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 |
|
A3 F11 I1 R1
|
56 |
79.5 |
3383150 |
98.4% |
3329019 |
146.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
499,203 |
A→G |
intergenic (+47/‑249) |
uhpA → / → PP_0411 |
two‑component system response regulator UhpA/polyamine ABC transporter ATP‑binding protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 499,203 | 0 | A | G | 100.0%
| 68.2
/ NA
| 20 | intergenic (+47/‑249) | uhpA/PP_0411 | two‑component system response regulator UhpA/polyamine ABC transporter ATP‑binding protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (4/16); total (4/16) |
CAAGACCATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCAGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCATGCCC > NC_002947_CJ‑RC/499057‑499271
|
cAAGACCATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCggg > 7:1177/1‑149 (MQ=255)
gACCATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCAt > 5:377086/1‑149 (MQ=255)
gACCATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCAt > 5:195639/1‑149 (MQ=255)
aTCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCgggggggggg > 4:13640/1‑142 (MQ=255)
aCCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAAc < 7:110480/149‑1 (MQ=255)
acaAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGggc < 7:260231/149‑1 (MQ=255)
acaAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGggc < 5:62995/149‑1 (MQ=255)
aaGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGggcct < 2:203260/149‑1 (MQ=255)
aGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGggcctg > 7:126726/1‑149 (MQ=255)
ggCACGCCTGATGCAGAAGTTTAAAGTGAACTGGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGGGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGggcctgg < 5:55886/149‑1 (MQ=255)
gCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGggcctggc < 7:79754/149‑1 (MQ=255)
aTGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGAt < 3:127927/148‑1 (MQ=255)
cAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATctct < 7:405788/149‑1 (MQ=255)
gAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGggc < 2:279226/130‑1 (MQ=255)
gAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGggc > 1:279226/1‑130 (MQ=255)
aGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATgt < 6:195639/149‑2 (MQ=255)
aGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATgg < 6:377086/149‑1 (MQ=255)
gCTGGGGGAGCTGGTGTAGTTCGCCATGGAGCACAAGCTCATCTCATTGCGACATACGCGTGCCCGAAACTTGCCGAAGCCTTTGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCctct < 4:295669/147‑1 (MQ=255)
cTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTcg < 1:405812/149‑1 (MQ=255)
aGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCAt < 8:126726/149‑1 (MQ=255)
gtttaattACCCCTTGGACCACAAGCTGATTTTATTGCCACTTAGGGGTGCCCCAAAGTTCCCTACGCATTTGGGGGCGGGGGCAGCCCCGCGACCGGGCCTGGCCTGCTGATCTCTATGGCTGCGCCGGCCTCTTCGCGGGCATGccc < 2:207589/142‑1 (MQ=255)
ggTGATGTACGCCATGGAGCACACGCTGATCTGATTGCTATATTCGGGTGCCCGAAAGTTGCCTTACCCTTTGTGGGTGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCATGccc < 6:359752/149‑1 (MQ=255)
|
CAAGACCATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCAGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCATGCCC > NC_002947_CJ‑RC/499057‑499271
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CGAGCAAGACCATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCAGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCATGCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCATTCCAATCCCGCCATCC > NC_002947_CJ‑RC/499053‑499323
|
CGAGCAAGACCATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATAGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCG > NB501016:282:H2V7GAFX2:3:11510:14023:16699/1‑151 (MQ=60)
AGACCATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATG > NB501016:282:H2V7GAFX2:3:21605:13382:1592/1‑151 (MQ=60)
AGACCATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATCTGGGAGCGGGCATG > NB501016:282:H2V7GAFX2:3:11609:6056:11182/1‑151 (MQ=60)
CACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACG < NB501016:282:H2V7GAFX2:4:11506:25965:14533/151‑1 (MQ=60)
CACAAGGCACGCCTGATGCAGATGTTTAAAGTGAACTGGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGGGCC < NB501016:282:H2V7GAFX2:3:11411:19718:18456/151‑1 (MQ=60)
CACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGGGCC < NB501016:282:H2V7GAFX2:4:21407:11595:15225/151‑1 (MQ=60)
AAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGGGCCTGG > NB501016:282:H2V7GAFX2:4:11509:3982:7614/1‑151 (MQ=60)
CGGCACGCCTGATGCAGAAGTTTAAAGTGAACTGGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGGGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGC < NB501016:282:H2V7GAFX2:3:11410:2706:13556/151‑1 (MQ=60)
GGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCC < NB501016:282:H2V7GAFX2:4:11501:11446:12927/151‑1 (MQ=60)
GATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATC < NB501016:282:H2V7GAFX2:2:11210:16894:14737/150‑1 (MQ=60)
GCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTA < NB501016:282:H2V7GAFX2:4:21607:19071:15129/151‑1 (MQ=60)
AGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGGGCC > NB501016:282:H2V7GAFX2:1:21111:16322:8970/1‑132 (MQ=60)
AGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGGGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATG < NB501016:282:H2V7GAFX2:2:21107:26151:13800/151‑1 (MQ=60)
gaagtggctggctgtggtgtttaagtaggccatgttcctcaaggttttctgattgcttcttacgggtcccagaaacttgcataaggcttTGTGGGAGCGGGCAAGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCC < NB501016:282:H2V7GAFX2:3:21403:16551:17495/61‑1 (MQ=60)
GCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGC < NB501016:282:H2V7GAFX2:1:21310:20959:6001/151‑1 (MQ=60)
ACGCCATGCAGCAAAAGCTGATCTGATTGCGACATACGGGTGCCCCAAACTTGCCGAAGCCTTTGTGGCCGCGGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGG < NB501016:282:H2V7GAFX2:2:11304:18850:19407/134‑1 (MQ=60)
CCCGAAACTTGCCGAAGCCTATGTGGGAGCGGGCATGCCCccccaccgggcaggccggcggctcgcaatggctgagccgggcgcaacgcgggcaagagcgggaccccacggttggtggtgggggagccacgggcttacacacccccccgac > NB501016:282:H2V7GAFX2:3:21505:1559:20305/1‑40 (MQ=60)
|
CGAGCAAGACCATCAGCACCCACAAGGCACGCCTGATGCAGAAGTTGAAAGTGAACTCGCTGGCGGAGCTGGTGAAGTACGCCATGGAGCACAAGCTGATCTGATTGCGACATACGGGTGCCCGAAACTTGCCGAAGCCTATGTGGGAGCAGGCATGCCCGCGAACGGGCCTGGCCTGCTGATCTCTATGGCTGAGCCGGCCTCTTCGCGGGCATGCCCGCTCCCACAGGTTTCGTGGTTGGCTCGCAAGGGCATTCCAATCCCGCCATCC > NC_002947_CJ‑RC/499053‑499323
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
