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 |
|
A7 F74 I1 R1
|
20 |
64.4 |
2271604 |
93.9% |
2133036 |
140.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913_3_hsa_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_hsa_tpiA | 2,173,361 | 0 | C | . | 95.7%
| 196.2
/ ‑0.0
| 47 | 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 (1/1); new base . (21/24); total (22/25) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.92e-01 |
| * | NC_000913_3_hsa_tpiA | 2,173,362 | 0 | C | . | 95.7%
| 196.0
/ ‑0.4
| 47 | 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 (1/1); new base . (21/24); total (22/25) |
| 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 |
CAGATTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGA‑TTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCACCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTGGCATTA > NC_000913_3_hsa_tpiA/2173218‑2173503
||
cAGATTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGA‑TTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAAGCTTGCCGATaccaccgccg > 1:359851/1‑145 (MQ=255)
aCGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGA‑TTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACAA‑‑CCGCCGTATGTGCca > 1:657726/1‑149 (MQ=255)
aCGAGGCACGGCGACCGTCATGGCTACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGA‑TTACCCGGCACACAAACAGCAATTAAAATGGTGAGTCGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCca < 1:66212/149‑1 (MQ=255)
cGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGA‑TTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCcag < 2:1126516/149‑1 (MQ=255)
gATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGA‑TTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGACTTGCCGATACCA‑‑CCGCCGTATGTCCcagc > 1:546722/1‑149 (MQ=255)
gATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGA‑TTACCCGGCACACAAACAGCAATTAAAATGGTGAACGGGATAAAAATCAAGCATCCCCATACCACCCCCCC‑‑ATGTCCcaac > 2:177993/1‑147 (MQ=255)
gACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGA‑TTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGTCGTATGTCCCAGCAGCAACGCCg < 2:130815/149‑1 (MQ=255)
gACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGA‑TTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCg < 2:694231/149‑1 (MQ=255)
gCCATCGCCACGAATAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGA‑TTACCCGGCACACAAACAGCAACTAAAATGGTGAGTGGTATAAAAACCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATc < 2:456578/149‑1 (MQ=255)
ccATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGA‑TTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCa > 2:725074/1‑149 (MQ=255)
aTCGGCACGAAGAAGCCGGTGGGGGCAAGAATGCCAAACGGCAGCACCTGA‑GTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCGTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAg < 2:1032302/149‑1 (MQ=255)
cACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGA‑TTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCaa > 1:869628/1‑149 (MQ=255)
aCGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGA‑TTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAAt < 1:187071/149‑1 (MQ=255)
gaagCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGA‑TTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAggc > 1:890494/1‑148 (MQ=255)
aagCAGATGTGGGCAAGGTCGCCAAACGGTAGCACCTGA‑TTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGAGAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCTACGCCGGATCAAGGCCAATCAGGaa < 2:1097620/149‑1 (MQ=255)
gCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGA‑TTACCCGGCACACAAACAGCAGTTAAAAGGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCACGGCCAATCAGGAACt > 1:542761/1‑149 (MQ=255)
gATGGTGGCAAGATCGCCAAACGGCAGCACCTGA‑TTACCCGGCACACAAACAGCAATTAACAGGCGGAGTGGGGTAAAAATCAGGATTGATGTTACCA‑‑CGGCCGTGTTGCCCATCAGCAACTCCGGATCAAGGCCAATAAGGAACTCCt > 2:526966/1‑149 (MQ=255)
gCAAGATCGCCAAACGGCAGCACCTGA‑TTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCTACGCCGGATCAAGGCCAATCACGAACTCCTGaccacc > 1:1046359/1‑149 (MQ=255)
gCAAGATCGCCAAACGGCAGCACCTGA‑TTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCa > 1:860828/1‑133 (MQ=255)
gCAAGATCGCCAAACGGCAGCACCTGA‑TTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCa < 2:860828/133‑1 (MQ=255)
gCAAGATCGCCAAACGGCAGCACCTGA‑TTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGAccgcc > 1:979965/1‑149 (MQ=255)
gATCGCCAAACGGCAGCACCTGA‑TTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAAc > 1:166355/1‑149 (MQ=255)
cGCCAAACGGCAGCACCTGA‑TTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTc < 2:607108/149‑1 (MQ=255)
gCCAAACGGCAGCACCTGA‑TTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCagcagc > 1:442989/1‑103 (MQ=255)
gCCAAACGGCAGCACCTGA‑TTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCagcagc < 2:442989/103‑1 (MQ=255)
ccAAACGGCAGCACCTGA‑TTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGCTCAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTAAGTCCCAGACGCAACGCCGGATACAGGCCAATACGGGACCCCTGACCGACGCACTCCga > 1:519918/1‑148 (MQ=255)
ccAAACGGCAGCACCTGA‑TTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGc < 2:618370/149‑1 (MQ=255)
ccAAACGGCAGCA‑CTGAGTGACGCATCACAGTAACAGCAATGAAAATCGTGAGTGGTATAAAAATCAGGCGTGCCGATACCA‑‑CCGCCGTATGTCCTAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTgcgc < 2:519918/149‑1 (MQ=255)
aCGGCAGCACCTGA‑TTGCCCGGCACACAAACAGCAATTAAAAGGGTGAGTGGGATAGAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGGCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGt < 2:983474/149‑1 (MQ=255)
a‑TTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTCCGCCTGTAAACGACAACGAg > 1:635850/1‑149 (MQ=255)
ttACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGc < 1:725074/149‑1 (MQ=255)
cGGCACACAAAAAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCt < 2:478832/149‑1 (MQ=255)
ccacaaaAACTGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGCAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTa < 1:170012/148‑1 (MQ=255)
acaAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGc < 2:446221/120‑1 (MQ=255)
acaAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGc > 1:446221/1‑120 (MQ=255)
aCAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATggg > 1:840062/1‑149 (MQ=255)
cAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGc < 1:526966/149‑1 (MQ=255)
aTTAAAATGGTGAGTGGGATAAAAATCAGGGTTGCCCATACAA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCAATGGGCGTTaa > 2:193107/1‑149 (MQ=255)
ttAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAAATCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTaaa < 2:637079/149‑1 (MQ=255)
aaTGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAAccat > 2:888732/1‑149 (MQ=255)
gTGGTATAAAAAACAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGCACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCatgatg < 1:228643/149‑1 (MQ=255)
tGGGCTAAACATCACGCTTGCGCATAC‑‑CCGCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACGTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATgg < 2:789121/149‑1 (MQ=255)
gATAAAATTCAGGCTTGCCGATACCA‑‑CTGTCGTATGTCCCAGCATCAACGCTGGTTCTAGTCCAATGGGGGACTCTTGACCGTCGGACTTTGCCTGTATATGGTTACGAGCCTGCTTTGCGGTTGGTGTTTAGCCATTCATGATGGGtt > 2:222173/1‑149 (MQ=255)
aaaaaTCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTaa < 2:979965/149‑1 (MQ=255)
aaaTCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGATTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATc < 2:890494/149‑1 (MQ=255)
aaaTCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATc > 2:487584/1‑149 (MQ=255)
ccGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTGGCAtt < 1:487584/149‑1 (MQ=255)
cGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCCTGGCCttt > 2:73898/1‑148 (MQ=255)
||
CAGATTTCCACGATGCACGGCGACCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGA‑TTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCACCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTGGCATTA > NC_000913_3_hsa_tpiA/2173218‑2173503
|
| 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
