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 F15 I1 R1
|
10 |
34.7 |
1290222 |
96.6% |
1246354 |
128.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,173,363 |
Δ2 bp |
intergenic (‑1/+1) |
gatC ← / ← gatC |
pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,173,361 | 0 | C | . | 100.0%
| 119.2
/ NA
| 27 | pseudogene (2/442 nt) | gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base . (13/14); total (13/14) |
| * | NC_000913 | 2,173,362 | 0 | C | . | 100.0%
| 119.2
/ NA
| 27 | pseudogene (1/442 nt) | gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base . (13/14); total (13/14) |
ATTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCACCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTT > NC_000913/2173221‑2173486
||
aTTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATaccaccgccgtat > 2:125803/1‑142 (MQ=255)
aTGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCcagca < 1:125803/149‑1 (MQ=255)
gCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGc < 1:5495/149‑1 (MQ=255)
cACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCa > 6:129444/1‑148 (MQ=255)
cGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATc < 5:129444/149‑1 (MQ=255)
gCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCca < 1:180987/106‑1 (MQ=255)
gCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCca > 2:180987/1‑106 (MQ=255)
gATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCaa < 8:109560/120‑1 (MQ=255)
gATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCaa > 7:109560/1‑120 (MQ=255)
aTCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACt > 2:170397/1‑149 (MQ=255)
cagcaCCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAAc < 4:54211/149‑1 (MQ=255)
cTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTAc > 8:97263/1‑149 (MQ=255)
ccGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCt > 2:23429/1‑129 (MQ=255)
ccGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCt < 1:23429/129‑1 (MQ=255)
acacaAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGc > 2:11288/1‑140 (MQ=255)
acacaAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGc < 1:11288/140‑1 (MQ=255)
acaAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAg > 7:3886/1‑96 (MQ=255)
acaAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAg < 8:3886/96‑1 (MQ=255)
acaAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGa > 4:88018/1‑149 (MQ=255)
aaaCAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAg < 2:186417/144‑1 (MQ=255)
aaaCAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAg > 1:186417/1‑144 (MQ=255)
aaTTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGc > 5:69884/1‑80 (MQ=255)
aaTTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGc < 6:69884/80‑1 (MQ=255)
aaTTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGc > 5:86641/1‑111 (MQ=255)
aaTTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGc < 6:86641/111‑1 (MQ=255)
gTGGGATAATAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATg > 3:17616/1‑128 (MQ=255)
gTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATg < 4:17616/128‑1 (MQ=255)
aTAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGttt < 3:88018/149‑1 (MQ=255)
||
ATTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCACCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTT > NC_000913/2173221‑2173486
|
| 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
GATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCACCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTA > NC_000913/2173229‑2173487
|
GATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAG < NB501016:228:HFK2FAFXY:1:21112:9376:17647/151‑1 (MQ=60)
GGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCC < NB501016:228:HFK2FAFXY:1:11103:19934:1140/151‑1 (MQ=60)
CCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATG > NB501016:228:HFK2FAFXY:3:21602:22741:5808/1‑127 (MQ=60)
ACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCA < NB501016:228:HFK2FAFXY:3:21507:12788:16726/151‑1 (MQ=60)
GGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAG < NB501016:228:HFK2FAFXY:1:21310:9252:8258/108‑1 (MQ=60)
AGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAG > NB501016:228:HFK2FAFXY:4:21507:5952:9440/1‑122 (MQ=60)
CCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTG < NB501016:228:HFK2FAFXY:1:11109:4901:12932/131‑1 (MQ=60)
CACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCC < NB501016:228:HFK2FAFXY:1:11105:11533:3118/142‑1 (MQ=60)
CACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGG > NB501016:228:HFK2FAFXY:4:11402:21492:18948/1‑98 (MQ=60)
CAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGC > NB501016:228:HFK2FAFXY:1:21312:12559:9846/1‑146 (MQ=60)
CAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCC > NB501016:228:HFK2FAFXY:3:11612:17467:19654/1‑113 (MQ=60)
CAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCC > NB501016:228:HFK2FAFXY:3:11606:3600:2509/1‑82 (MQ=60)
AGTGGGATAATAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGG > NB501016:228:HFK2FAFXY:2:11110:13179:1249/1‑130 (MQ=60)
GTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCGCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGG < NB501016:228:HFK2FAFXY:3:11605:1805:17319/151‑1 (MQ=60)
GATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTA < NB501016:228:HFK2FAFXY:2:21108:19759:5160/151‑1 (MQ=60)
ccaCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAG < NB501016:228:HFK2FAFXY:2:21305:6933:1812/84‑1 (MQ=60)
|
GATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCACCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTA > NC_000913/2173229‑2173487
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
