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 F14 I0 R1
|
206 |
76.7 |
3255580 |
98.8% |
3216513 |
146.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
4,586,137 |
2 bp→TC |
100% |
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%
| 49.7
/ NA
| 16 | 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 (1/15); total (1/15) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| * | NC_002947_CJ‑RC | 4,586,138 | 0 | T | C | 100.0%
| 52.9
/ NA
| 16 | 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 (1/15); total (1/15) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
GAGCCAGGAGCCACCGGTGAAGGCTTAAGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTCTGC‑GGTAAACCCGCTCCTACCAGGGA‑CGTGCCGGCCTTGAATGCGGCGCTGCCCCTGGTAGGAGCGGGTTTACCCGC > NC_002947_CJ‑RC/4585997‑4586214
||
gAGCCAGGAGCCACCGGTGAAGGCTTAAGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCctctcgcgg > 3:298051/1‑141 (MQ=255)
gAGCCAGGAGCCACCGGTGAAGGCTTAAGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCctctcgcgg < 4:298051/145‑5 (MQ=255)
cGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATg < 7:119807/148‑1 (MQ=39)
cGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATg < 8:207864/148‑1 (MQ=39)
gCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATgcgg < 3:342531/149‑1 (MQ=39)
gCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATgcgg < 4:190654/149‑1 (MQ=39)
aCAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGC‑GGGAAACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATGCGGCGCTGCCCCTg < 7:108566/147‑1 (MQ=255)
aGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATGCGGCGCTGCCCCTGGTa < 3:319008/149‑1 (MQ=39)
aGCTGATCTGCGCTGCTCCATTGAAAGGATGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATGCGGCGCTGCCCCTGGTa < 3:373802/149‑1 (MQ=38)
gCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATGCGGCGCTGCCCCTGGTa < 7:63489/148‑1 (MQ=39)
aTCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATGCGGCGCTGCCCCTGGTAgg < 7:340963/146‑1 (MQ=39)
cgcTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATGCGGCGCTGCCCCTGGTAGGAg < 8:420330/143‑1 (MQ=38)
cgcTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATGCGGCGCTGCCCCTGGTAGGAGc < 3:63292/144‑1 (MQ=38)
gctgctCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATGCGGCGCTGCCCCTGGTAGGAGCGGGttt < 2:36866/149‑1 (MQ=38)
tgctCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATGCGGCGCTg < 7:263212/127‑1 (MQ=38)
tgctCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATGCGGCGCTg > 8:263212/1‑127 (MQ=38)
ctCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATGCGGCGCTGCCCCTGGTAGGAGCGGGTTTAcc < 8:57953/148‑1 (MQ=38)
ccATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGAGCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACCGGGCCGGCCTTGAATGCGGCGCTGCCCCTGGTAGGAGCGGGTTTACCcgc < 1:315070/149‑1 (MQ=37)
||
GAGCCAGGAGCCACCGGTGAAGGCTTAAGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTCTGC‑GGTAAACCCGCTCCTACCAGGGA‑CGTGCCGGCCTTGAATGCGGCGCTGCCCCTGGTAGGAGCGGGTTTACCCGC > NC_002947_CJ‑RC/4585997‑4586214
|
| 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
CGAGCCAGGAGCCACCGGTGAAGGCTTAAGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTCTGC‑GGTAAACCCGCTCCTACCAGGGA‑CGTGCCGGCCTTGAATGCGGCGCTGCCCCTGGTAGGAGCGGGTTTACCCGCG > NC_002947_CJ‑RC/4585996‑4586215
|
CGAGCCAGGAGCCACCGGTGAAGGCTTAAGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTCgcggg > NB501016:282:H2V7GAFX2:2:21207:8336:19638/1‑142 (MQ=60)
CCGGTGAAGGCTTAAGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCTGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCA < NB501016:282:H2V7GAFX2:2:21301:18485:2927/151‑1 (MQ=60)
GGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACCGTGCCGGCC > NB501016:282:H2V7GAFX2:2:21306:14407:16393/1‑151 (MQ=60)
ACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATGCG < NB501016:282:H2V7GAFX2:4:11508:4936:19414/151‑1 (MQ=60)
GGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATGCGGC < NB501016:282:H2V7GAFX2:2:21304:4924:11738/151‑1 (MQ=60)
AACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGC‑GGGAAACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATGCGGCGCTGCCCCTGGT < NB501016:282:H2V7GAFX2:4:11507:19946:2245/150‑1 (MQ=60)
CAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATGCGGCGCTGCCCCTGGTAG < NB501016:282:H2V7GAFX2:2:21211:12718:14425/151‑1 (MQ=60)
CAGCTGATCTGCGCTGCTCCATTGAAAGGATGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATGCGGCGCTGCCCCTGGTAG < NB501016:282:H2V7GAFX2:2:21309:16886:19713/151‑1 (MQ=60)
AGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATGCGGCGCTGCCCCTGGTAGG < NB501016:282:H2V7GAFX2:4:11411:15550:8917/151‑1 (MQ=60)
GATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATGCGGCGCTGCCCCTGGTAGGAG < NB501016:282:H2V7GAFX2:4:21510:20423:16920/149‑1 (MQ=60)
GCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGgcagcgccgcattcaaggccggcacggtccctggtaggagcg < NB501016:282:H2V7GAFX2:3:11608:18913:6476/146‑43 (MQ=60)
GCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATGCGGCGCTGCCCCTGGTAGGAGCG < NB501016:282:H2V7GAFX2:2:11112:8891:8690/146‑1 (MQ=60)
GCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACCGTGCCGGCCTTGAATGCGGCGCTGCC < NB501016:282:H2V7GAFX2:4:21409:10132:15364/131‑1 (MQ=60)
ACCATTGAACGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGAGCGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACCAGGGACCGGGCCGGCCTTGAATGCGGCGCTGCCCCTGGTAGGAGCGGGTTTACCCGCG < NB501016:282:H2V7GAFX2:1:21207:19272:15040/151‑1 (MQ=60)
|
CGAGCCAGGAGCCACCGGTGAAGGCTTAAGGGTAGACCACGGCACCGGCGTGAACAGCTGATCTGCGCTGCTCCATTGAAAGGTTGAGGATGACCGGGTGCTTGGCAAGGTGAAGATCTTGCATTGATCGGGCCGGCCTCTCTGC‑GGTAAACCCGCTCCTACCAGGGA‑CGTGCCGGCCTTGAATGCGGCGCTGCCCCTGGTAGGAGCGGGTTTACCCGCG > NC_002947_CJ‑RC/4585996‑4586215
|
| 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: ‑ |
