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 |
|
A4 F1 I0 R1
|
70 |
84.3 |
4123603 |
97.0% |
3999894 |
62.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,359,192 |
G→A |
9.4% |
noncoding (1903/2905 nt) |
rrlA ← |
23S ribosomal RNA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,359,192 | 0 | G | A | 9.4%
| 160.0
/ 6.8
| 53 | noncoding (1903/2905 nt) | rrlA | 23S ribosomal RNA |
| Reads supporting (aligned to +/- strand): ref base G (23/25); new base A (2/3); total (25/28) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.84e-01 |
GGAATTTCGCTACCTTAGGACCGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAACCCCATCAATTAACCTTCCGGCACCGGG > minE/2359152‑2359260
|
ggAATTTCGCTACCTTAGGACCGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGcc < 1:54287/71‑1 (MQ=31)
aaTTTCGCTACCTTAGGACCGTTATAGTTACGGCCGCCATTTACCGGGGCTTCGATCAAGAGCTTCGCCtt < 1:330479/71‑1 (MQ=21)
aaTTTCGCTACCTTAGGACCGTTATAGTTACGGCCACCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCtt < 1:3910911/71‑1 (MQ=21)
aTTTCGCTACCTTAGGACCGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTg < 1:2221075/71‑1 (MQ=35)
aTTTCGCTACCTTAGGACCGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTg < 1:1837316/71‑1 (MQ=35)
tttCGCTACCTTAGGACCGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTg < 1:2890329/70‑1 (MQ=37)
tttCGCTACCTTAGGACCGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGc < 1:2356164/71‑1 (MQ=38)
tttCGCTACCTTAGGACCGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCATGc < 1:3789037/71‑1 (MQ=17)
tCGCTACCTTAGGACCGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCtt > 1:1995009/1‑67 (MQ=35)
tCGCTACCTTAGGACCGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCgg > 1:1051032/1‑71 (MQ=40)
tCGCTACCTTAGGACCGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCgg > 1:3504383/1‑71 (MQ=40)
tCGCTACCTTAGGACCGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCgg > 1:1129778/1‑71 (MQ=40)
tCGCTACCTTAGGACCGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCgg > 1:604651/1‑71 (MQ=40)
gCTACCTTAGGACCGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCt < 1:2594300/71‑1 (MQ=255)
cTACCTTAGGACCGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTa < 1:1676600/71‑1 (MQ=255)
cTACCTTAGGACCGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTa < 1:1552586/71‑1 (MQ=255)
ccTTAGGACCGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCt < 1:1096695/67‑1 (MQ=255)
ccTTAGGACCGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAAcc > 1:47942/1‑71 (MQ=255)
ccTTAGGACCGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAAcc > 1:374506/1‑71 (MQ=255)
ccTTAGGACCGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAAcc < 1:579514/71‑1 (MQ=255)
ccTTAGGACCGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAAcc > 1:83154/1‑71 (MQ=255)
ccTTAGGACCGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAAcc > 1:1111072/1‑71 (MQ=255)
ccTTAGGACCGTTATAGTTACGGCCGCCATTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTaa < 1:313215/69‑1 (MQ=255)
cTTAGGACCGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAAccc > 1:2203474/1‑71 (MQ=255)
cTTAGGACCGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAAccc > 1:3703257/1‑71 (MQ=255)
aGGACCGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAACCCCAt > 1:166549/1‑71 (MQ=255)
aGGACCGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAACCCCAt > 1:643194/1‑71 (MQ=255)
aGGACCGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAACCCCAt > 1:2492013/1‑71 (MQ=255)
ggACCGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAACCCCATc < 1:3633561/71‑1 (MQ=255)
ggACCGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAACCCCATc < 1:3107030/71‑1 (MQ=255)
gACCGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAACCCCATc > 1:472049/1‑70 (MQ=255)
gACCGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAACCCCATCa < 1:505478/71‑1 (MQ=255)
gACCGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAACCCCATCa < 1:500512/71‑1 (MQ=255)
aCCGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTaa < 1:2948673/62‑1 (MQ=255)
ccGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAACCCCATCAAt > 1:2992004/1‑71 (MQ=255)
cGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAACCCCATCaa > 1:4076101/1‑69 (MQ=255)
cGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAACCCCATCAAtt < 1:3266887/71‑1 (MQ=255)
cGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAACCCCATCAAt > 1:3237983/1‑70 (MQ=255)
cGTTATAGTTACGGCCGCCATTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAACCCCATCAAtt < 1:1656841/71‑1 (MQ=255)
cGTTATAGTTACGGCCGCCATTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAACCCCATCAAt > 1:1440001/1‑70 (MQ=255)
gTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAACCCCATCAATTa < 1:3080639/71‑1 (MQ=255)
gTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGAGCAAGAGCTTCGCCTTGCGGCTAACCCCATCAAtt < 1:1944055/70‑1 (MQ=255)
ttATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAACCCCATCa < 1:3469721/66‑1 (MQ=255)
ataGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAACCCCATCAATTAAcc > 1:3073077/1‑71 (MQ=255)
ataGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAACCCCATCAATTAAcc > 1:3598536/1‑71 (MQ=255)
ataGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAACCCCATCAATTAAcc > 1:2647659/1‑71 (MQ=255)
taGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAACCCCATCAATTAACCt < 1:2566815/71‑1 (MQ=255)
taGTTACGGCCGCCATTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAACCCCATCAATTAACCt > 1:619140/1‑71 (MQ=255)
gTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAACCCCATCAATTAACCTTc < 1:2408286/71‑1 (MQ=255)
ttACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAACCCCATCAATTAACCTTcc < 1:2181979/71‑1 (MQ=255)
ttACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAACCCCATCAATTAACCTTcc < 1:667563/71‑1 (MQ=255)
aCGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAACCCCATCAAt > 1:1011671/1‑60 (MQ=255)
aCGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAACCCCATCAATTAACCTTCCgg > 1:3789708/1‑71 (MQ=255)
ccgccgTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAACCCCATCAATTAACCTTCCGGCAcc > 1:546612/1‑71 (MQ=255)
ccgccgTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAACCCCATCAATTAACCTTCCGGCAcc > 1:258950/1‑71 (MQ=255)
gccgTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAACCCCATCAATTAACCTTCCGGCACCg > 1:3773029/1‑70 (MQ=255)
ccgTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAACCCCATCAATTAACCTTCCGGCAcc < 1:2492182/68‑1 (MQ=255)
cgTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAACCCCATCAATTAACCTTCCGGCACCggg < 1:3725030/70‑1 (MQ=255)
gTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAACCCCATCAATTAACCTTc > 1:3530052/1‑59 (MQ=255)
gTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAACCCCATCAATTAACCTTCCGGCACCggg > 1:3965606/1‑69 (MQ=255)
|
GGAATTTCGCTACCTTAGGACCGTTATAGTTACGGCCGCCGTTTACCGGGGCTTCGATCAAGAGCTTCGCCTTGCGGCTAACCCCATCAATTAACCTTCCGGCACCGGG > minE/2359152‑2359260
|
| 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
