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 |
|
A17 F109 I0 R1
|
32 |
27.2 |
584098 |
96.5% |
563654 |
139.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
CP000730 |
463,014 |
C→A |
66.9% |
E47* (GAA→TAA) |
USA300HOU_0437 ← |
hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | CP000730 | 463,014 | 0 | C | A | 66.9%
| 18.7
/ 14.1
| 24 | E47* (GAA→TAA) | USA300HOU_0437 | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base C (3/5); new base A (5/11); total (8/16) |
| 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 |
TCTTGTTTAGCTTTGTTGATAATGTCTTTGATTGAATGTAGTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTCTAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTACCATTGCCGTAGCTACTAAAACCTTTTTAAAT > CP000730/462881‑463147
|
tCTTGTTTAGCTTTGTTGATAATGTCTTTGATTGAATGTAGTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATaagaa > 2:76821/1‑140 (MQ=255)
ttgttgATAATGTCTTTGATTGAATGTAGTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGcatcatc < 1:136444/140‑1 (MQ=255)
tgttgATAATGTCTTTGATTGAATGTAGTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGcatcatca > 2:217509/1‑140 (MQ=255)
gttgATAATGTCTTTGATTGAATGTAGTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTCTAAGAAGTTTGcatcatcat < 1:49196/140‑1 (MQ=255)
gttgATAATGTCTTTGATTGAATGTAGTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGcatcatcat < 1:248657/140‑1 (MQ=255)
ttgaATGTAGTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTCTAAGAAGTTTGCATCATCATGTAGTACGAGTCCAttt > 2:261415/1‑140 (MQ=255)
gtcgtacTTTATCGGCGAATGCTGATTTTCAGTTGTCTTTTGTAGCTTTGTCAGCATTCTTATCTAATAACATATCAATATAACTTAATTCATTTTCTAAGAAGTTTGCATCATCATGTAGTACGAGTCTATTTTGAGaa < 2:153839/134‑1 (MQ=255)
aGTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTCGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATa > 1:186916/1‑140 (MQ=255)
gTCCTTTATCGTGGAAGTATGATTTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATaa < 1:150042/140‑1 (MQ=255)
tATGATCTGAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAAGACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTg > 2:214253/1‑140 (MQ=255)
ttcgatcctcgTCTGCATTCTTATCTAATAACACGCTAATATAACTTAATTCATTTTATAAGCAGTTTGCATCATCATGTACTACGAGTCCATTTTGATAATAAACTTTCTCATCTGCTTCATTACCATATCCAACAACg < 2:189059/130‑1 (MQ=255)
ggTCAGTATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCt < 2:270695/140‑1 (MQ=255)
ggTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCt < 1:283053/140‑1 (MQ=255)
tCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTaa < 1:76821/140‑1 (MQ=255)
aTTTTTATCTAATAACACATCAATATAACTTAATTCATGTTCTAAGAAGTTTACATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCGTATGCAACAAGGCCAGTTGCCAAAacac < 1:184637/140‑1 (MQ=255)
tATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTAcc < 1:214253/140‑1 (MQ=255)
aataaCACATCATTATCACTTAATTCATGTTCTAAGAAGTTTGCTTCATCATGTAGTACGAGTCCATTTTGAGAATAAACGGTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCGAAAACACCTACCATTGc < 1:129434/140‑1 (MQ=255)
ataaCACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTACCATTGcc < 2:252526/140‑1 (MQ=255)
aaCACATCAATATAACTAAATTCATGTTCTAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACACCAGTCGCTAAAACACCTCCCATTGCCGt > 2:52966/1‑140 (MQ=255)
aaCTTAATTCATGTTCTAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTACCATTGCCGTAGCTACTaaaaac > 1:256364/1‑138 (MQ=255)
aCTTAATTCATGTTATAAGAAGTTTGCATCATCATGTATTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGAGTACCCTATCCAACAACGCCAGTTGCTAAAACACCTACCATTGCCGTAGCTACTAAAACCt < 1:148565/140‑1 (MQ=255)
aaTTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTACCATTGCCGTAGCTACTAAAACCttttt > 2:184461/1‑140 (MQ=255)
aTTCATGTTCTAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTACCATTGCCGTAGCTACTAAAACCTTTTTa < 1:256584/140‑1 (MQ=255)
taTGTTATAAGAAGGTTGCATCATCATGTAGTACGAGTCCCTTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTACCATTGCCGTAGCTACTAAAACCTTTTTAAAt < 2:141551/139‑1 (MQ=255)
|
TCTTGTTTAGCTTTGTTGATAATGTCTTTGATTGAATGTAGTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTCTAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTACCATTGCCGTAGCTACTAAAACCTTTTTAAAT > CP000730/462881‑463147
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
