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 |
|
A2 F59 I1 R1
|
58 |
78.7 |
3339874 |
98.5% |
3289775 |
147.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
3,951,161 |
A→T |
intergenic (‑125/+70) |
PP_3486 ← / ← PP_3487 |
cytochrome c/hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 3,951,161 | 0 | A | T | 100.0%
| 49.1
/ NA
| 16 | intergenic (‑125/+70) | PP_3486/PP_3487 | cytochrome c/hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (13/3); total (13/3) |
GGCTGAGGTCGAAGTTGCCATGCCAAGCACGCAGGTAAGCCATATCGCAAGCCCTGTGGGAGCGGCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCTTATCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTGCATCCG > NC_002947_CJ‑RC/3951016‑3951298
|
gggtGATGTCGAAGTTGCCATGCCAAGCACGGAGGTAAGCCATATGGCTAGCCGTGTGGGAGCGGCCTTGCGTCGCGAAAGGGCTGCGCAGCTGCCCCGGCAGTGGCAGCTCTAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTcg < 2:395881/146‑1 (MQ=38)
ggcTGTGGTCGAAGTTGCCATGCCAAGCACGCAGGTAAGCCATATCGCAAGCCCTGTGGGAGCGGCCTTGCGTCGCTAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTcg < 8:91137/149‑1 (MQ=255)
gTCGCGAAAGGGTTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGAAGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAAATCCCAAGGAGGCCCATGATAATCacc > 2:225428/1‑149 (MQ=38)
tCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCacc > 8:76070/1‑148 (MQ=255)
gcCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCaa > 7:33592/1‑149 (MQ=255)
ccGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAg > 6:200656/1‑149 (MQ=255)
ccGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAg > 8:163089/1‑149 (MQ=255)
ccGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTACTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAg > 3:111313/1‑149 (MQ=255)
cGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGAAACTCACCGACCGGCCAGCGGCTGGGTCAACAGc > 8:168730/1‑149 (MQ=255)
aGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAGTTACCCAGGCGGCCCCTGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCt > 3:394927/1‑149 (MQ=39)
aGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCaa > 7:323816/1‑149 (MQ=255)
gcAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATcg > 7:249309/1‑149 (MQ=255)
aGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATcgcc > 8:307099/1‑149 (MQ=255)
agagGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTg < 7:307099/149‑1 (MQ=255)
gAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTg > 3:350279/1‑149 (MQ=255)
tGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTGCATCCg > 4:316349/1‑149 (MQ=255)
|
GGCTGAGGTCGAAGTTGCCATGCCAAGCACGCAGGTAAGCCATATCGCAAGCCCTGTGGGAGCGGCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCTTATCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTGCATCCG > NC_002947_CJ‑RC/3951016‑3951298
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AGGTCGAAGTTGCCATGCCAAGCACGCAGGTAAGCCATATCGCAAGCCCTGTGGGAGCGGCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCTTATCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTGCATCCGGGCGAATCTTGCT > NC_002947_CJ‑RC/3951021‑3951311
|
cggcccccctgccacccccaccccccccgtaacccaaaaccccccccccgggggccgcggcctggcgccccaaccgggcggccccccccCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCA < NB501016:282:H2V7GAFX2:4:11604:7976:19541/62‑1 (MQ=60)
gcggggcttgctgtcttcgcgcgtgtgcctctccctctcccccgcgcccccccccccccCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAG < NB501016:282:H2V7GAFX2:2:11207:5493:6630/92‑1 (MQ=60)
CGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCCCACCTTTGCCGACCCAAGGCCGCTGCCACAAAAGCCGATGGCACAGAGGCCAATTTCCCAGGCCGCCCAagaagatcggaagaggacacctctgga > NB501016:282:H2V7GAFX2:2:11101:14656:4270/1‑123 (MQ=60)
AGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAAC > NB501016:282:H2V7GAFX2:4:11406:18678:9234/1‑151 (MQ=60)
CCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTACTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGC > NB501016:282:H2V7GAFX2:2:11208:17208:6958/1‑151 (MQ=60)
CAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAGTTACCCAGGCGGCCCCTGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTG > NB501016:282:H2V7GAFX2:2:21311:15535:5862/1‑151 (MQ=60)
AAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAAT > NB501016:282:H2V7GAFX2:4:21507:8702:4502/1‑151 (MQ=60)
CGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGC > NB501016:282:H2V7GAFX2:4:21406:7068:15761/1‑151 (MQ=60)
AAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGG < NB501016:282:H2V7GAFX2:4:21504:11108:7842/151‑1 (MQ=60)
GGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTGC > NB501016:282:H2V7GAFX2:2:21303:4678:15364/1‑151 (MQ=60)
CTCCTTTCGCGACGCAAGGCCGCTCACACAAAAGCGGATGCCACAGAGGCCAATTCCCAAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGAATGCGCAGCGCAATCGCCGCTGGCGGTGCATCCGGGCGAATC > NB501016:282:H2V7GAFX2:4:11503:15170:11063/1‑151 (MQ=60)
TTTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTGCATCCGGGCGAATCTTGC > NB501016:282:H2V7GAFX2:2:11108:3240:1813/1‑151 (MQ=60)
TTCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTGCATCCGGGCGAATCTTGAT > NB501016:282:H2V7GAFX2:3:11405:21066:13478/1‑151 (MQ=60)
|
AGGTCGAAGTTGCCATGCCAAGCACGCAGGTAAGCCATATCGCAAGCCCTGTGGGAGCGGCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCTTATCGCGACGCAAGGCCGCTCCCACAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTGCATCCGGGCGAATCTTGCT > NC_002947_CJ‑RC/3951021‑3951311
|
| 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: ‑ |
