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
|
150 |
26.0 |
2053212 |
90.0% |
1847890 |
107.8 |
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%
| 105.4
/ NA
| 28 | 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 (18/10); total (18/10) |
CGAGCATGGACCGCAACCGATGCGCGCCTGACTGCCCGTCAGTCCGGTGCGTGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACG‑CCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTGGCGGCGAAGCATCC > AM260479/1354517‑1354766
|
cGAGCATGGACCGCAACCGATGCGCGCCTGACTGCCCGTCAGTCCGGTGCGTGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACG‑ccctgga > 1:465522/1‑129 (MQ=255)
cAACCGATGCGCGCCTGACTGCCCGTCAGTCCGGTGCGTGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGAt > 2:268518/1‑133 (MQ=255)
gTCCGGTGCGTGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATg < 2:465522/134‑1 (MQ=255)
cAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCt < 2:551847/133‑1 (MQ=255)
aTAACAGGGAGCTAGATCATGCAGTACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTg > 1:621182/1‑132 (MQ=255)
aTAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTg > 1:558825/1‑132 (MQ=255)
aTAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTg > 2:604890/1‑132 (MQ=255)
tAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAg > 1:989483/1‑134 (MQ=255)
aCAGGGAGCTAGATCATGCAGTACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCa < 2:621182/134‑1 (MQ=255)
aCAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCa < 2:558825/134‑1 (MQ=255)
aTCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCgg > 2:485151/1‑134 (MQ=255)
tGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCgg < 1:883805/123‑1 (MQ=255)
tGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCgg > 2:883805/1‑123 (MQ=255)
ggACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAg < 1:829927/61‑1 (MQ=255)
ggACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAg > 2:829927/1‑61 (MQ=255)
ggACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCgg > 2:496906/1‑133 (MQ=255)
tACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAg > 2:193678/1‑61 (MQ=255)
tACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAg < 1:193678/61‑1 (MQ=255)
aTTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTc > 2:686434/1‑132 (MQ=255)
tgtgGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCtgctgc > 1:756678/1‑54 (MQ=39)
tgtgGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCtgctgc < 2:756678/54‑1 (MQ=39)
tgtgGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTggcggc > 1:647459/1‑133 (MQ=255)
ggCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTGGCGGCGAAg > 1:937978/1‑134 (MQ=255)
ggCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTGGCGGCGAAg > 1:8876/1‑134 (MQ=255)
cAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTg < 2:235349/84‑1 (MQ=255)
cAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTg > 1:235349/1‑84 (MQ=255)
gCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTGGCGGCGaa > 2:528869/1‑128 (MQ=255)
gCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTGGCGGCGaa < 1:528869/128‑1 (MQ=255)
gCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTGGCGGCGAAGCATcc > 1:570976/1‑134 (MQ=255)
|
CGAGCATGGACCGCAACCGATGCGCGCCTGACTGCCCGTCAGTCCGGTGCGTGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACG‑CCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTGGCGGCGAAGCATCC > AM260479/1354517‑1354766
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ 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
GAACGGTCCCGCTCTCGAGCATGGACCGCAACCGATGCGCGCCTGACTGCCCGTCAGTCCGGTGCGTGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACG‑CCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTGGCGGCGAAGCATCCGGACACGCC > AM260479/1354502‑1354775
|
caagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacaGTGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGAC < GWNJ‑0478:712:GW2002102894th:2:2203:4627:95410/85‑1 (MQ=60)
GAACGGTCCCGCTCTCGAGCATGGACCGCAACCGATGCGCGCCTGACTGCCCGTCAGTCCGGTGCGTGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGAC > GWNJ‑0478:712:GW2002102894th:2:1215:20679:24048/1‑150 (MQ=60)
ttattttttatcttttttttttttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGAC < GWNJ‑0478:712:GW2002102894th:2:2213:11691:68193/51‑1 (MQ=60)
aagacggcatacgagctgtagctccgtctcgtgggctcggagatgtgtataagagacaGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCAT < GWNJ‑0478:712:GW2002102894th:2:2205:17835:28008/92‑1 (MQ=60)
aagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAG < GWNJ‑0478:712:GW2002102894th:2:1112:18699:43213/91‑1 (MQ=60)
GTGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACG‑CCctggacctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgctt > GWNJ‑0478:712:GW2002102894th:2:2205:15122:76627/1‑79 (MQ=60)
TGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGTACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGG > GWNJ‑0478:712:GW2002102894th:2:2108:14205:28248/1‑148 (MQ=60)
TGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGG > GWNJ‑0478:712:GW2002102894th:2:2105:10372:17862/1‑148 (MQ=60)
GCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGC > GWNJ‑0478:712:GW2002102894th:2:2214:14997:87563/1‑150 (MQ=60)
gacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCA < GWNJ‑0478:712:GW2002102894th:2:2103:3944:31659/93‑1 (MQ=60)
GGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGC < GWNJ‑0478:712:GW2002102894th:2:2207:17674:66189/150‑1 (MQ=60)
agctccgtctcgtgggctcggagatgtgtataagagacagcgcCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGC < GWNJ‑0478:712:GW2002102894th:2:2204:13067:57134/107‑1 (MQ=60)
GTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttg > GWNJ‑0478:712:GW2002102894th:2:2116:18653:39898/1‑84 (MQ=60)
GTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTGGCGGCG > GWNJ‑0478:712:GW2002102894th:2:2109:15340:92923/1‑149 (MQ=60)
CTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTGGCGGCGAAGC > GWNJ‑0478:712:GW2002102894th:2:2210:14029:93722/1‑150 (MQ=60)
CTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTGGCGGCGAAGC > GWNJ‑0478:712:GW2002102894th:2:1101:6529:64641/1‑150 (MQ=60)
ATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCctgtctcttatacacatctccgagcccacgagacgg > GWNJ‑0478:712:GW2002102894th:2:1114:7358:87211/1‑114 (MQ=60)
GAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTGGCGGCGAAGCATCCG > GWNJ‑0478:712:GW2002102894th:2:2105:8668:99554/1‑150 (MQ=60)
GTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTGGCGGCGAAGCATCCGGACACGCC < GWNJ‑0478:712:GW2002102894th:2:2103:10544:5858/150‑1 (MQ=60)
|
GAACGGTCCCGCTCTCGAGCATGGACCGCAACCGATGCGCGCCTGACTGCCCGTCAGTCCGGTGCGTGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACG‑CCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTGGCGGCGAAGCATCCGGACACGCC > AM260479/1354502‑1354775
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
