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 |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,561,043 |
C→T |
33.2% |
H350H (CAC→CAT) |
evgS → |
hybrid sensory histidine kinase in two‑component regulatory system with EvgA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,561,043 | 0 | C | T | 33.2%
| 47.0
/ 29.5
| 60 | H350H (CAC→CAT) | evgS | hybrid sensory histidine kinase in two‑component regulatory system with EvgA |
| Reads supporting (aligned to +/- strand): ref base C (17/23); new base T (6/14); total (23/37) |
| Fisher's exact test for biased strand distribution p-value = 4.08e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-01 |
GGGACATTCTTAATATTATTACCTTGCAAACAGGTTTAAATTTTTCTCCGATCACCGTTTCACACAATATCCATGCTGGAACACAGCTTAGCCCCGGAGGATGGGATATAATACCTGGCGC > minE/1560979‑1561099
|
gggACATTCTTAATATTATTACCTTGCAAACAGGTTTAAATTTTTCTCCGATCACCGTTTCACACaa < 1:3190273/67‑1 (MQ=255)
cTTAATATTATTACCTTGCAAACAGGTTTAAATTTTTCTCCGATCACCGTTTCACACAATATCCATGc > 1:2090237/1‑68 (MQ=255)
cTTAATATTATTACCTTGCAAACAGGTTTAAATTTTTCTCCGATCACCGTTTCACACAATATCCATGc > 1:1139391/1‑68 (MQ=255)
cTTAATATTATTACCTTGCAAACAGGTTTAAATTTTTCTCCGATCACCGTTTCACACAATATCCATGc > 1:1550895/1‑68 (MQ=255)
cTTAATATTATTACCTTGCAAACAGGTTTAAATTTTTCTCCGATCACCGTTTCACACAATATCCATGc > 1:1757019/1‑68 (MQ=255)
ttattaCCTTGCAAACAGGTTTAAATTTTTCTCCGATCACCGTTTCACACAATATCCa < 1:1079813/58‑1 (MQ=255)
ttattaCCTTGCAAACAGGTTTAAATTTTTCTCCGATCACCGTTTCACACAATATCCa < 1:1964776/58‑1 (MQ=255)
ttattaCCTTGCAAACAGGTTTAAATTTTTCTCCGATCACCGTTTCACACAATATCCa < 1:413381/58‑1 (MQ=255)
ttattaCCTTGCAAACAGGTTTAAATTTTTCTCCGATCACCGTTTCACACAATATCCa < 1:1890835/58‑1 (MQ=255)
ttattaCCTTGCAAACAGGTTTAAATTTTTCTCCGATCACCGTTTCACACAATATCCa < 1:2116561/58‑1 (MQ=255)
ttattaCCTTGCAAACAGGTTTAAATTTTTCTCCGATCACCGTTTCACACAATATCCa < 1:1716603/58‑1 (MQ=255)
ttattaCCTTGCAAACAGGTTTAAATTTTTCTCCGATCACCGTTTCACACAATATCCa < 1:1376444/58‑1 (MQ=255)
ttattaCCTTGCAAACAGGTTTAAATTTTTCTCCGATCACCGTTTCACACAATATCCa < 1:850665/58‑1 (MQ=255)
ttattaCCTTGCAAACAGGTTTAAATTTTTCTCCGATCACCGTTTCACACAATATCCa < 1:2992425/58‑1 (MQ=255)
ttattaCCTTGCAAACAGGTTTAAATTTTTCTCCGATCACCGTTCCACACAATATCCa < 1:591888/58‑1 (MQ=255)
attaCCTTGCAAACAGGTTTAAATTTTTCTCCGATCACCGTTTCACACAATATc > 1:3335182/1‑54 (MQ=255)
attaCCTTGCAAACAGGTTTAAATTTTTCTCCGATCACCGTTTCACACAATATc > 1:717032/1‑54 (MQ=255)
attaCCTTGCAAACAGGTTTAAATTTTTCTCCGATCACCGTTTCACACAATATc > 1:1835321/1‑54 (MQ=255)
attaCCTTGCAAACAGGTTTAAATTTTTCTCCGATCACCGTTTCACACAATATc > 1:3101336/1‑54 (MQ=255)
attaCCTTGCAAACAGGTTTAAATTTTTCTCCGATCACCGTTTCACACAATATCCATGCTGGAACACAg > 1:2826853/1‑69 (MQ=255)
attaCCTTGCAAACAGGTTTAAATTTTTCTCCGATCACCGTTTCACACAATATCCATGCTGGAACACAg > 1:1975683/1‑69 (MQ=255)
attaCCTTGCAAACAGGTTTAAATTTTTCTCCGATCACCGTTTCACACAATATCCATGCTGGAACACAg > 1:608100/1‑69 (MQ=255)
attaCCTTGCAAACAGGTTTAAATTTTTCTCCGATCACCGTTTCACACAATATCCATGCTGGAACACAg > 1:1707230/1‑69 (MQ=255)
attaCCTTGCAAACAGGTTTAAATTTTTCTCCGATCACCGTTTCACACAATATCCATGCTGGAACACAg > 1:930588/1‑69 (MQ=255)
aCAGG‑TTAAATTTTTCTCCGATCACCGTTTCACACAATATCCATGCTGGAACACAGCTTAGCCCCggag < 1:2366251/69‑1 (MQ=255)
cAGGTTTAAATTTTTCTCCGATCACCGTTTCACACAATATCCATGCTGGAACACAGCTTAGCCCCggag < 1:1883466/69‑1 (MQ=255)
cAGGTTTAAATTTTTCTCCGATCACCGTTTCACACAATATCCATGCTGGAACACAGCTTAGCCCCggag < 1:2223725/69‑1 (MQ=255)
cAGGTTTAAATTTTTCTCCGATCACCGTTTCACACAATATCCATGCTGGAACACAGCTTAGCCCCggag < 1:791409/69‑1 (MQ=255)
cAGGTTTAAATTTTTCTCCGATCACCGTTTCACACAATATCCATGCTGGAACACAGCTTAGCCCCggag < 1:133349/69‑1 (MQ=255)
cAGGTTTAAATTTTTCTCCGATCACCGTTTCACACAATATCCATGCTGGAACACAGCTTAGCCCCggag < 1:3070791/69‑1 (MQ=255)
cAGGTTTAAATTTTTCTCCGATCACCGTTTCACACAATATCCATGCTGGAACACAGCTTAGCCCCggag < 1:2702613/69‑1 (MQ=255)
tttAAATTTTTCTCCGATCACCGTTTCACACAATATCCATGCTGGAACACAGCTTAGCCCCGGAGGAt > 1:3374128/1‑68 (MQ=255)
tttAAATTTTTCTCCGATCACCGTTTCACACAATATCCATGCTGGAACACAGCTTAGCCCCGGAGGAt > 1:254356/1‑68 (MQ=255)
ttAAATTTTTCTCCGATCACCGTTTCACATAATATTCATGCt < 1:2914537/42‑1 (MQ=255)
ttAAATTTTTCTCCGATCACCGTTTCACATAATATTCATGCt < 1:739864/42‑1 (MQ=255)
ttAAATTTTTCTCCGATCACCGTTTCACATAATATTCATGCt < 1:1825543/42‑1 (MQ=255)
ttAAATTTTTCTCCGATCACCGTTTCACATAATATTCATGCt < 1:698674/42‑1 (MQ=255)
ttAAATTTTTCTCCGATCACCGTTTCACATAATATTCATGCt < 1:681734/42‑1 (MQ=255)
ttAAATTTTTCTCCGATCACCGTTTCACATAATATTCATGCt < 1:1915221/42‑1 (MQ=255)
ttAAATTTTTCTCCGATCACCGTTTCACATAATATTCATGCt < 1:565050/42‑1 (MQ=255)
ttAAATTTTTCTCCGATCACCGTTTCACATAATATTCATGCt < 1:32501/42‑1 (MQ=255)
ttAAATTTTTCTCCGATCACCGTTTCACATAATATTCATGCt < 1:1229613/42‑1 (MQ=255)
ttAAATTTTTCTCCGATCACCGTTTCACATAATATTCATGCt < 1:3107849/42‑1 (MQ=255)
ttAAATTTTTCTCCGATCACCGTTTCACATAATATTCATGCt < 1:2393304/42‑1 (MQ=255)
ttAAATTTTTCTCCGATCACCGTTTCACATAATATTCATGCt < 1:2940034/42‑1 (MQ=255)
ttAAATTTTTCTCCGATCACCGTTTCACACAATATCCATGCTGGAACACAGCTTAGCCCCGGAGGATgg < 1:1334282/69‑1 (MQ=255)
ttAAATTTTTCTCCGATCACCGTTTCACACAATATCCATGCTGGAACACAGCTTAGCCCCGGAGGATgg < 1:2225227/69‑1 (MQ=255)
ttAAATTTTTCTCCGATCACCGTTTCACACAATATCCATGCTGGAACACAGCTTAGCCCCGGAGGATgg < 1:2908700/69‑1 (MQ=255)
tAAATTTTTCTCCGATCACCGTTTCACATAATATTCATGc > 1:200649/1‑40 (MQ=255)
tAAATTTTTCTCCGATCACCGTTTCACATAATATTCATGCt < 1:2968925/41‑1 (MQ=255)
tAAATTTTTCTCCGATCACCGTTTCACATAATATTCATGCTGGGACACAGCTTAACCCCGGTGGATgg > 1:3242945/1‑68 (MQ=255)
tAAATTTTTCTCCGATCACCGTTTCACATAATATTCATGCTGGGACACAGCTTAACCCCGGTGGATgg > 1:2092329/1‑68 (MQ=255)
tAAATTTTTCTCCGATCACCGTTTCACATAATATTCATGCTGGGACACAGCTTAACCCCGGTGGATgg > 1:516805/1‑68 (MQ=255)
tAAATTTTTCTCCGATCACCGTTTCACATAATATTCATGCTGGGACACAGCTTAACCCCGGTGGATgg > 1:226175/1‑68 (MQ=255)
tAAATTTTTCTCCGATCACCGTTTCACATAATATTCATGCTGGGACACAGCTTAACCCCGGTGGATgg > 1:1002280/1‑68 (MQ=255)
aTTTTTCTCCGATCACCGTTTCACATAATATTCATGCt < 1:392103/38‑1 (MQ=38)
tttttCTCCGATCACCGTTTCACACAATATCCATGCTGGAACACAGCTTAGCCCCGGAGGATGGGatat < 1:2241453/69‑1 (MQ=255)
tttttCTCCGATCACCGTTTCACACAATATCCATGCTGGAACACAGCTTAGCCCCGGAGGATGGGatat < 1:2245446/69‑1 (MQ=255)
cACCGTTTCACACAATATCCATGCTGGAACACAGCTTAGCCCCGGAGGATGGGATATAATACCTGgcgc > 1:971639/1‑69 (MQ=255)
cACCGTTTCACACAATATCCAAGCTGGAACACAGCTTAGCCCCGGAGGATGGGATATAATACCTGgcgc > 1:1226410/1‑69 (MQ=255)
|
GGGACATTCTTAATATTATTACCTTGCAAACAGGTTTAAATTTTTCTCCGATCACCGTTTCACACAATATCCATGCTGGAACACAGCTTAGCCCCGGAGGATGGGATATAATACCTGGCGC > minE/1560979‑1561099
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
