcgtcgCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTtgtct < 2:1025731/129‑3 (MQ=255)
ggcatcgtcgCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTtgtct < 1:908486/129‑3 (MQ=255)
cgCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTTGTCTACACCTTCa > 1:1018506/1‑134 (MQ=255)
gCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTTGTCTACACCTTCAt < 1:142426/134‑1 (MQ=255)
ccTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTTGTCTACACCTTCATCGAGCTGTtc < 2:360318/134‑1 (MQ=255)
tgccGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTTGTCTACACCTTCATCGAGCTGTTCTCGCCGa < 1:1008078/132‑1 (MQ=255)
cgcgA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTTGTCTACACCTTCATCGAGCTGTTCTCGCCGACGCTCaa > 1:755216/1‑134 (MQ=255)
ctgcgcGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTTGTCTACACCTTCATCGAGCTGTTCTCGCCGACGCTCAACCGCAAGCTGGt < 1:324813/129‑1 (MQ=255)
gCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTTGTCTACACCTTCATCGAGCTGTTCTCGCCGACGCTCAACCGCAAGCTGGTTGAGCAg > 2:416669/1‑134 (MQ=255)
gCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CATGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTTGTCTACACCTTCATCGAGCTGTTCTCGCCGACGCTCAAcc < 1:464977/117‑1 (MQ=255)
gCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CATGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTTGTCTACACCTTCATCGAGCTGTTCTCGCCGACGCTCAAcc > 2:464977/1‑117 (MQ=255)
ggccggccACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTTGTCTACACCTTCATCGAGCTGTTCTCGCCGACGCTCAACCGCAAGCTGGTTGAGCAGGCCATGt < 2:1018506/134‑1 (MQ=255)
gcagcaA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTTGTCTACACCTTCATCGAGCTGTTCTCGCCGACGCTCAACCGCAAGCTGGTTGAGCAGGCCATGTCCGGCGAACACGAAGcc < 1:416669/134‑1 (MQ=255)
gcagcaA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTTGTCTACACCTTCATCGAGCTGTTCTCGCCGACGCTCAACCGCAAGCTGGTTGAGCAGGCCATGTCCGGCGAACACGAAGcc < 2:755216/134‑1 (MQ=255)
cagcaA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTTGTCTACACCTTCATCGAGCTGTTCTCGCCGACGCTCAACCGCAAGCTGGTTGAGCAGGCCATGTCCGGCGAACACGAAGCCt < 2:578095/134‑1 (MQ=255)
|
CCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGATTCGTCGCCGGCGTCGCCTATGATGCCCGAGCCGCGACCCGCAACCTTGCCCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAACCGTGACGCACCTGGCCGTC‑AGCAGGGTGCCTACCTGCGCAGCTTTGTGTACACCTTCATCGAGCTGTTCTCGCCGACGCTCAACCGCAAGCTGGTTGAGCAGGCCATGTCCGGCGAACACGAAGCCT > AM260479/3247907‑3248171
|
| 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
ACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGATTCGTCGCCGGCGTCGCCTATGATGCCCGAGCCGCGACCCGCAACCTTGCCCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAACCGTGACGCACCTGGCCGTC‑AGCAGGGTGCCTACCTGCGCAGCTTTGTGTACACCTTCATCGAGCTGTTCTCGCCGACGCTCAACCGCAAGCTGGTTGAGCAGGCCATGTCCGGCGAACACGAAGCCTACGAACTCTGAGGA > AM260479/3247892‑3248185
|
ACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAACG > GWNJ‑0478:712:GW2002102894th:2:2205:14959:71318/1‑150 (MQ=60)
TCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTG > GWNJ‑0478:712:GW2002102894th:2:1208:10401:3672/1‑149 (MQ=60)
GTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACG > GWNJ‑0478:712:GW2002102894th:2:2216:16875:51475/1‑150 (MQ=60)
GCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGC < GWNJ‑0478:712:GW2002102894th:2:1211:10369:7968/149‑1 (MQ=60)
ttttttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagcctatgatgccgagcgcgaccgcaacctgcgCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGA < GWNJ‑0478:712:GW2002102894th:2:2204:7201:51077/38‑1 (MQ=60)
GCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAG < GWNJ‑0478:712:GW2002102894th:2:2213:7691:84675/150‑1 (MQ=60)
ATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTAC > GWNJ‑0478:712:GW2002102894th:2:1116:16610:50997/1‑150 (MQ=60)
ATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTAC > GWNJ‑0478:712:GW2002102894th:2:2213:17483:5408/1‑150 (MQ=60)
TACGTGGAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCctg > GWNJ‑0478:712:GW2002102894th:2:2110:11091:29136/1‑147 (MQ=60)
GAGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTTGTC > GWNJ‑0478:712:GW2002102894th:2:1216:14342:70192/1‑150 (MQ=60)
AGATCGGGCTGGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTTGTCT < GWNJ‑0478:712:GW2002102894th:2:1202:4144:65985/150‑1 (MQ=60)
GGGCGTGGGCATCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTTGTCTACACCTTCAT > GWNJ‑0478:712:GW2002102894th:2:2216:13111:13356/1‑150 (MQ=60)
gggcaTCGTCGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTTGTCTACACCTTCATCGAGC < GWNJ‑0478:712:GW2002102894th:2:2208:2088:86983/144‑1 (MQ=60)
CGCCGGCGTCGCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTTGTCTACACCTTCATCGAGCTGTTCTCGCC < GWNJ‑0478:712:GW2002102894th:2:1111:8248:40711/150‑1 (MQ=60)
GCCTATGATG‑CCGAG‑CGCGA‑CCGCAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTTGTCTACACCTTCATCGAGCTGTTCTCGCCGACGCTCAAC > GWNJ‑0478:712:GW2002102894th:2:2114:15651:95999/1‑150 (MQ=60)
atgccgagcgcgaccgcaacctgcgCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTTGTCTACACCTTCATCGAGCTGTTCTCGCCGACGCTCAACCGCAAGC < GWNJ‑0478:712:GW2002102894th:2:2215:17778:54199/125‑1 (MQ=60)
cagaccgcaacctgcgCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CATGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTTGTCTACACCTTCATCGAGCTGTTCTCGCCGACGCTCAACCGCAAGCTGGTTGAGC < GWNJ‑0478:712:GW2002102894th:2:1215:19457:9207/134‑1 (MQ=60)
CAACC‑TGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaa > GWNJ‑0478:712:GW2002102894th:2:1108:3591:25519/1‑80 (MQ=60)
CCTGCGCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTTGTCTACACCTTCATCGAGCTGTTCTCGCCGACGCTCAACCGCAAGCTGGTTGAGCAGGCCATGTC < GWNJ‑0478:712:GW2002102894th:2:1204:12364:77493/150‑1 (MQ=60)
GTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTTGTCTACACCTTCATCGAGCTGTTCTCGCCGACGCTCAACCGCAAGCTGGTTGAGCAGGCCATGTCCtgtctcttatacacatctccgagccc > GWNJ‑0478:712:GW2002102894th:2:2208:20364:57705/1‑124 (MQ=60)
GTTTGGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTTGTCTACACCTTCATCGAGCTGTTCTCGCCGACGCTCAACCGCAAGCTGGTTGAGCAGGCCATGTCCGGCGAACACGAAGCCTACGAACTCTG > GWNJ‑0478:712:GW2002102894th:2:1111:19157:35310/1‑150 (MQ=60)
GGCAGCAA‑CGTGACGCACCTGGCCGTCAAGCAGGGTGCCTACCTGCGCAGCTTTGTCTACACCTTCATCGAGCTGTTCTCGCCGACGCTCAACCGCAAGCTGGTTGAGCAGGCCATGTCCGGCGAACACGAAGCCTACGAACTCTGAGGA < GWNJ‑0478:712:GW2002102894th:2:1210:12286:37225/150‑1 (MQ=60)
|
ACATCGTGCTGGAGGCCATCGACGCGGACGTGATCAAGACGTACGTGGAGATCGGGCTGGGCGTGGGATTCGTCGCCGGCGTCGCCTATGATGCCCGAGCCGCGACCCGCAACCTTGCCCGGCATCTCGGCCGGCCACCTGTTTGGCAGCAACCGTGACGCACCTGGCCGTC‑AGCAGGGTGCCTACCTGCGCAGCTTTGTGTACACCTTCATCGAGCTGTTCTCGCCGACGCTCAACCGCAAGCTGGTTGAGCAGGCCATGTCCGGCGAACACGAAGCCTACGAACTCTGAGGA > AM260479/3247892‑3248185
|
| 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: ‑ |
