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 |
1,354,645 |
+C |
intergenic (+98/‑15) |
h16_A1248 → / → h16_A1249 |
predicted signal transduction protein containingCHASE, PAS, GGDEF and EAL domains/Hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 1,354,643 | 1 | . | C | 100.0%
| 110.5
/ NA
| 29 | intergenic (+96/‑17) | h16_A1248/h16_A1249 | predicted signal transduction protein containingCHASE, PAS, GGDEF and EAL domains/Hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (18/11); total (18/11) |
CCGCTCTCGAGCATGGACCGCAACCGATGCGCGCCTGACTGCCCGTCAGTCCGGTGCGTGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACG‑CCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTGGCGGCGAAGCATCCGGA > AM260479/1354510‑1354769
|
ccGCTCTCGAGCATGGACCGCAACCGATGCGCGCCTGACTGCCCGTCAGTCCGGTGCGTGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACg > 1:816439/1‑134 (MQ=255)
cAACCGATGCGCGCCTGACTGCCCGTCAGTCCGGTGCGTGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGAt > 1:684966/1‑133 (MQ=255)
gcgcCTGACTGCCCGTCAGTCCGGTGCGTGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAgc < 2:816439/134‑1 (MQ=255)
aaGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCg > 2:218700/1‑133 (MQ=255)
gTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACttt < 2:499136/77‑1 (MQ=255)
gTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACttt > 1:499136/1‑77 (MQ=255)
aTAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGc < 1:28680/121‑1 (MQ=255)
aTAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGc > 2:28680/1‑121 (MQ=255)
aTAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTg > 2:219552/1‑132 (MQ=255)
aTAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTg > 2:1016137/1‑132 (MQ=255)
aTGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTa > 2:804577/1‑134 (MQ=255)
cAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCg < 2:684966/134‑1 (MQ=255)
ggACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAg < 1:141769/67‑1 (MQ=255)
ggACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAg > 2:141769/1‑67 (MQ=255)
ggACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCgg > 1:166468/1‑133 (MQ=255)
cTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCt > 2:124264/1‑133 (MQ=255)
aTTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAg < 1:534114/44‑1 (MQ=38)
aTTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAg > 2:534114/1‑44 (MQ=38)
aTTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCg > 2:782645/1‑122 (MQ=255)
aTTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCg < 1:782645/122‑1 (MQ=255)
aaTCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTgg > 2:800579/1‑134 (MQ=255)
aaTCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTgg > 1:280335/1‑134 (MQ=255)
tCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTggcg < 1:1016137/134‑1 (MQ=255)
tgtgGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCAt > 1:885378/1‑56 (MQ=39)
tgtgGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCAt < 2:885378/56‑1 (MQ=39)
tgtgGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTggcggc > 1:349029/1‑133 (MQ=255)
tgGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTGGCGGCGaa < 1:219552/134‑1 (MQ=255)
ggCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTGGCGGCGAAGCATc < 1:124264/134‑1 (MQ=255)
tCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTGGCGGCGAAGCATCCGGa > 1:940022/1‑133 (MQ=255)
tCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTGGCGGCGAAGCATCCGGa > 1:680634/1‑133 (MQ=255)
|
CCGCTCTCGAGCATGGACCGCAACCGATGCGCGCCTGACTGCCCGTCAGTCCGGTGCGTGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACG‑CCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTGGCGGCGAAGCATCCGGA > AM260479/1354510‑1354769
|
| 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
CATGGAGAACGGTCCCGCTCTCGAGCATGGACCGCAACCGATGCGCGCCTGACTGCCCGTCAGTCCGGTGCGTGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACG‑CCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTGGCGGCGAAGCATCCGGACACGCCCGTCG > AM260479/1354496‑1354780
|
CATGGAGAACGGTCCCGCTCTCGAGCATGGACCGCAACCGATGCGCGCCTGACTGCCCGTCAGTCCGGTGCGTGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACG‑CC > GWNJ‑0478:712:GW2002102894th:2:1210:13074:59955/1‑150 (MQ=60)
CTCGAGCATGGACCGCAACCGATGCGCGCCTGACTGCCCGTCAGTCCGGTGCGTGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATG > GWNJ‑0478:712:GW2002102894th:2:2110:19525:93883/1‑149 (MQ=60)
tttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCT < GWNJ‑0478:712:GW2002102894th:2:2103:4759:10451/74‑1 (MQ=60)
gcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacaGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAG < GWNJ‑0478:712:GW2002102894th:2:1111:4833:36735/98‑1 (MQ=60)
GTGCGTGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCctgtctcttatacacatctccgagcccacgagacggagctac > GWNJ‑0478:712:GW2002102894th:2:1214:16420:89171/1‑107 (MQ=60)
GCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGC < GWNJ‑0478:712:GW2002102894th:2:1105:2379:2888/150‑1 (MQ=60)
GAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGC > GWNJ‑0478:712:GW2002102894th:2:1110:2329:83974/1‑149 (MQ=60)
ATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaaaaaaaaaaaagcaagaatc > GWNJ‑0478:712:GW2002102894th:2:2215:16680:63334/1‑62 (MQ=60)
GCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCT < GWNJ‑0478:712:GW2002102894th:2:2201:15182:68935/150‑1 (MQ=60)
GGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTGGC > GWNJ‑0478:712:GW2002102894th:2:1203:4253:79508/1‑150 (MQ=60)
GTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgct > GWNJ‑0478:712:GW2002102894th:2:2207:21162:42647/1‑86 (MQ=60)
GTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTGGCGGCG > GWNJ‑0478:712:GW2002102894th:2:1206:12370:32113/1‑149 (MQ=60)
CTATTGAAATCATGTGGCAGGCCATCGACG‑CCctggacctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaaaaaaaaaaaaaaaataatgggtcagactgcaataacagaaca > GWNJ‑0478:712:GW2002102894th:2:2214:6666:65929/1‑32 (MQ=60)
ATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTGGCGGCGAAGCATCCGGAC < GWNJ‑0478:712:GW2002102894th:2:2215:11111:100123/150‑1 (MQ=60)
TCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTGGCGGCGAAGCATCCGGAC > GWNJ‑0478:712:GW2002102894th:2:2110:6746:68708/1‑149 (MQ=60)
TCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTGGCGGCGAAGCATCCGGAC > GWNJ‑0478:712:GW2002102894th:2:2210:6148:73515/1‑149 (MQ=60)
GTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTGGCGGCGAAGCATCCGGACACGCC < GWNJ‑0478:712:GW2002102894th:2:1115:4195:88664/150‑1 (MQ=60)
AGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTGGCGGCGAAGCATCCGGACACGCCCGTCG < GWNJ‑0478:712:GW2002102894th:2:1109:7062:31033/150‑1 (MQ=60)
|
CATGGAGAACGGTCCCGCTCTCGAGCATGGACCGCAACCGATGCGCGCCTGACTGCCCGTCAGTCCGGTGCGTGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACG‑CCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTGGCGGCGAAGCATCCGGACACGCCCGTCG > AM260479/1354496‑1354780
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
