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 F9 I0 R1
|
58 |
62.8 |
1514203 |
84.7% |
1282529 |
220.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_000913 |
2,173,361 |
Δ2 bp |
100% |
pseudogene (1‑2/442 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 |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,173,361 | 0 | C | . | 85.7%
| 63.1
/ 3.1
| 21 | 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 (3/0); new base . (14/4); total (17/4) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. |
| * | NC_000913 | 2,173,362 | 0 | C | . | 85.7%
| 63.6
/ 1.8
| 21 | 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 (3/0); new base . (14/4); total (17/4) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. |
TAGTTTGCGTCGCGATCCACAGGGTGATGCTCATAATGATGACACCCGAGATTAAGGTGCGGAACAGATTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCACCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTGGCATTAGCAGCATCACTGCCGCCGTTTTTACCGCCAGCTGCAATACACCTTTGACATCGTAACCCGCGAGGATGCCGATAATCA > NC_000913/2173154‑2173581
||
tAGTTTGCGTCGCGATCCACAGGGTGATGCTCATAATGATGACACCCGAGATTAAGGTGCGGAACAGATTTCCACGATGCACGTCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGCCAGCACCTGATTACCCGGCACCCAAACAGCAATTAAAATGGGGACTGGGTTAAACATCAGGCTGCCCGCAACC‑CCCC‑CCGTATGttcacgcccaaa > 2:650167/1‑218 (MQ=255)
acccccggggTGATGCCCAGAATGATAACCCCCGGAATTAAGGTGCGAAACAGTTTCCCCGGAGGCACGGCGACCGCCAGCGCCACGAAGAAGCCGATGGTGGAAAGATCGCAAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAgg < 1:141517/221‑1 (MQ=255)
ggggTGAGGCCCAAAATGATGACCCCCGAGTTTAAGGTGCGGACCAGATTCCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATc < 1:7375/227‑1 (MQ=255)
ggTGATGCTCATAATGATGACACCCGAGATTAAGGTGCGGAACAGATTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACCCAAACGGCAATTAAAAGGGTGAGTGGGATAAAAAACCAGCTTGCAGCAACCACCC‑‑CCGAATGTCCCAGGACCAACACGCGGTCAAGGCaaaaaaa > 2:237539/1‑224 (MQ=255)
gATGCTCATAATGATGACACACGAGATTAAGGTGCGGAACAGATTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGGGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGGAGCAACGCGGGAACAAGGCAAATCAGGaa > 1:608585/1‑228 (MQ=255)
tGCTCATAATGATGACACCCGAGATTAAGGTGCGGAACAGATTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCCCACAACCAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTTCCGATACCA‑‑ACGCCGGATGTCCCAGCAGAAACACCGGATAAAGGCCAACCAGGAAATc > 1:376140/1‑229 (MQ=255)
tGCTCATAATGATGACACCCGAGATTAAGGTGCGGAACAGATTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAACCAGACATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTCAGGCCCAGCAGCAACGCCGGACCAAGGCCACACAGGaaacc > 2:660569/1‑226 (MQ=255)
tgaCACCCGCGATTAAGGTGCGGAACAGATTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGCTTACCCGGCACACAAACAGCAATTAAAATGGTGAGCGGGATAAAAATCAGGCTTGCCGAAACCACCC‑‑CCGTATGTCCCCGCAGCAACGCCGCGACAAGGCCAATCAGGAACCACTGACCCCCGaa > 2:495095/1‑229 (MQ=255)
ggTGCGGAACAGATTTCCACGATGCACGTCGACCGCCATCGCCACGAAGAAGCCGATGGCGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAATCAGCAATTAAAATGGTGCGTGGGAAACGAATCAGGCTTACCGATACCA‑‑CCGCCGACTGTCCCAGCAGCAACGCCGGATCACGGCCCATACGGAAGTCCTCACCGCCGAACCTCCCCTGGAAAcca > 2:556073/1‑227 (MQ=255)
cGGAACAGATTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACACCGGATCAAGGCCAATCAGGACACCCTGCCCGCCGAACTTCGCCTGTAaacaacaac > 2:19243/1‑229 (MQ=255)
cGGAACAGATTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGAAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCCCCGACATTCGCCTGTAAACGACTa > 1:442771/1‑228 (MQ=255)
ccGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCCGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGCCTACGAGCCTGCTTAGCGATCGGCGTTAAAca > 1:379682/1‑228 (MQ=255)
aTGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAACCAGCAATTAAAATGGTGAGTGGGATAAAAAGCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCAccc < 1:19243/229‑1 (MQ=255)
ggCCCACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACAACGACCCTGCTTAGCGATCGGCGGTAACCCATCCATGCTGGGTTTAATACCCCTTGGCCTTGGCGGCATCCCTCCCGCCGTTTTTACCTCCa > 2:484870/1‑229 (MQ=255)
cacacaAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCACAGCAGCAACGCCGGATCAAGGCCAATAAGGAACTCCTGACCGCCGAACTTCGCCTGTAAAAAACTCCGAACCTGCTTAGCACGGGGCGTTAAACCATCCACATTGGGTTTAATACCCCGTGGACTTCGCCGAATCCCTACCGCCGGTTTTCCCTCCAg > 2:539586/1‑228 (MQ=255)
cacacaAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACAA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGCACTGCGCCTGTAAACGACTACGAACCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTGGCATTAGCAGCTTCACTGCCGCCGTTTTTTACGcccg > 1:373223/1‑226 (MQ=255)
acacaACCAGAAATTAAAATGGTGAGTGGGAAAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGAccgc < 2:512516/112‑1 (MQ=255)
acacaAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGAccgc > 1:512516/1‑112 (MQ=255)
acacaAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTGGCATTAGCAGCATCACTGCCGCCGTTTTTACCGCCAg > 1:5633/1‑227 (MQ=255)
gAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTGGCATTAGCAGCATCACTGCCGCCGTTTTTACACCCACCTGACAAACACCTTTGAccaccaaa > 2:719421/1‑222 (MQ=255)
gCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTGGCATTGGCAGCATCACTGCCGCCGGTTTTACGGCAAGCTGCAATACACCTTTTACATCGTAACCCCCGAGGATGCCGAAAAtaa > 1:69684/1‑227 (MQ=255)
||
TAGTTTGCGTCGCGATCCACAGGGTGATGCTCATAATGATGACACCCGAGATTAAGGTGCGGAACAGATTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCACCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTGGCATTAGCAGCATCACTGCCGCCGTTTTTACCGCCAGCTGCAATACACCTTTGACATCGTAACCCGCGAGGATGCCGATAATCA > NC_000913/2173154‑2173581
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
