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 |
|
A6 F1 I0 R1
|
2892 |
75.3 |
5698161 |
66.1% |
3766484 |
59.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
821,535 |
G→T |
23.5% |
intergenic (‑72/+382) |
ldrA ← / ← ldrC |
toxic polypeptide, small/toxic polypeptide, small |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 821,535 | 0 | G | T | 23.5%
| 117.1
/ 20.6
| 51 | intergenic (‑72/+382) | ldrA/ldrC | toxic polypeptide, small/toxic polypeptide, small |
| Reads supporting (aligned to +/- strand): ref base G (16/23); new base T (4/8); total (20/31) |
| Fisher's exact test for biased strand distribution p-value = 7.43e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01 |
GCCGCCTTGTTGTAATGACAACATTTTGCGGCTATTCTTGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAGGTTTTACCTCTCAACGTGCGGGGGTTTTCTCT > minE/821493‑821604
|
gccgccTTGTTGTAATGACAACATTTTGCGGCTATTCTTGAAGTG‑TCTGGTTTCAAAATTAGCCCCCGTTc < 1:3016986/71‑1 (MQ=14)
cgccTTGTTGTAATGACAACATTTTGCGGCTATTCTTGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCtg < 1:4219937/71‑1 (MQ=34)
ccTTGTTGTAATGACAACATTTTGCGGCTATTCTTGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCtgtt > 1:4893763/1‑71 (MQ=34)
ccTTGTTGTAATGACAACATTTTGCGGCTATTCTTGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCtgt > 1:589954/1‑70 (MQ=35)
cTTGTTGTAATGACAACATTTTGCGGCTATTCTTGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCtgttg < 1:2806379/71‑1 (MQ=34)
cTTGTTGTAATGACAACATTTTGCGGCTATTCTTGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCtgttg < 1:1714718/71‑1 (MQ=34)
tgttgtAATGACAACATTTTGCGGCTATTCTTGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCtgtt < 1:940135/68‑1 (MQ=35)
gttgtAATGACAACATTTTGCGGCTATTCTTGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCtgttgt > 1:374624/1‑69 (MQ=35)
gtAATGACAACATTTTGCGGCTATTCTTGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAgg < 1:3061370/70‑1 (MQ=35)
gtAATGACAACATTTTGCGGCTATTCTTGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAgg < 1:4660628/70‑1 (MQ=35)
aTGACAACATTTTGCGGCTATTCTTGAATTGTTCTGG‑TTCAAGATTAGCCCCCGTTCTGTTGTCAGGttgt < 1:155652/71‑3 (MQ=11)
aTGACAACATTTTGCGGCTATTCTTGAATTGTTCTGG‑TTCAAGATTAGCCCCCGTTCTGTTGTCAGGttg > 1:3273401/1‑69 (MQ=11)
aTGACAACATTTTGCGGCTATTCTTGAATTGTTCTGG‑TTCAAGATTAGCCCCCGTTCTGTTGTCAGGttg > 1:1338530/1‑69 (MQ=11)
aTGACAACATTTTGCGGCTATTCTTGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAGGtttt < 1:1909009/71‑1 (MQ=34)
aTGACAACATTTTGCGGCTATTCTTGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAGGttt > 1:4937720/1‑70 (MQ=35)
aTGACAACATTTTGCGACTATTCTTGAATTGTTCTGG‑TTCAAGATTAGCCCCCGTTCTGTTGTCAGGttgt < 1:3754784/71‑3 (MQ=11)
tGACAACATTTTGCGGCTATTCTTGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAg < 1:2893014/65‑1 (MQ=35)
aacaTTTTGCGGCTATTCTTGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAGGTTTTACctc > 1:762428/1‑71 (MQ=34)
aacaTTTTGCGGCTATTCTTGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAGGTTTTACctc > 1:1018866/1‑71 (MQ=34)
aacaTTTTGCGGCTATTCTTGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAGGTTTTACctc > 1:4271205/1‑71 (MQ=34)
acaTTTTGCGGCTATTCTTGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAGGTTTTACctc < 1:5348219/70‑1 (MQ=35)
caTTTTGCGGCTATTCTTGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAGGTTTTACctc < 1:2749988/69‑1 (MQ=35)
aTTTTGCGGCTATTCTTGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAGGTTTTACCtctc > 1:4164091/1‑70 (MQ=35)
ttGCGGCTATTCTTGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAGGTTTTACCTCTCAACg > 1:1730592/1‑71 (MQ=34)
cGGCTATTCTTGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAGGTTTTACCTCTCAACGt < 1:753174/69‑1 (MQ=35)
gCTATTCTTGAATTG‑TTCTGTTTCAAGATTAGCCCCCGTTCTGTTGTCAGGTTGTACct < 1:1570890/59‑1 (MQ=11)
gCTATTCTTGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAGGTTTTACCTCTCAACGTg < 1:1546760/68‑1 (MQ=35)
gCTATTCTTGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAGGTTTTACCTCTCAACGTg < 1:1553419/68‑1 (MQ=35)
gCTATTCTTGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAGGTTTTACCTCTCAACGTg < 1:3472529/68‑1 (MQ=35)
gCTATTCTTGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAGGTTTTACCTCTCAACGTg < 1:2987968/68‑1 (MQ=35)
gCTATTCTTGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAGGTTTTACCTCTCAACGTg < 1:4483300/68‑1 (MQ=35)
cTATTCTTGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAGGTTTTACCTCTCAACGTGCggg > 1:1886804/1‑71 (MQ=34)
cTATTCTTGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAGGTTTTACCTCTCAACGTGCgg < 1:175163/70‑1 (MQ=35)
tATTCTTGAATTGTTCTGG‑TTCAAGATTAGCCCCCGTTCTGTTGTCAGGttgt < 1:3070741/53‑3 (MQ=11)
ttCTTGAATTGTTCTGG‑TTCAAGATTAGCCCCCGTTCtgtt < 1:148253/41‑1 (MQ=9)
ttCTTGAATTGTTCTGG‑TTCAAGATTAGCCCCCGTTCTGTTGTCAg < 1:4106768/46‑1 (MQ=11)
ttCTTGAATTGTTCTGG‑TTCAAGATTAGCCCCCGTTCTGTTGTCAg < 1:281134/46‑1 (MQ=11)
ttCTTGAATTGTTCTGG‑TTCAAGATTAGCCCCCGTTCTGTTGTCAGGTTGTACCTCTCAACGTGCGGGGGt > 1:1870206/1‑71 (MQ=11)
ttCTTGAATTGTTCTGG‑TTCAAGATTAGCCCCCGTTCTGTTGTCAGGTTGTACCTCTCAACGTGCGGGGGt > 1:1290788/1‑71 (MQ=11)
ttCTTGAATTG‑TTCAGGTTCAAGATTAGCCCCCGTTCTGTTGTCAGGTTGTACCTCTCaa < 1:1278158/60‑1 (MQ=11)
tCTTGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCa < 1:3543476/44‑1 (MQ=38)
tCTTGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAGGTTTTACCTCTCAACGTGCGGGGGtt > 1:5693301/1‑71 (MQ=34)
cTTGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAGGTTTTAc > 1:2826786/1‑51 (MQ=35)
ttGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAgg > 1:1133119/1‑44 (MQ=38)
ttGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAgg > 1:1922856/1‑44 (MQ=38)
ttGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCATGTTTTACCTCTCAACGTGCGGGGGtt < 1:3721880/69‑1 (MQ=25)
ttGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAGGttt < 1:1544248/47‑1 (MQ=38)
ttGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAGGtt > 1:640946/1‑46 (MQ=38)
ttGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAGGTTTTa < 1:3133947/49‑1 (MQ=38)
ttGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAGGTTTTACCTCTCAACGTGCGGGGGttt > 1:756040/1‑70 (MQ=35)
aGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAGGTTTTACCTCTCAACGTGCGGGGGTTTTctct < 1:459328/71‑1 (MQ=34)
gtg‑tCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAGGTTTTAc > 1:759367/1‑45 (MQ=38)
|
GCCGCCTTGTTGTAATGACAACATTTTGCGGCTATTCTTGAAGTG‑TCTGGTTTCAAGATTAGCCCCCGTTCTGTTGTCAGGTTTTACCTCTCAACGTGCGGGGGTTTTCTCT > minE/821493‑821604
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
