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 F1 I2 R1
|
777 |
59.2 |
2955938 |
92.5% |
2734242 |
106.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
3,432,994 |
(C)6→8 |
coding (567/1125 nt) |
smf ← |
DNA recombination‑mediator A family protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 3,432,988 | 1 | . | C | 92.2%
| 156.3
/ 6.1
| 51 | coding (573/1125 nt) | smf | DNA recombination‑mediator A family protein |
| Reads supporting (aligned to +/- strand): ref base . (2/2); new base C (23/24); total (25/26) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.48e-01 |
| * | NC_000913 | 3,432,988 | 2 | . | C | 83.7%
| 136.6
/ 20.0
| 51 | coding (573/1125 nt) | smf | DNA recombination‑mediator A family protein |
| Reads supporting (aligned to +/- strand): ref base . (4/4); new base C (20/21); total (25/26) |
| 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 |
GAACCACTACGCAAAGCCGCTTCCACCACCAGTACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCG‑‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTAAGGCTGCTTTATGCGCTACA > NC_000913/3432863‑3433111
||
gAACCACTACGCAAAGCCGCTTCCACCACCAGTACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCG‑‑cccccccctgttc < 2:704395/139‑8 (MQ=255)
aCGCAAAGCCGCTTCCACCACCAGTACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGAc < 2:693324/139‑1 (MQ=255)
aGCCGCTTCCACCACCAGTACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGT‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAg > 1:707017/1‑139 (MQ=255)
tACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGAcggc > 2:898693/1‑139 (MQ=255)
cacCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGAcggcgg > 1:1205005/1‑139 (MQ=255)
tACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGa > 2:1195045/1‑139 (MQ=255)
aCTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGaa < 2:1263687/139‑1 (MQ=255)
cTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAAt < 2:659045/139‑1 (MQ=255)
ttAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATg < 2:1205005/139‑1 (MQ=255)
aCCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTAt > 2:655713/1‑139 (MQ=255)
aCCACTGATAATGCGATTTCTCCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGTGCC‑‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGa > 1:329529/1‑120 (MQ=255)
aCCACTGATAATGCGATTTCATCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTAt > 2:997667/1‑139 (MQ=255)
aCCACGGATAATGCGATTTCTTCGTAGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGAGTGCC‑‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGa < 2:329529/120‑1 (MQ=255)
aCTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTaa < 2:1285265/139‑1 (MQ=255)
cTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCGCTCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAg > 2:1244731/1‑139 (MQ=255)
cTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAg > 1:232581/1‑139 (MQ=255)
cTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGACGAGAGC‑‑GCC‑‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTc > 1:421722/1‑139 (MQ=255)
tGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTa < 2:12870/136‑1 (MQ=255)
tGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTa > 1:12870/1‑136 (MQ=255)
tGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGt > 2:835090/1‑139 (MQ=255)
tGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTc > 1:732933/1‑139 (MQ=255)
tGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCG‑‑cccccccctgt > 2:1208349/1‑80 (MQ=255)
tGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCG‑‑cccccccctgt < 1:1208349/85‑6 (MQ=255)
gATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTc < 1:898693/139‑1 (MQ=255)
gATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGACGAGAGC‑‑GCC‑‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCa < 2:421722/139‑1 (MQ=255)
tAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCa < 2:1469559/139‑1 (MQ=255)
tAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCa < 1:997667/139‑1 (MQ=255)
aTGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAg > 2:400369/1‑100 (MQ=255)
aTGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAg < 1:400369/100‑1 (MQ=255)
aTGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCG‑‑cccccc > 2:1173982/1‑75 (MQ=255)
aTGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCG‑‑cccccc < 1:1173982/75‑1 (MQ=255)
aTGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCG‑‑cc > 1:779517/1‑71 (MQ=255)
aTGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCG‑‑cc < 2:779517/71‑1 (MQ=255)
cGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTccc < 2:867928/139‑1 (MQ=255)
cGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTccc < 1:655713/139‑1 (MQ=255)
ggAGATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGTCGGCgggg > 1:947630/1‑102 (MQ=255)
ggAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCgggg < 2:947630/102‑1 (MQ=255)
ttGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACg < 2:732933/139‑1 (MQ=255)
tAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCG‑‑cccccc < 1:394603/51‑1 (MQ=255)
tAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCG‑‑cccccc > 2:394603/1‑51 (MQ=255)
cAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCAttt < 1:835090/139‑1 (MQ=255)
ggggTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTAcc > 1:847631/1‑139 (MQ=255)
gggTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGAt > 1:1079410/1‑88 (MQ=255)
gggTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGAt < 2:1079410/88‑1 (MQ=255)
gggTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCG‑‑ccccccc > 1:484542/1‑43 (MQ=255)
gggTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCG‑‑ccccccc < 2:484542/44‑2 (MQ=255)
gTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGt > 1:7281/1‑139 (MQ=255)
ggAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTaa > 2:255940/1‑139 (MQ=255)
aaCATCGAGGGGAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCa > 2:231926/1‑99 (MQ=255)
aaCATCGAGGGGAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCa < 1:231926/99‑1 (MQ=255)
aaCATCGAGGGGAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTAAgg < 1:255940/139‑1 (MQ=255)
tCGAGGGGAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTc < 2:892856/93‑1 (MQ=255)
tCGAGGGGAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTc > 1:892856/1‑93 (MQ=255)
aGGGGAAATTCCGAGACGAGA‑‑GCGCTCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTAAGGCTGCttt < 1:1244731/139‑1 (MQ=255)
aGGGGAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTAAGGCTGCttt > 1:1233833/1‑139 (MQ=255)
ggAAATTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTAAGGCTGCTTTATg < 2:232581/139‑1 (MQ=255)
aaaTTCCGAGACGAGA‑‑GCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCaa < 2:356200/94‑1 (MQ=255)
aaaTTCCGAGACGAGA‑‑GCGC‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCaa > 1:356200/1‑94 (MQ=255)
aaTTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTc < 1:701573/51‑1 (MQ=255)
aaTTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTc > 2:701573/1‑51 (MQ=255)
aaTTCCGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTAAGGCTGCTTTATgcgc > 1:980356/1‑139 (MQ=255)
ccGAGACGAGA‑‑GCGCCCCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTAAGGCTGCTTTATGCGCTaca < 1:253897/139‑1 (MQ=255)
||
GAACCACTACGCAAAGCCGCTTCCACCACCAGTACACCTTTACTTAGACCACTGATAATGCGATTTCTTCGTGGGAAATTGTAAGCAAGGGGTGGAACATCGAGGGGAAATTCCGAGACGAGA‑‑GCG‑‑CCCCCCTGTTCAAGCAGACTGGCAGCCAGTCGGGCATGACGGCGGGGATGAATGGTATTAAGTCCATTCCCCAATACAGCAATGCTGACGCCATTTACCTGTAAGGCTGCTTTATGCGCTACA > NC_000913/3432863‑3433111
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
