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 |
|
A11 F56 I1 R1
|
155 |
65.2 |
3164312 |
95.9% |
3034575 |
99.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
3,840,547 |
T→C |
intergenic (+39/+2) |
yicS → / ← nepI |
putative periplasmic protein/putative transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 3,840,547 | 0 | T | C | 98.3%
| 195.8
/ ‑4.2
| 60 | intergenic (+39/+2) | yicS/nepI | putative periplasmic protein/putative transporter |
| Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (27/32); total (28/32) |
| Fisher's exact test for biased strand distribution p-value = 4.67e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.65e-01 |
TAATAATCAGAGCAATTATTGGGAAGCGTTGGGTAAGGTAGAATGCCCGGATATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGATATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCCGGACAACATCAACGGCGAAGTCAGACC > NC_000913/3840451‑3840638
|
taataaTCAGAGCAATTATTGGGAAGCGTTGGGTAAGGTAGAATGCCCGGATATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGACATc > 1:477693/1‑100 (MQ=255)
aataatCAGAGCAATTATTGGGAAGCGTTGGGTAAGGTAGAATGCCCGGATATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGACATCa < 1:263317/100‑1 (MQ=255)
taatCAGAGCAATTATTGGGAAGCGTTGGGTAAGGTAGAATGCCCGGATATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGATATCAgg > 1:837008/1‑100 (MQ=255)
aaacAGAGCAATTATGGGGAACCGTTGGGTAAGGTAGAATGCCCGGATAGGTAAGGACAGAAAAAGGTAATGACCAACGCTTCTTTAAATGACATccgca > 2:1417412/4‑96 (MQ=255)
agagCAATTATTGGGAAGCGTTGGGTAAGGTAGAATGCCCGGATATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATttc < 1:221493/100‑1 (MQ=255)
gagCAATTATTGGGAAGCGTTGGGTAAGGTAGAATGCCCGGATATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATttct > 1:54397/1‑100 (MQ=255)
gCAATTATTGGGAAGCGTTGGGTAAGGTAGAATGCCCGGATATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATttcttc < 1:921875/100‑1 (MQ=255)
cAATTATTGGGAAGCGTTGGGTAAGGTAGAATGCCCGGATATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCa > 1:761444/1‑100 (MQ=255)
aaTTATTGGGAAGCGTTGGGTAAGGTAGAATGCCCGGATATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCAt > 1:29253/1‑100 (MQ=255)
attattGGGAAGCGTTGGGTAAGGTAGAATGCCCGGATATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCAtt < 1:1461939/100‑1 (MQ=255)
tattGGGAAGCGTTGGGTAAGGTAGAATGCCCGGATATGTAAGCACAGCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCAtttt < 2:1009081/100‑1 (MQ=255)
ttGGGAAGCGTTGGGTAAGGTAGAATGCCCGGATATGTAAGAACAGCAACAACTACTGACCGCCGCTTCTTTACCTGACATCAGGATTTCTTCAttttn < 2:644729/99‑2 (MQ=255)
ttGGGAAGCGTTGGGTAAGGTAGAATGCCCGGATATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCa < 1:1184480/100‑1 (MQ=255)
ttGGGAAGCGTTGGGTAAGGTAGAATGCCCGGATATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCa < 1:1493528/100‑1 (MQ=255)
tGGGAAGCGTTGGGTAAGGTAGAATGCCCGGATATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCAc < 1:814572/100‑1 (MQ=255)
gggAAGCGTTGGGTAAGGTAGAATGCCCGGATATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATTGCTTCATTTTCAcc < 2:977216/100‑1 (MQ=255)
gCGTTGGGTAAGGTAGAATGCCCGGATATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCACCTTTGc < 1:1487201/100‑1 (MQ=255)
tGGGTAAGGTAGAATGCCCGGATATCTCAGAACAGAAACAACTCCTCACCCCCGCTTCTTTACCTGACATCACGATTTCCTCATTTTCACCTTTGCAGTa < 2:130308/100‑1 (MQ=255)
ggTAAGGTAGAATGCCCGGATATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAAc > 1:558174/1‑100 (MQ=255)
ggTAAGGTAGAATGCCCGGATATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAAc < 1:209190/100‑1 (MQ=255)
gTAAGGTAGAATGCCCGGATATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAAcc < 1:515836/100‑1 (MQ=255)
tAAGGTAGAATGCCCGGATATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAACca > 2:351248/1‑100 (MQ=255)
ggTAGAATGCCCGGATATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAACcaaca > 2:952342/1‑100 (MQ=255)
ggTAGAATGCCCGGATATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAACcaaca > 2:871745/1‑100 (MQ=255)
ggTAGAATGCCCGGATATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAACcaaca > 1:191637/1‑100 (MQ=255)
ggTAGAAGGCCCGGATATGTAAGAGCAGCCACAACTACTGACCAGCGAGTCTTTACCTGACATCAGGATTTCTTCAGTGTCAGCTTTGCAGTAACcaac > 2:704848/1‑99 (MQ=255)
gTAGAATGCCCGGATATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAACcaac < 1:1014321/98‑1 (MQ=255)
aGAATGCCCGGATATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATg > 2:233696/1‑100 (MQ=255)
aTGCCCGGATATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAg > 1:1132884/1‑100 (MQ=255)
aTGCCCGGAGATGTAAGAACAGCAACAACTACTGACCAACGCGTCTTTACCTGACATTAGGATTTCTTCATTGTCACCTTTGCAGTAACCAACAATGCAg > 2:1108069/1‑100 (MQ=255)
gCCCGGCTATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCCCCTTTGCAGTAACCAACAATGCAGTc > 2:1099514/1‑100 (MQ=255)
gccGGATATGTAAGAACAGCGACCACTACTGACCAACGCTTCTTTACCTGACATCAGGGTTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCa > 2:174171/2‑100 (MQ=255)
cGGATATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGc < 2:724752/100‑1 (MQ=255)
atGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACAt > 2:752398/1‑100 (MQ=255)
tGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATc > 1:522598/1‑100 (MQ=255)
tGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATc > 2:555049/1‑100 (MQ=255)
gTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCa > 2:663425/1‑100 (MQ=255)
aaGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAAt < 2:1509940/100‑1 (MQ=255)
gAACAGCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAAtgt > 1:943427/1‑100 (MQ=255)
aaCAGCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAAtgtg < 2:891410/100‑1 (MQ=255)
aaCAGCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAAtgtg < 1:952347/100‑1 (MQ=255)
aaCAGCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAAtgtg > 2:758219/1‑100 (MQ=255)
aCAGCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGc > 1:502217/1‑100 (MQ=255)
aGCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCCg < 1:662677/100‑1 (MQ=255)
gCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCCgg > 2:499366/1‑100 (MQ=255)
gCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCCgg < 1:1575335/100‑1 (MQ=255)
gCAACAACTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCCgg > 1:48614/1‑100 (MQ=255)
caacaaCTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCCGGa < 2:550424/100‑1 (MQ=255)
aacTACTGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCCGGacaac < 2:54397/100‑1 (MQ=255)
actactGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCCGGacaaca < 2:869551/100‑1 (MQ=255)
ctGACCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCCGGACAACATCaa > 1:463/1‑100 (MQ=255)
gACCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCCGGACAACATCAACg > 1:342487/1‑100 (MQ=255)
aCCAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCCGGACAACATCAACgg < 2:558173/100‑1 (MQ=255)
cAACGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTACCCAACACTGCAGTCAGCAACATCACTGTGCCGGACAACATCAACGGCg < 2:860920/100‑1 (MQ=255)
cGCTTCTTTACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCCGGACAACATCAACGGCGAAg < 2:343519/100‑1 (MQ=255)
ttgttttCCTGTCATCATTATTTCTTCATTTTCTCCTTCGCAGTAACCAACTAGGCAGTCAGCAACATCAATGTGCTGGACAACATCAACGGCGAAg < 2:210927/94‑1 (MQ=255)
ttcttTACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCCGGACAACATCAACGGCGAAGTCa < 2:1140944/100‑1 (MQ=255)
tcttTACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCCGGACAACATCAACGGCGAAGTCAg < 1:196665/100‑1 (MQ=255)
tttACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCCGGACAACATCAACGGCGAAGTCAGAc < 2:1219148/100‑1 (MQ=255)
ttACCTGACATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCCGGACAACATCAACGGCGAAGTCAGAcc < 1:907614/100‑1 (MQ=255)
|
TAATAATCAGAGCAATTATTGGGAAGCGTTGGGTAAGGTAGAATGCCCGGATATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGATATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCCGGACAACATCAACGGCGAAGTCAGACC > NC_000913/3840451‑3840638
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
