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 F26 I1 R1
|
16 |
35.0 |
1240938 |
93.0% |
1154072 |
143.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913_3_pae_tpiA |
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_3_pae_tpiA | 2,173,361 | 0 | C | . | 96.9%
| 134.7
/ ‑1.5
| 33 | 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 (1/0); new base . (18/13); total (19/14) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01 |
| * | NC_000913_3_pae_tpiA | 2,173,362 | 0 | C | . | 96.9%
| 135.1
/ ‑2.5
| 33 | 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 (1/0); major base . (18/13); minor base T (0/1); total (19/14) |
| Fisher's exact test for biased strand distribution p-value = 4.38e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GAACAGATTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCA‑GCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCACCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCC > NC_000913_3_pae_tpiA/2173215‑2173494
||
aaaCAGATAACCACGATGCACGACGACCGCGATCGCCACGAAGAAGCCGATGGTGGCAAGAGCACCAAACAGCA‑ACACCGGATTACCCGGCACACAAACAGCAATAAAAATGTGTAGTCGGATAAAAATCAGGCTTGCGGATACCAccc > 2:18902/2‑149 (MQ=255)
aGATTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCA‑GCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATaccaccgccgt < 1:135787/149‑6 (MQ=255)
cACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCA‑GCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGACCGTGGGGTACAAATCAGGCTTGCCGATACCA‑‑CCGCCGTCTGTccc > 2:130057/1‑149 (MQ=255)
cACGGCGACCGCCATCGCCACGAAGAAGACGAGGGGGACAAGCTGGCCAAGCGGCA‑GCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑ACGCCGTATGTCCCAgcagca > 1:89426/1‑149 (MQ=255)
ccGGCGACCGCGATCGGCACGAAGAAGCCGAGGGTGGCAAGATCGCCAAACGGCA‑GCACCTGATTACCCGGCACACAAACAGCAATGAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCaa < 2:548327/148‑1 (MQ=255)
cGACCGCCATAGCCACGAAGAAGCCGCTGGTGGCAAGACCGCCAAACGGCA‑GCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATAC‑‑CCCCGCCGCATGTCCCAGCATCAACGcc > 2:284145/1‑149 (MQ=255)
gCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCA‑GGACCTGATTACCCGGCACACAAACAGCAATTAAAAGGGGGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATc < 1:284145/149‑1 (MQ=255)
aTCGCCACGAAGAAGCCGATGGTGGCAAGACCGCCAAACGGCA‑GCCCATGATTACCCGGCACACAAACAGCAATTAAAATGGTGGGCTCGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAg < 1:518979/149‑1 (MQ=255)
tCGCCACGAAGAAGCCGAGGGTGGCAAGATCGCCAAACGGCA‑GCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAgg < 1:430688/149‑1 (MQ=255)
cACGAATAATCTGATGGTGCCATATACTCCAAACGGCA‑GCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCaa > 2:601477/1‑149 (MQ=255)
cACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCA‑GCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCaa > 1:526623/1‑149 (MQ=255)
aCGAAGAAGCTGTTGGTGGCAAGATCGCCAAACGGCA‑GCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAAt > 2:149700/1‑149 (MQ=255)
aCGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCA‑GCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAAt < 1:149700/149‑1 (MQ=255)
cGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCA‑GCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAAGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCCACGCCGCATCAATGCCAATc > 2:239796/1‑149 (MQ=255)
aaataagCCGATGGGGGCAAGATCGCCAAAGGGCA‑GCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCa < 2:554247/145‑1 (MQ=255)
aagaagCCGATGGTGGCAAGATCGCGAAACGGCA‑GCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAg < 2:464709/149‑1 (MQ=255)
aagCCGATGGTGGCAAGATCGCCAAACGGCA‑GCACCTGATTACCCGGCACACAGACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGaa > 1:370381/1‑149 (MQ=255)
aagCCGATGGTGGCAAGATCGCCAAACGGCA‑GCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGaa < 2:248517/149‑1 (MQ=255)
gCCGATGATGGCAAGATCGCCCACCAGAATGCACC‑GATTACCCGGCACACAAACAGCCATTAAAATGGTAAGTAGGACAAAAATCAGCCTTGCCGATTTCA‑‑CCGCCCTATCTCCCACCAGCAACTCCCGACCACGCCCCATCTGCAAcc > 2:135383/1‑148 (MQ=255)
aTGGTGGCAAGATCGCCAAACGGCA‑GCACCTGAGTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGGCCCAGCAGCAGCGCCGGATCAAGGCCAATCAGGAACTCCTg > 2:3636/1‑149 (MQ=255)
tggtggCAAGATCGCCAAACGGCA‑GCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGa > 1:465352/1‑149 (MQ=255)
cAAACGGCA‑GCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGcc > 1:77589/1‑149 (MQ=255)
gATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGa > 2:23876/1‑149 (MQ=255)
cccGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGa < 1:506405/90‑1 (MQ=255)
cccGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGa > 2:506405/1‑90 (MQ=255)
ccGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCTGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGc > 1:608964/1‑149 (MQ=255)
ccGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGc > 1:80957/1‑149 (MQ=255)
acaAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTa < 2:549440/145‑1 (MQ=255)
acaAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTa > 1:549440/1‑145 (MQ=255)
acaAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGa > 1:393453/1‑149 (MQ=255)
aGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCg > 2:418795/1‑149 (MQ=255)
gTGGGACAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCatgatg < 1:23876/149‑1 (MQ=255)
aaaaaTCAGGATTGCCGATAC‑‑GTTCGCCGTATGTCCCAGCAGCATCGCCGGATCAAGGCCAATCAGGAACTCCTGCCCGCCGAACTCCGCCTGTAAACGACGACGAGCCTGCTGAGCGATGGGCGTTAAACCATCCATGATGGGTTTaa < 2:580910/149‑1 (MQ=255)
aaTCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCa < 1:567726/149‑1 (MQ=255)
cAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCAccc < 1:601477/149‑1 (MQ=255)
||
GAACAGATTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCA‑GCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCACCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCC > NC_000913_3_pae_tpiA/2173215‑2173494
|
| 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
