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 |
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%
| 111.6
/ NA
| 30 | 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 (18/12); total (18/12) |
CAACCGATGCGCGCCTGACTGCCCGTCAGTCCGGTGCGTGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACG‑CCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTGGCG > AM260479/1354530‑1354755
|
cAACCGATGCGCGCCTGACTGCCCGTCAGTCCGGTGCGTGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGAt > 2:265717/1‑133 (MQ=255)
gATGCGCGCCTGACTGCCCGTCAGTCCGGTGCGTGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCa < 1:163757/124‑1 (MQ=255)
gATGCGCGCCTGACTGCCCGTCAGTCCGGTGCGTGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCa > 2:163757/1‑124 (MQ=255)
gTCCGGTGCGTGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACttt > 2:473430/1‑97 (MQ=255)
gTCCGGTGCGTGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACttt < 1:473430/97‑1 (MQ=255)
gTCCGGTGCGTGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATg > 1:659731/1‑134 (MQ=255)
cTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGc < 2:659731/134‑1 (MQ=255)
gTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCa < 2:455002/81‑1 (MQ=255)
gTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCa > 1:455002/1‑81 (MQ=255)
aTAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATgcgc > 1:411238/1‑112 (MQ=255)
aTAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATgcgc < 2:411238/112‑1 (MQ=255)
aTAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACG‑cc > 2:952414/1‑63 (MQ=255)
aTAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACG‑cc < 1:952414/63‑1 (MQ=255)
gCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCg > 2:878969/1‑131 (MQ=255)
gCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCg > 1:725771/1‑131 (MQ=255)
gATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGc < 2:725771/133‑1 (MQ=255)
ggACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAg > 2:259650/1‑67 (MQ=255)
ggACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAg < 1:259650/67‑1 (MQ=255)
gTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTc > 1:498704/1‑134 (MQ=255)
aTTGAAATCATGTGGCAGGCCATCGACGCCCTGGACtt > 1:1091981/1‑38 (MQ=25)
aTTGAAATCATGTGGCAGGCCATCGACGCCCTGGACtt < 2:1091981/38‑1 (MQ=25)
aTTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGgaga < 2:423550/112‑1 (MQ=255)
aTTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGgaga > 1:423550/1‑112 (MQ=255)
aTTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTc > 1:426217/1‑132 (MQ=255)
aTTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTc > 1:407835/1‑132 (MQ=255)
aTTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTc > 2:112639/1‑132 (MQ=255)
aTTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTc > 1:779434/1‑132 (MQ=255)
tCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTggcg < 2:498704/134‑1 (MQ=255)
cATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCt > 2:453669/1‑90 (MQ=255)
cATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCt < 1:453669/90‑1 (MQ=255)
tgtgGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGc < 2:484006/78‑1 (MQ=255)
tgtgGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGc > 1:484006/1‑78 (MQ=255)
|
CAACCGATGCGCGCCTGACTGCCCGTCAGTCCGGTGCGTGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACG‑CCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTGGCG > AM260479/1354530‑1354755
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 37 ≤ 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‑CCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTGGCGGCG > AM260479/1354502‑1354758
|
gagtgtctcgtgggctcggagatgtgtataagagacagGCGCCTGACTGCCCGTCAGTCCGGTGCGTGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGAC < GWNJ‑0478:712:GW2002102894th:2:1101:3974:12562/112‑1 (MQ=60)
gacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacaGTGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGG < GWNJ‑0478:712:GW2002102894th:2:2209:20814:98613/94‑1 (MQ=60)
cggagatgtgtataagagacaGCCTGACTGCCCGTCAGTCCGGTGCGTGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCC < GWNJ‑0478:712:GW2002102894th:2:1213:20708:3841/128‑1 (MQ=60)
GGACCGCAACCGATGCGCGCCTGACTGCCCGTCAGTCCGGTGCGTGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGC < GWNJ‑0478:712:GW2002102894th:2:1111:8752:78726/150‑1 (MQ=60)
gcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacaGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAG < GWNJ‑0478:712:GW2002102894th:2:1114:14533:74102/98‑1 (MQ=60)
CCTGACTGCCCGTCAGTCCGGTGCGTGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGC > GWNJ‑0478:712:GW2002102894th:2:2107:15892:46592/1‑150 (MQ=60)
GTGCGTGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCctgtctcttatacacatctccgagcccacgagacactcg > GWNJ‑0478:712:GW2002102894th:2:1210:2256:7639/1‑111 (MQ=60)
TGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCtgtctct > GWNJ‑0478:712:GW2002102894th:2:1208:16620:75335/1‑143 (MQ=60)
GTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGG > GWNJ‑0478:712:GW2002102894th:2:2111:6507:28819/1‑147 (MQ=60)
cgtgggctcggagatgtgtataagagacagCCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAG < GWNJ‑0478:712:GW2002102894th:2:1211:3999:99845/120‑1 (MQ=60)
cgagattagcgagtgtctcgtgggctcggagatgtgtataagagacagGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAG < GWNJ‑0478:712:GW2002102894th:2:1214:16897:11994/102‑1 (MQ=60)
AGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCC > GWNJ‑0478:712:GW2002102894th:2:1212:2731:28858/1‑150 (MQ=60)
ATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCtgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaaaaaaaaccac > GWNJ‑0478:712:GW2002102894th:2:2214:20734:55348/1‑69 (MQ=60)
ATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATctgtctct > GWNJ‑0478:712:GW2002102894th:2:1209:14532:41892/1‑142 (MQ=60)
ATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCA > GWNJ‑0478:712:GW2002102894th:2:1209:6210:56619/1‑148 (MQ=60)
ATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCA > GWNJ‑0478:712:GW2002102894th:2:2112:15846:14255/1‑148 (MQ=60)
ATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCA > GWNJ‑0478:712:GW2002102894th:2:1208:11982:57633/1‑148 (MQ=60)
GTACTATTGAAATCATGTGGCAGGCCATCGACGCCCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCctgtctcttatacacatctccgagcccacgagacactcgct > GWNJ‑0478:712:GW2002102894th:2:1213:21027:55010/1‑108 (MQ=60)
|
GAACGGTCCCGCTCTCGAGCATGGACCGCAACCGATGCGCGCCTGACTGCCCGTCAGTCCGGTGCGTGCTTAAGCAGTCCAATAACAGGGAGCTAGATCATGCAGGACCGTACTATTGAAATCATGTGGCAGGCCATCGACG‑CCTGGACTTTTCCAGGATGAAGGCCAAGCTGCTGCATCAGAAGCATGCGCATTGGTCGCCGGAATCGCTGGAGCAGGCGGAGAGCGGCTACCGGCAATTCCTCAAGCTGGCGGCG > AM260479/1354502‑1354758
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
