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 F28 I1 R1
|
159 |
86.7 |
3040088 |
95.7% |
2909364 |
138.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,734,543 |
(C)8→10 |
coding (492/732 nt) |
pgeF ← |
polyphenol oxidase YfiH |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,734,535 | 1 | . | C | 93.2%
| 142.2
/ 3.5
| 44 | coding (500/732 nt) | pgeF | polyphenol oxidase YfiH |
| Reads supporting (aligned to +/- strand): ref base . (1/2); new base C (22/19); total (23/21) |
| Fisher's exact test for biased strand distribution p-value = 5.99e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01 |
| * | NC_000913 | 2,734,535 | 2 | . | C | 88.6%
| 133.6
/ 10.9
| 44 | coding (500/732 nt) | pgeF | polyphenol oxidase YfiH |
| Reads supporting (aligned to +/- strand): ref base . (2/3); new base C (21/18); total (23/21) |
| Fisher's exact test for biased strand distribution p-value = 6.58e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.49e-01 |
CGCCGAAAATTTGCTCAACACCCACGTTCGCCAGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGA‑‑ACCT‑‑‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACGCCAGCCAGCA > NC_000913/2734398‑2734663
||
cgccgAAAATTTGCTCAACACCCACGTTCGCCAGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGA‑‑ACCT‑‑‑cc < 1:395771/140‑1 (MQ=255)
aaTTTGCTCAACACCCACGTTCGCCAGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGA‑‑ACCT‑‑‑cccc‑‑ccccc < 1:1055461/140‑2 (MQ=255)
aaCACCCACGTTCGCCAGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGaa < 1:836260/140‑1 (MQ=255)
aCGTTCGCCAGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGt > 2:74880/1‑140 (MQ=255)
gCCAGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCCCCATGCTGAATGAAAGCTGCCCTTGCTTTAGCGTCTACTGCCATAAACCCCTCGCGACCCCCC‑‑‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCa < 1:604272/140‑1 (MQ=255)
aGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGA‑‑ACCT‑‑‑CCCC‑‑CCCCCACTCGAACGCGCGTGGACCAATTGc < 1:297771/140‑1 (MQ=255)
gACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGA‑‑ACCTC‑‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGc < 1:1135929/140‑1 (MQ=255)
aCGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGc < 1:378463/140‑1 (MQ=255)
cGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTTCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGcc > 2:124152/1‑140 (MQ=255)
ccGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGA‑‑ACCTCCCCCCC‑‑CCCCACTTCGAACGCGCGTGGTCCAATTGCCGGcc < 1:1478652/140‑1 (MQ=255)
gCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAAc < 1:867209/140‑1 (MQ=255)
aTACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGAtt < 1:501877/140‑1 (MQ=255)
tCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCa > 2:38534/1‑140 (MQ=255)
tCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCa > 2:1472185/1‑140 (MQ=255)
cATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAAc > 2:1403968/1‑140 (MQ=255)
cATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAAc > 2:1159911/1‑140 (MQ=255)
tGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAg > 1:550247/1‑140 (MQ=255)
aatgaaAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAAc > 1:259770/1‑140 (MQ=255)
aatgaaAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAAc > 1:880932/1‑140 (MQ=255)
tgaaAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCg > 2:187889/1‑140 (MQ=255)
tgaaAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCg > 2:1104011/1‑140 (MQ=255)
gaaAGCTTCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGt < 1:124152/140‑1 (MQ=255)
gaaAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGt < 2:259770/140‑1 (MQ=255)
aaaGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGtc < 2:550247/140‑1 (MQ=255)
aGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGA‑‑ACCT‑‑‑CCCCCACCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGtctc > 2:1032373/1‑140 (MQ=255)
gCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTctct > 2:2332/1‑140 (MQ=255)
gCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTcc > 1:1071672/1‑140 (MQ=255)
gCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTcc > 2:1385110/1‑140 (MQ=255)
ttGCTTTAGCGTCTACTGCCATAAACGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCa < 1:38534/140‑1 (MQ=255)
ttGCTTTAGCGTCTACTGCCATAAACGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCa < 1:1472185/140‑1 (MQ=255)
gCTTTAGCGTCTACTGCCATAAACGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACg > 1:5524/1‑140 (MQ=255)
aGCGTCTACTGCCATAAACGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTgc > 2:1516613/1‑140 (MQ=255)
gTCTACTGCCATAAACGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGca < 1:1159911/140‑1 (MQ=255)
gTCTACTGCCATAAACGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGca < 2:1071672/140‑1 (MQ=255)
gTCTACTGCCATAAACGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGca < 1:1403968/140‑1 (MQ=255)
gTCTACTGCCATAAACGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGca < 1:1385110/140‑1 (MQ=255)
aCTGCCATAAACGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGt < 1:187889/140‑1 (MQ=255)
cATAAACGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCAcc > 1:446937/1‑139 (MQ=255)
cATAAACGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACg > 1:527095/1‑140 (MQ=255)
aTAAACGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACgc < 1:490752/140‑1 (MQ=255)
aTAAACGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACgc < 1:1178160/140‑1 (MQ=255)
aaaCGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCCCTTCGAACCCCCGGGGACCAATTCCCGGCCCTAACCAGGCGGAAATATTTTCCGGTTTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACCCCTCCCCACAGCCCACgcca > 2:497743/1‑140 (MQ=255)
aaaCGCCTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGT‑CACgccag < 1:2332/140‑1 (MQ=255)
cTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACGCcagccagc > 2:932294/1‑140 (MQ=255)
cTCGCGA‑‑ACCTCC‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACGCcagccagc > 1:824963/1‑140 (MQ=255)
cTCGCGA‑‑ACCTC‑‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACGCCAGCCAGCa > 1:626284/1‑140 (MQ=255)
||
CGCCGAAAATTTGCTCAACACCCACGTTCGCCAGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGA‑‑ACCT‑‑‑CCCC‑‑CCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACGCCAGCCAGCA > NC_000913/2734398‑2734663
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
