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 F29 I1 R1
|
57 |
65.8 |
2790598 |
98.6% |
2751529 |
146.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
4,586,137 |
2 bp→TC |
intergenic (+113/+101) |
PP_4061 → / ← PP_4063 |
hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 4,586,137 | 0 | C | T | 100.0%
| 72.5
/ NA
| 23 | intergenic (+113/+102) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (5/18); total (5/18) |
| * | NC_002947_CJ‑RC | 4,586,138 | 0 | T | C | 100.0%
| 75.1
/ NA
| 23 | intergenic (+114/+101) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (5/18); total (5/18) |
GCCGAGCCAGGAGCCACCGGTGAAGGCTTAAGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTCTGC‑GGTAAACCCGCTCCTACCAGGGA‑C‑GTGCCGGCCTTGAATG‑CGGCGCTGCCCCTGGTAGGAGCGGGTT > NC_002947_CJ‑RC/4585994‑4586207
||
gccgAGCCAGGAGCCACCGGTGAAGGCTTAAGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGC‑gg > 3:20791/1‑149 (MQ=255)
gccgAGCCAGGAGCCACCGGTGAAGGCTTAAGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGC‑gg < 5:137935/149‑1 (MQ=255)
gccgAGCCAGGAGCCACCGGTGAAGGCTTAAGGGTAGACCACGGCACCGGCGGGAACAGCTGATCTGCGCTGCGCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGC‑gg < 4:125870/149‑1 (MQ=255)
cAGGAGCCACCGGTGAAGGCTTAAGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAAcc > 6:156026/1‑149 (MQ=255)
gAGCCACCGGTGAAGGCTTAAGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGc < 5:156026/149‑1 (MQ=255)
aGCCACCGGTGAAGGCTTAAGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCt < 4:252594/149‑1 (MQ=255)
ccGGTGAAGGCTTAAGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTAc > 2:76597/1‑149 (MQ=255)
tAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACC‑GTGCCGGCCt < 4:20791/149‑1 (MQ=39)
aCCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACC‑GTGCCGGCCTTGa < 6:282920/149‑1 (MQ=39)
cACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACC‑GTGCCGGCCTTGAAt < 1:30956/149‑1 (MQ=39)
gTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACC‑GTGCCGGCCTTGAATG‑CGGCGCTGccc < 2:103810/149‑1 (MQ=39)
tGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACC‑GTGCCGGCCTTGAATG‑CGGCGCTGcccc < 1:80848/149‑1 (MQ=39)
aGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACC‑GTGCCGGCCTTGAATG‑CGGCGCTGCCCCTGGTa < 8:218602/149‑1 (MQ=39)
aGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACC‑GTGCCGGCCTTGAATG‑CGGCGCTGCCCCTGGTa < 5:275741/149‑1 (MQ=39)
gCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACC‑GTGCCGGCCTTGAATG‑CGGCGCTGCCCCTGGTAg < 4:115815/149‑1 (MQ=39)
gCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACC‑GTGCCGGCCTTGAATG‑CGGCGCTGCCCCTGGTAg > 4:306902/1‑149 (MQ=39)
cgcTGCTCCATTGAAAGGTTGAGGATGCCCGGTTGCTTGGCAAGGTGAAGATCTTGCATTGCTCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACC‑GTGCCGGCCTTGAATG‑CGGCGCTGCCCCTGGTAGGAGCGGGt < 7:291324/148‑1 (MQ=37)
cgcTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGG‑CAGCGCC‑GCATTCAAGGCCGGCACGGTCCCTGGTAGGAGc < 7:282114/144‑1 (MQ=14)
cgcTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACC‑GTGCCGGCCTTGAATG‑CGGCGCTGCCCCTGGTAGGAGCgg < 3:306902/146‑1 (MQ=38)
cgcTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACC‑GTGCCGGCCTTGAATG‑CGGCGCTGCCCCTGGTAGGAGCGGGtt < 8:244478/149‑1 (MQ=38)
cgcTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACC‑GTGCCGGCCTTGAATG‑CGGCGCTGCCCCTGGTAGGAGCGGGt < 1:76597/148‑1 (MQ=38)
ctCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACC‑GTGCCGGCCTTGAATG‑CGGCGCTGcccc > 6:12295/1‑129 (MQ=38)
ctCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACC‑GTGCCGGCCTTGAATG‑CGGCGCTGcccc < 5:12295/129‑1 (MQ=38)
||
GCCGAGCCAGGAGCCACCGGTGAAGGCTTAAGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTCTGC‑GGTAAACCCGCTCCTACCAGGGA‑C‑GTGCCGGCCTTGAATG‑CGGCGCTGCCCCTGGTAGGAGCGGGTT > NC_002947_CJ‑RC/4585994‑4586207
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ 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
CGACCCGCCGAGCCAGGAGCCACCGGTGAAGGCTTAAGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTC‑TCTGC‑GGTAAACCCGCTCCTACCAGGGA‑CGTGCCGGCCTTGAATGCGGCGCTGCCCCTGGTAGGAGCGGGTT > NC_002947_CJ‑RC/4585988‑4586207
|
CGACCCGCCGAGCCAGGAGCCACCGGTGAAGGCTTAAGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTC‑TT > NB501016:282:H2V7GAFX2:1:11209:21324:5213/1‑150 (MQ=60)
GGAGCCACCGGTGAAGGCTTAAGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTC‑TTCGCGGGTAAACCCGCT < NB501016:282:H2V7GAFX2:3:11608:3554:8163/151‑1 (MQ=60)
CACCGGTGAAGGCTTAAGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGAGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATATTGCATTGATAGGGCCGGCCACTTCGCC‑GGTAAACCCGCTCCAAC > NB501016:282:H2V7GAFX2:1:21104:19187:11994/1‑151 (MQ=60)
CCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTC‑TTCGCGGGTAAACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATG < NB501016:282:H2V7GAFX2:1:11106:7832:17765/151‑1 (MQ=60)
GTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTC‑TTCGCGGGTAAACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATGCGGCGCTGCCCCT < NB501016:282:H2V7GAFX2:1:11204:26451:12163/151‑1 (MQ=60)
CAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTC‑TTCGCGGGTAAACCCGCTCCTACCAGGGgcagcgccgcattcaaggccggcacggtccctggtag < NB501016:282:H2V7GAFX2:4:11603:19122:2880/151‑38 (MQ=60)
CAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTC‑TTCGCGGGTAAACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATGCGGCGCTGCCCCTGGTAG < NB501016:282:H2V7GAFX2:3:21509:22772:14760/151‑1 (MQ=60)
AGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTC‑TTCGCGGGTAAACCCGCTCCTACCAGGGgcagcgccgcattcaaggccggcacggtccctggtagg < NB501016:282:H2V7GAFX2:1:21304:20567:1719/151‑39 (MQ=58)
GCGCTGCTCCATTGAAAGGTTGAGGATGCCCGGTTGCTTGGCAAGGTGAAGATCTTGCATTGCTCGGGCCGGCCTC‑TTCGCGGGTAAACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATGCGGCGCTGCCCCTGGTAGGAGCGGGTT < NB501016:282:H2V7GAFX2:4:21511:24936:2402/150‑1 (MQ=60)
GCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTC‑TTCGCGGGTAAACCCGCTCCTACCAGGGgcagcgccgcattcaaggccggcacggtccctggtaggagcg < NB501016:282:H2V7GAFX2:4:21509:15251:5764/146‑43 (MQ=60)
GCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTC‑TTCGCGGGTAAACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATGCGGCGCTGCCCCTGGTAGGAGCGGGTT < NB501016:282:H2V7GAFX2:1:11203:10321:15471/150‑1 (MQ=60)
GCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTC‑TTCGCGGGTAAACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATGCGGCGCTGCCCCTGGTAGGAGCGGG < NB501016:282:H2V7GAFX2:2:21307:17069:4033/148‑1 (MQ=60)
GCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTC‑TTCGCGGGTAAACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATGCGGCGCTGCCCCT < NB501016:282:H2V7GAFX2:3:11403:13902:11464/131‑1 (MQ=60)
|
CGACCCGCCGAGCCAGGAGCCACCGGTGAAGGCTTAAGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTC‑TCTGC‑GGTAAACCCGCTCCTACCAGGGA‑CGTGCCGGCCTTGAATGCGGCGCTGCCCCTGGTAGGAGCGGGTT > NC_002947_CJ‑RC/4585988‑4586207
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
