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 |
1,444,430 |
C→G |
21.4% |
intergenic (+51/+149) |
rcsB → / ← rcsC |
DNA‑binding response regulator in two‑component regulatory system with RcsC and YojN/hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,444,430 | 0 | C | G | 21.4%
| 134.2
/ 28.1
| 70 | intergenic (+51/+149) | rcsB/rcsC | DNA‑binding response regulator in two‑component regulatory system with RcsC and YojN/hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| Reads supporting (aligned to +/- strand): ref base C (42/13); new base G (8/7); total (50/20) |
| Fisher's exact test for biased strand distribution p-value = 1.09e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.83e-01 |
GATAAAGACTAATCACCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGATTCCCATTATTTCAACAAATTA > minE/1444368‑1444492
|
gATAAAGAGTAATCACCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGc > 1:2597892/1‑69 (MQ=255)
gATAAAGAGTAATCACCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGc > 1:2601903/1‑69 (MQ=255)
gATAAAGACTAATCACCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGc > 1:2944601/1‑69 (MQ=255)
gATAAAGACTAATCACCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGc > 1:2027446/1‑69 (MQ=255)
gATAAAGACTAATCACCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGc > 1:1901866/1‑69 (MQ=255)
gATAAAGACTAATCACCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGc > 1:2933300/1‑69 (MQ=255)
gATAAAGACTAATCACCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGc > 1:1720620/1‑69 (MQ=255)
gATAAAGACTAATCACCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGc > 1:436451/1‑69 (MQ=255)
gATAAAGACTAATCACCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGc > 1:806417/1‑69 (MQ=255)
gATAAAGACTAATCACCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGc > 1:1046368/1‑69 (MQ=255)
gATAAAGACTAATCACCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGc > 1:525597/1‑69 (MQ=255)
tAAAGACTAATCACCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGc > 1:2441978/1‑67 (MQ=255)
tAAAGACTAATCACCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGCCg > 1:377829/1‑69 (MQ=255)
tAAAGACTAATCACCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGCCg < 1:2273227/69‑1 (MQ=255)
tAAAGACTAATCACCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGCCg < 1:2226829/69‑1 (MQ=255)
tAAAGACTAATCACCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGCCg > 1:2076557/1‑69 (MQ=255)
tAAAGACTAATCACCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGCCg < 1:2612080/69‑1 (MQ=255)
tAAAGACTAATCACCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGCCg > 1:2670922/1‑69 (MQ=255)
tAAAGACTAATCACCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGCCg < 1:2732643/69‑1 (MQ=255)
tAAAGACTAATCACCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGCCg > 1:461247/1‑69 (MQ=255)
tAAAGACTAATCACCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGCCg < 1:3165062/69‑1 (MQ=255)
tAAAGACTAATCACCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGCCg < 1:3255908/69‑1 (MQ=255)
tAAAGACTAATCACCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGCCg > 1:361808/1‑69 (MQ=255)
aTCACCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGCCGGATgcggc > 1:1760216/1‑68 (MQ=255)
cACCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGCCGGATGCGGCGTa < 1:1771922/69‑1 (MQ=255)
cACCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGCCGGATGCGGCGTa < 1:109368/69‑1 (MQ=255)
cACCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGCCGGATGCGGCGTa < 1:1904732/69‑1 (MQ=255)
cACCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGCCGGATGCGGCGTa < 1:798335/69‑1 (MQ=255)
cACCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGCCGGATGCGGCGTa < 1:2036891/69‑1 (MQ=255)
aCCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGCCGGATGCGGCGTa > 1:2699582/1‑68 (MQ=255)
aCCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGCCGGATGCGGCGTa > 1:981841/1‑68 (MQ=255)
aCCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGCCGGATGCGGCGTa > 1:299598/1‑68 (MQ=255)
aCCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGCCGGATGCGGCGTa > 1:3227628/1‑68 (MQ=255)
aCCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGCCGGATGCGGCGTa > 1:1190377/1‑68 (MQ=255)
aCCTGTAGGCCAGATAAGACGCGTCAGTGTCTTATCTGGCATTTGCACGGATTGCCGGATGCGGCGTaa < 1:325906/69‑1 (MQ=17)
aCCTGTAGGCCAGATAAGACGCGTCAGTGTCTTATCTGGCATTTGCACGGATTGCCGGATGCGGCGTaa < 1:333855/69‑1 (MQ=17)
aCCTGTAGGCCAGATAAGACGCGTCAGTGTCTTATCTGGCATTTGCACGGATTGCCGGATGCGGCGTaa < 1:1820579/69‑1 (MQ=17)
aCCTGTAGGCCAGATAAGACGCGTCAGTGTCTTATCTGGCATTTGCACGGATTGCCGGATGCGGCGTaa < 1:562383/69‑1 (MQ=17)
aCCTGTAGGCCAGATAAGACGCGTCAGTGTCTTATCTGGCATTTGCACGGATTGCCGGATGCGGCGTaa < 1:3302397/69‑1 (MQ=17)
aCCTGTAGGCCAGATAAGACGCGTCAGTGTCTTATCTGGCATTTGCACGGATTGCCGGATGCGGCGTaa < 1:3330116/69‑1 (MQ=17)
cTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCg > 1:1059327/1‑48 (MQ=255)
cTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCg > 1:1404360/1‑48 (MQ=255)
cTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCg > 1:3174937/1‑48 (MQ=255)
cTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCg > 1:74186/1‑48 (MQ=255)
cTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCg > 1:854162/1‑48 (MQ=255)
cTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCg > 1:1815596/1‑48 (MQ=255)
cTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCg > 1:963078/1‑48 (MQ=255)
cTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCg > 1:1923458/1‑48 (MQ=255)
cTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCg > 1:1400349/1‑48 (MQ=255)
cAGATAAGACGCGTCAGTGTCTTATCTGGCATTTGCACGGATTGCCGGATGCGGCGTAAACGCCTTATc > 1:1246244/1‑69 (MQ=14)
cAGATAAGACGCGTCAGTGTCTTATCTGGCATTTGCACGGATTGCCGGATGCGGCGTAAACGCCTTATc > 1:2451674/1‑69 (MQ=14)
cAGATAAGACGCGTCAGTGTCTTATCTGGCATTTGCACGGATTGCCGGATGCGGCGTAAACGCCTTATc > 1:1499699/1‑69 (MQ=14)
cAGATAAGACGCGTCAGTGTCTTATCTGGCATTTGCACGGATTGCCGGATGCGGCGTAAACGCCTTATc > 1:2994096/1‑69 (MQ=14)
cAGATAAGACGCGTCAGTGTCTTATCTGGCATTTGCACGGATTGCCGGATGCGGCGTAAACGCCTTATc > 1:1764188/1‑69 (MQ=14)
cAGATAAGACGCGTCAGTGTCTTATCTGGCATTTGCACGGATTGCCGGATGCGGCGTAAACGCCTTATc > 1:187617/1‑69 (MQ=14)
cAGATAAGACGCGTCAGTGTCTTATCTGGCATTTGCACGGATTGCCGGATGCGGCGTAAACGCCTTATc > 1:2530442/1‑69 (MQ=14)
cAGATAAGACGCGTCAGTGTCTTATCTGGCATTTGCA‑GGATTGCCGGATGCGGCGTAAACGCCTTATcc > 1:2449126/1‑69 (MQ=14)
cgcgTTAGTGTCTTATCTGGCATTTGCACCGATTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTAc < 1:3260300/68‑1 (MQ=255)
tCTTATCTGGCATTTGCACCGATTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGATTCCCatta > 1:431233/1‑69 (MQ=255)
tCTTATCTGGCATTTGCACCGATTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGATTCCCatta > 1:3414798/1‑69 (MQ=255)
tCTTATCTGGCATTTGCACCGATTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGATTCCCatta > 1:1542004/1‑69 (MQ=255)
tCTTATCTGGCATTTGCACCGATTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGATTCCCatta > 1:68104/1‑69 (MQ=255)
tCTTATCTGGCATTTGCACCGATTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGATTCCCatta > 1:1807058/1‑69 (MQ=255)
ttATCTGGCATTTGCACGGATTGCCGGATGCGGCGTaa < 1:1024765/38‑1 (MQ=255)
ttGCACCGATTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGATTCCCATTATTTCAACAAATTa < 1:1015276/69‑1 (MQ=255)
tGCACCGATTGCCGGATGCGGCGTAAACGCCTTATCCGGGCTACGATTCCCATTATTTCAACAAATTa > 1:1378062/1‑68 (MQ=255)
tGCACCGATTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGATTCCCATTATTTCAACAAATTa > 1:1116688/1‑68 (MQ=255)
tGCACCGATTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGATTCCCATTATTTCAACAAATTa > 1:163312/1‑68 (MQ=255)
tGCACCGATTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGATTCCCATTATTTCAACAAATTa > 1:2771460/1‑68 (MQ=255)
tGCACCGATTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGATTCCCATTATTTCAACAAATTa > 1:1882922/1‑68 (MQ=255)
|
GATAAAGACTAATCACCTGTAGGCCAGATAAGACGCGTTAGTGTCTTATCTGGCATTTGCACCGATTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACGATTCCCATTATTTCAACAAATTA > minE/1444368‑1444492
|
| 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
