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 |
2,374,528 |
A→T |
26.8% |
C178S (TGC→AGC) |
tatD ← |
DNase, magnesium‑dependent |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,374,528 | 0 | A | T | 26.8%
| 88.6
/ 38.2
| 56 | C178S (TGC→AGC) | tatD | DNase, magnesium‑dependent |
| Reads supporting (aligned to +/- strand): ref base A (21/20); new base T (6/9); total (27/29) |
| Fisher's exact test for biased strand distribution p-value = 5.52e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.89e-01 |
GATCAGTAATTTTTCCGCCGGAATCAACGGCAAAAGTTCCCGCAGCTCCAGTCCGCGTCGTTCATCGCAAACCCAACCGGTAATGCCGATATAAATTCCATGCGCCACGCACGCCTGCATCTCTTCGCGTGTG > minE/2374460‑2374592
|
gATCAGTAATTTTTCCGCCGGAATCAACGGCAAAAGTTCCCGCAGCTCCAGTCCGCGTCGTTCATCGCaa < 1:2829695/70‑1 (MQ=255)
aTTTTTCCGCCGGAATCAACGGCAAAAGTTCCCGCAGCTCCAGTCCGCGTCGTTCATCGCAAACCCa < 1:892568/67‑1 (MQ=255)
aTTTTTCCGCCGGAATCAACGGCAAAAGTTCCCGCAGCTCCAGTCCGCGTCGTTCATCGCAAACCCAACCg > 1:459562/1‑71 (MQ=255)
aTTTTTCCGCCGGAATCAACGGCAAAAGTTCCCGCAGCTCCAGTCCGCGTCGTTCATCGCAAACCCAACCg > 1:2122918/1‑71 (MQ=255)
ttttCCGCCGGAATCAACGGCAAAAGTTCCCGCAGCTCCAGTCCGCGTCGTTCATCGCAAACCCAACCgg > 1:4014855/1‑70 (MQ=255)
tttCCGCCGGAATCAACGGCAAAAGTTCCCGCAGCTCCAGTCCGCGTCGTTCATCGCAAACCCaa > 1:4789500/1‑65 (MQ=255)
tttCCGCCGGAATCAACGGCAAAAGTTCCCGCAGCTCCAGTCCGCGTCGTTCATCGCAAACCCaa > 1:337177/1‑65 (MQ=255)
gccgGAATCAACGGCAAAAGTTCCCGCAGCTCCAGTCCGCGTCGTTCATCGCAAACCCAACCGGTAATGcc < 1:1942003/71‑1 (MQ=255)
cgGAATCAACGGCAAAAGTTCCCGCAGCTCCAGTCCGCGTCGTTCATCGCaa < 1:216411/52‑1 (MQ=255)
aaTCAACGGCAAAAGTTCCCGCAGCTCCAGTCCGCGTCGTTCATCGCAAACCCAAcc > 1:4629738/1‑57 (MQ=255)
aaTCAACGGCAAAAGTTCCCGCAGCTCCAGTCCGCGTCGTTCATCGCAAACCCAACCGGTaa > 1:5239245/1‑62 (MQ=255)
aaTCAACGGCAAAAGTTCCCGCAGCTCCAGTCCGCGTCGTTCATCGCAAACCCAACCGGTAAAGCCGata > 1:1593150/1‑70 (MQ=255)
tCAACGGCAAAAGTTCCCGCAGCTCCAGTCCGCGTCGTTCATCGCAAACCCAACCgg < 1:4400274/57‑1 (MQ=255)
aaCGGCAAAAGTTCCCGCAGCTCCAGTCCGCGTCGTTCATCGCAAAc > 1:375258/1‑47 (MQ=255)
aaCGGCAAAAGTTCCCGCAGCTCCAGTCCGCGTCGTTCATCGCAAAc > 1:832681/1‑47 (MQ=255)
aCGGCAAAAGTTCCCGCAGCTCCAGTCCGCGTCGTTCATCGCAAACCCAACCGGTAATGCCGATATAAAtt < 1:1523984/71‑1 (MQ=255)
cGGCAAAAGTTCCCGCAGCTCCAGTCCGCGTCGTTCATCGCAAACCCAACCGGTAATGCCGATATAAATTc < 1:599344/71‑1 (MQ=255)
cccGCAGCTCCAGTCCGCGTCGTTCATCGCAAACCCAACCGGTAATGCCGATATAAATTCCATGCGCcacg > 1:4840939/1‑71 (MQ=255)
cccGCAGCTCCAGTCCGCGTCGTTCATCGCAAACCCAACCGGTAATGCCGATATAAATTCCATGCGCcacg > 1:5587776/1‑71 (MQ=255)
ccGCAGCTCCAGTCCGCGTCGTTCATCGCAAACCCAACCGGTAATGCCGATATAAATTCCATGCGCcacgc < 1:4234168/71‑1 (MQ=255)
ccGCAGCTCCAGTCCGCGTCGTTCATCGCAAACCCAACCGGTAATGCCGATATAAATTCCATGCGCcacg > 1:1948260/1‑70 (MQ=255)
cGCAGCTCCAGTCCGCGTCGTTCATCGCAAACCCAACCGGTAATGCCGATATAAATTCCATGCGCcacgca > 1:2726293/1‑71 (MQ=255)
gCAGCTCCAGTCCGCGTCGTTCATCGCAAACCCAACCGGTAATGCCGATATAAATTCCATGCGCcacgc > 1:560556/1‑69 (MQ=255)
actgcgtcttttactggctcttcTCGCTAACCCaa < 1:5464082‑M1/12‑1 (MQ=255)
actgcgtcttttactggctcttcTCGCTAACCCaa < 1:3815422‑M1/12‑1 (MQ=255)
actgcgtcttttactggctcttcTCGCTAACCCAAc < 1:4304800‑M1/13‑1 (MQ=255)
actgcgtcttttactggctcttcTCGCTAACCCAAc < 1:5605238‑M1/13‑1 (MQ=255)
actgcgtcttttactggctcttcTCGCTAACCCAACCg < 1:296584‑M1/15‑1 (MQ=255)
actgcgtcttttactggctcttcTCGCTAACCCAACCg < 1:3476691‑M1/15‑1 (MQ=255)
actgcgtcttttactggctcttcTCGCTAACCCAACCGGt > 1:311424‑M1/24‑40 (MQ=255)
actgcgtcttttactggctcttcTCGCTAACCCAACCGGt > 1:5203469‑M1/24‑40 (MQ=255)
actgcgtcttttactggctcttcTCGCTAACCCAACCGGt > 1:4638053‑M1/24‑40 (MQ=255)
actgcgtcttttactggctcttcTCGCTAACCCAACCGGt > 1:221378‑M1/24‑40 (MQ=255)
actgcgtcttttactggctcttcTCGCTAACCCAACCGGTa < 1:315000‑M1/18‑1 (MQ=255)
actgcgtcttttactggctcttcTCGCTAAACCAACCGGTa < 1:4281735‑M1/18‑1 (MQ=255)
tgcgtcttttactggctcttcTCGCTAACCCAACCGGt > 1:1569305‑M1/22‑38 (MQ=255)
gcgtcttttactggctcttcTCGCTAACCCAACCGGt > 1:181526‑M1/21‑37 (MQ=255)
gCTCCAGTCCGCGTCGTTCATCGCAAACCCAACCGGt < 1:2417244/37‑1 (MQ=255)
gCTCCAGTCCGCGTCGTTCATCGCAAACCCAACCGGt < 1:2252053/37‑1 (MQ=255)
tcttttactggctcttcTCGCTAACCCAACCGGTaa < 1:4290858‑M1/19‑1 (MQ=255)
ccAGTCCGCGTCGTTCATCGCAAACCCAACCGGTAATGCCGATATaaa > 1:5040273/1‑48 (MQ=255)
cAGTCCGCGTCGTTCATCGCAAACCCAACCGGTAATGCCGATATAAATTCCATGCGCCACGCACGCCTGc < 1:4269696/70‑1 (MQ=255)
gTCCGCGTCGTTCATCGCAAACCCAACCGGTAATGCCGATATAAAt < 1:4933495/46‑1 (MQ=255)
gTCCGCGTCGTTCATCGCAAACCCAACCGGTAATGCCGATATAAATTc < 1:1785000/48‑1 (MQ=255)
cgcgTCGTTCATCGCAAACCCAACCGGTAATGCCGATATaa > 1:616850/1‑41 (MQ=255)
cgcgTCGTTCATCGCAAACCCAACCGGTAATGCCGATATaa > 1:1964198/1‑41 (MQ=255)
cgcgTCGTTCATCGCAAACCCAACCGGTAATGCCGATATAAATTCCAt > 1:3188071/1‑48 (MQ=255)
cgcgTCGTTCATCGCAAACCCAACCGGTAATGCCGATATAAATTCCATGCGCCACGCACGCCTGCATctct > 1:989722/1‑71 (MQ=255)
cgcgTCGTTCATCGCAAACCCAACCGGTAATGCCGATATAAATTCCATGCGCCACGCACGCCTGCATctct > 1:4817289/1‑71 (MQ=255)
gtcgtTCATCGCAAACCCAACCGGTAATGCCGATATAAATTCCATGCGCCACGCACGCCTGCATCTCTTc < 1:1363117/70‑1 (MQ=255)
ttCATCGCAAACCCAACCGGTAATGCCGATATAAATTCCATGCGCCACGCACGCCTGCATctct < 1:2836345/64‑1 (MQ=255)
ttCATCGCAAACCCAACCGGTAATGCCGATATAAATTCCATGCGCCACGCACGCCTGCATCTCTTCGCgt < 1:5316504/70‑1 (MQ=255)
aTCGCAAACCCAACCGGTAATGCCGATATAAATTCCATGCGCCACGCACGCCTGCATCTCTTCGCGtgtg < 1:2937724/70‑1 (MQ=255)
tCGCAAACCCAACCGGTAATGCCGATATAAATTCCATGCGCCACGCACGCCTGCATCTCTTcgc < 1:774073/64‑1 (MQ=255)
cGCAAACCCAACCGGTAATGCCGATATAAATTCCATGCGCcacg < 1:4241340/44‑1 (MQ=255)
cGCAAACCCAACCGGTAATGCCGATATAAATTCCATGCGCcacg < 1:340252/44‑1 (MQ=255)
cGCAAACCCAACCGGTAATGCCGATATAAATTCCATGCGCcacg < 1:3248664/44‑1 (MQ=255)
cGCAAACCCAACCGGTAATGCCGATATAAATTCCATGCGCcacg < 1:825951/44‑1 (MQ=255)
aaaCCCAACCGGTAATGCCGATATAAATTCCATGCGCCACGCACGcc > 1:4064237/1‑47 (MQ=255)
|
GATCAGTAATTTTTCCGCCGGAATCAACGGCAAAAGTTCCCGCAGCTCCAGTCCGCGTCGTTCATCGCAAACCCAACCGGTAATGCCGATATAAATTCCATGCGCCACGCACGCCTGCATCTCTTCGCGTGTG > minE/2374460‑2374592
|
| 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
