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 |
|
A1 F8 I0 R2
|
422 |
46.8 |
3726540 |
94.7% |
3529033 |
61.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,927,287 |
T→C |
100% |
L45P (CTT→CCT) |
yobB → |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,927,287 | 0 | T | C | 87.5%
| 64.0
/ 1.2
| 24 | L45P (CTT→CCT) | yobB | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (1/2); new base C (8/13); total (9/15) |
| 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 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
ATCATCTGGAGTTTGTGAGGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGCTTTCTTTACTGGGGTGTGATTATTCGCGACGTGCCCTTCCTGCCCCACCCGATCTCTCACTGT > W3110S.gb/1927224‑1927349
|
atcatcTGGAGTTTGTGAGGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGccttctt < 1:2121064/69‑1 (MQ=255)
gTTTGTGAGGGCCGCCGCCAGGCGACAATGTCAGCTGTTAGTTTTTCCATCGCCTTCTTTACTGGGgtgt < 1:3495237/70‑1 (MQ=255)
tttGTGAGGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGcctt < 1:1135058/55‑1 (MQ=255)
tttGTGAGGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGcctt < 1:3298881/55‑1 (MQ=255)
tttGTGAGGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGcctt < 1:591030/55‑1 (MQ=255)
tgtgAGGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGCCTTCTTTACTGGGGTGTGat < 1:1635841/70‑1 (MQ=255)
gtgAGGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGCCTTCTTTACTGGGGTGTGat < 1:1203792/69‑1 (MQ=255)
tgAGGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGCTTTCTTTACTGGGGTGTGatta < 1:1219626/70‑1 (MQ=255)
tgAGGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGCTTTCTTTACTGGGGTGTGatta < 1:612698/70‑1 (MQ=255)
ggCAACAATGTCAGCTGTTAGTTTTTCCATCGCCTTCTTTACTGGGGTGTGATTATTCGCGACGTGCCCtt < 1:3104580/71‑1 (MQ=255)
ggCAACAATGTCAGCTGTTAGTTTTTCCATCGCCTTCTTTACTGGGGTGTGATTATTCGCGACGTGCCCtt < 1:3570594/71‑1 (MQ=255)
gCAACAATGTCAGCTGTTAGTTTTTCCATCGctttctt < 1:3372274/38‑1 (MQ=255)
gCAACAATGTCAGCTGTTAGTTTTTCCATCGctttctt < 1:3319595/38‑1 (MQ=255)
gCAACAATGTCAGCTGTTAGTTTTTCCATCGctttctt < 1:2575899/38‑1 (MQ=255)
gCAACAATGTCAGCTGTTAGTTTTTCCATCGctttctt < 1:2571495/38‑1 (MQ=255)
gCAACAATGTCAGCTGTTAGTTTTTCCATCGctttctt < 1:900648/38‑1 (MQ=255)
gCAACAATGTCAGCTGTTAGTTTTTCCATCGctttctt < 1:97377/38‑1 (MQ=255)
aacaaTGTCAGCTGTTAGTTTTTCCATCGCTTTCTTTACTGGGGTGTGATTATTCGCGACGTGCCCTTCCt > 1:3362366/1‑71 (MQ=255)
aaTGTCAGCTGTTAGTTTTTCCATCGCCTTCTTTACTGGGGTGTGATTATTCGCGACGTGCCCTTcc > 1:570021/1‑67 (MQ=255)
aaTGTCAGCTGTTAGTTTTTCCATCGCCTTCTTTACTGGGGTGTGATTATTCGCGACGTGCCCTTcc > 1:595566/1‑67 (MQ=255)
aaTGTCAGCTGTTAGTTTTTCCATCGCCTTCTTTACTGGGGTGTGATTATTCGCGACGTGCCCTTCCTGcc > 1:2593090/1‑71 (MQ=255)
cTGTTAGTTTTTCCATCGCCTTCTTTACTGGGGTGTGATTATTcgc < 1:249299/46‑1 (MQ=255)
ttAGTTTTTCCATCGCCTTCTTTACTGGGGTGTGATTATTcgc < 1:1192645/43‑1 (MQ=255)
ttAGTTTTTCCATCGCCTTCTTTACTGGGGTGTGATTATTcgc < 1:2702015/43‑1 (MQ=255)
ttAGTTTTTCCATCGCCTTCTTTACTGGGGTGTGATTATTcgc < 1:1917852/43‑1 (MQ=255)
ttAGTTTTTCCATCGCCTTCTTTACTGGGGTGTGATTATTCGCGACGTGCCCTTc < 1:460816/55‑1 (MQ=255)
tAGTTTTTCCATCGCCTTCTTTACTGGGGTGTGATTATTCGCGACGTGCCCTTCCTGCCCCACCCGAtctc > 1:1775006/1‑71 (MQ=255)
aGTTTTTCCATCGCCTTCTTTACTGGGGTGTGATTATTCGCGACGTGCCCTTCCTGCCACACCCGAtctct > 1:1515168/1‑71 (MQ=255)
tttCCATCGCCTTCTTTACTGGGGTGTGATTATTCGCGACGTGCCCTTCCTGCCCCACCCGATCTCTCAc > 1:3095877/1‑70 (MQ=255)
tCCATCGCCTTCTTTACTGGGGTGTGATTATTCGCGACGTGCCCTTCCTGCCCCACCCGATCTCTCACTGt > 1:3698364/1‑71 (MQ=255)
tCCATCGCCTTCTTTACTGGGGTGTGATTATTCGCGACGTGCCCTTCCTGCCCCACCCGATCTCTCACTGt > 1:805038/1‑71 (MQ=255)
ccATCGCCTTCTTTACTGGGGTGTGATTATTCGCGACGTGCCCTTCCTGCCCCACCCGATCTCTCACTGt < 1:2751007/70‑1 (MQ=255)
ccATCGCCTTCTTTACTGGGGTGTGATTATTCGCGACGTGCCCTTCCTGCCCCACCCGATCTCTCACTGt < 1:1422004/70‑1 (MQ=255)
cGCCTTCTTTACTGGGGTGTGATTATTCGCGACGTGCCCt < 1:1889786/40‑1 (MQ=255)
|
ATCATCTGGAGTTTGTGAGGGCCGCCGCCAGGCAACAATGTCAGCTGTTAGTTTTTCCATCGCTTTCTTTACTGGGGTGTGATTATTCGCGACGTGCCCTTCCTGCCCCACCCGATCTCTCACTGT > W3110S.gb/1927224‑1927349
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
