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 |
|
A21 F5 I0 R1
|
24 |
41.2 |
1474486 |
89.7% |
1322613 |
148.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_000913_3_pae_tpiA |
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_3_pae_tpiA | 2,173,361 | 0 | C | . | 97.1%
| 148.5
/ ‑3.2
| 35 | 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 (0/1); new base . (19/15); total (19/16) |
| Fisher's exact test for biased strand distribution p-value = 4.57e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| 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_3_pae_tpiA | 2,173,362 | 0 | C | . | 97.1%
| 148.3
/ ‑3.5
| 35 | 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 (0/1); new base . (19/15); total (19/16) |
| Fisher's exact test for biased strand distribution p-value = 4.57e-01 |
| 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: Frequency below/above cutoff threshold. |
| 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. |
AACAGATTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCACCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTGGCATTA > NC_000913_3_pae_tpiA/2173216‑2173503
||
aaCAGATTTCCACGATGCACGGCGACGGCCATCGCCACGAAGAAGCCGATGGTGGCCAGATGGCCACACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGATAGTGTTCAACATCAGGCTTGCCGATaccaccga > 2:316904/1‑147 (MQ=255)
aTTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATaccaccgccgtat > 1:523248/1‑142 (MQ=255)
aTTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATaccaccgccgtat > 1:297481/1‑142 (MQ=255)
aTTTCCACGATGCACGGCGACCGCCATCGCCACCAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATaccaccgccgtat < 2:656901/149‑8 (MQ=255)
tCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTc < 1:44283/149‑1 (MQ=255)
aTGCACGGCGACCGCCATCGCCACGAATAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACACCCCACTAAACGCTGAGGGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCcagca < 1:324091/149‑1 (MQ=255)
cGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGcc < 1:112736/149‑1 (MQ=255)
aCCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCgg < 1:735263/149‑1 (MQ=255)
ccATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCCCCTGATTACCCGGCACACAACCAGCAATTAAAATGGTGAGTGGGATAAAAATCCGGCGTGCCGATACCA‑‑CCGCCGAATGACCCCGCACCAccgccgcgtca > 2:144825/1‑144 (MQ=255)
ccATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCGGGATCa > 1:626334/1‑149 (MQ=255)
cATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCGAGCAGCAACGCCGGATCaa < 2:621184/149‑1 (MQ=255)
aacGCCACAAAGAATCCGATGGTGGCAAGATCGGCAAACGGCAGTACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAg < 1:584801/147‑1 (MQ=255)
tCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAAGTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAgc > 1:711938/1‑148 (MQ=255)
ccACGAAGAAGCCGATGATGGCAAGATCGCCAAACGGCAGCACCTGCTCACCCGGCACACAAACAGCAATTAAAATAGTGAGTGGGATAAAAATCAGGCTGGCCGATACCA‑‑CCGCCGTATGTCCCACCACCACCACCCGATCAAGGCCa > 2:685031/1‑149 (MQ=255)
accaagaagTCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCATACAAACCGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAAt < 1:517332/146‑1 (MQ=255)
gCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGAccgcc > 1:230987/1‑149 (MQ=255)
aaGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCATCAGCAACGCCGCATCAAGGCCAATCACGAACTCCTGACCGCCGa > 2:359586/1‑149 (MQ=255)
aaGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACCCCTCACCGCCGa > 2:656410/1‑149 (MQ=255)
aGATCGCAAACCGGCAGCACCTGATTACCCGGCACACAAACAGCAACTAAAATGGTGGGTGGGATAAAAATCAGGATTGCCTATACCA‑‑CCTCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGaa < 2:118112/149‑1 (MQ=255)
gATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAGGGCCAATCAGGAACTCCTGACCGCCGacc > 1:580585/1‑147 (MQ=255)
gCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCg > 1:660088/1‑149 (MQ=255)
gtaCCTGATTGCCCGGCACACAAACTGCAAATAAAATGGTGAGTGGGATAAAAATCCGGCTTGCCTATAC‑‑CCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGa < 2:408258/147‑1 (MQ=255)
caCCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATAAGGAACTCCTGACCGCCGAAATTCGCCTGTAAACGAc > 2:370091/1‑149 (MQ=255)
caCCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAACGCTAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTACACGAc > 2:462206/1‑149 (MQ=255)
aCCCTGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCt < 1:553405/149‑1 (MQ=255)
ccGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGc > 2:583298/1‑149 (MQ=255)
acacaAACAGGAACTAAAATGGGGAGTGGGATAAAAAGCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGc < 2:119425/149‑1 (MQ=255)
acacaAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTacc > 2:271988/1‑147 (MQ=255)
acaAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGa < 1:579931/149‑1 (MQ=255)
acaAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACAGACGCACTTCGCCTGTAGACGACTACGAGCCTGCTTAGCGa > 1:569466/1‑149 (MQ=255)
aaCATCAATCAAAATGTGCAGAGGGATAAACATCCGGCTGGCCTACACCA‑‑CCGCCGAATGTCCCTTCAGCCACGCCGGATCAAGGCCAATCAGCAACGCCTGTCCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATgg < 2:312897/149‑1 (MQ=255)
cAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGAGACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGTTCAAGGCCAATCAGGAACTCCGGACCGCCGAACTTCGCCTGTAAACGCCTCCGAGCCTGCTTAGCGATGGGc < 2:648676/149‑1 (MQ=255)
aGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGCACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCg > 1:280883/1‑149 (MQ=255)
aGCAATTAAAATGGTGAGTGGGATAAAAATCAAGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACAGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCg > 1:282450/1‑149 (MQ=255)
aTTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTaa > 1:548031/1‑149 (MQ=255)
tAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAAAATCGCGTGTAATCGACTACGAGCCCACTTAGCGATGGGCGTTAAAc > 1:200446/1‑149 (MQ=255)
aGTGGGATAAAAATCAGGCTGGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCatgat < 2:630871/149‑1 (MQ=255)
gCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTGTAATCACCCGTGGCAt < 1:642612/149‑1 (MQ=255)
cGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTGGCATTa > 2:731878/1‑149 (MQ=255)
||
AACAGATTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCACCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTGGCATTA > NC_000913_3_pae_tpiA/2173216‑2173503
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
