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 F3 I0 R2
|
232 |
76.3 |
4135488 |
90.9% |
3759158 |
60.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,827,932 |
C→T |
33.8% |
A392V (GCG→GTG) |
mutS → |
methyl‑directed mismatch repair protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,827,932 | 0 | C | T | 33.8%
| 76.8
/ 59.3
| 65 | A392V (GCG→GTG) | mutS | methyl‑directed mismatch repair protein |
| Reads supporting (aligned to +/- strand): ref base C (14/29); new base T (15/7); total (29/36) |
| Fisher's exact test for biased strand distribution p-value = 8.66e-03 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TCCAGCAACTGCCGGAGCTGCGTGCGCAGTTAGAAACTGTCGATAGTGCACCGGTACAGGCGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCTGCGCGATCTGCTGGAGCGAGCAATCATCGACAC > minE/1827872‑1827998
|
tCCAGCAACTGCCGGAGCTGCGTGCGCAGTTAGAAACTGTCGATAGTGCACCGGTACAGGCGCTACGTg < 1:2577564/69‑1 (MQ=255)
ccAGCAACTGCCGGAGCTGCGTGCGCAGTTAGAAACTGTCGATAGTGCACCGGTACAGGCGCTACGTgag < 1:3827069/70‑1 (MQ=255)
ccAGCAACTGCCGGAGCTGCGTGCGCAGTTAGAAACTGTCGATAGTGCACCGGTACAGGCGCTACGTg < 1:853388/68‑1 (MQ=255)
cAGCAACTGCCGGAGCTGCGTGCGCAGTTAGAAACTGTCGATAGTGCACCGGTACAGGCGCTACGTGagaa < 1:2919220/71‑1 (MQ=255)
gCAACTGCCGGAGCTGCGTGCGCAGTTAGAAACTGTCGATAGTGCACCGGTACAGGCGCTACGTGagaaga < 1:2980277/71‑1 (MQ=255)
gCAACTGCCGGAGCTGCGTGCGCAGTTAGAAACTGTCGATAGTGCACCGGTACAGGCGCTACGTGagaaga < 1:2350754/71‑1 (MQ=255)
gCAACTGCCGGAGCTGCGTGCGCAGTTAGAAACTGTCGATAGTGCACCGGTACAGGCGCTACGTGagaaga < 1:323222/71‑1 (MQ=255)
gCAACTGCCGGAGCTGCGTGCGCAGTTAGAAACTGTCGATAGTGCACCGGTACAGGCGCTACGTGagaaga < 1:1282255/71‑1 (MQ=255)
gCAACTGCCGGAGCTGCGTGCGCAGTTAGAAACTGTCGATAGTGCACCGGTACAGGCGCTACGTGagaaga < 1:1312685/71‑1 (MQ=255)
gCAACTGCCGGAGCTGCGTGCGCAGTTAGAAACTGTCGATAGTGCACCGGTACAGGCGCTACGTGagaaga < 1:3958847/71‑1 (MQ=255)
tGCCGGAGCTGCGTGCGCAGTTAGAAACTGTCGATAGTGCACCGGTACAGGCGCTATGTGAGAAGATGGGc > 1:1904629/1‑71 (MQ=255)
tGCCGGAGCTGCGTGCGCAGTTAGAAACTGTCGATAGTGCACCGGTACAGGCGCTACGTGAGAAGATGGGc > 1:1003374/1‑71 (MQ=255)
tGCCGGAGCTGCGTGCGCAGTTAGAAACTGTCGATAGTGCACCGGTACAGGCGCTACGTGAGAAGATGGGc > 1:2661979/1‑71 (MQ=255)
tGCCGGAGCTGCGTGCGCAGTTAGAAACTGTCGATAGTGCACCGGTACAGGCGCTACGTGAGAAGATGGGc > 1:1324848/1‑71 (MQ=255)
gCTGCGTGCGCAGTTAGAAACTGTCGATAGTGCACCGGTACAGGCGCTACGTGAGAAGATGGGCGAGTTTg > 1:1158519/1‑71 (MQ=255)
cTGCGTGCGCAGTTAGAAACTGTCGATAGTGCACCGGTACAGGCGCTACGTg > 1:3628369/1‑52 (MQ=255)
cTGCGTGCGCAGTTAGAAACTGTCGATAGTGCACCGGTACAGGCGCTACGTTAGAAGATGGGCGAGtt > 1:1909503/1‑68 (MQ=255)
tgcgtgcgCAGTTAGAAACTGTCGATAGTGCACCGGTACAGGCGCTACGTGAGAAGATGGGCGAg < 1:435707/65‑1 (MQ=255)
tgcgtgcgCAGTTAGAAACTGTCGATAGTGCACCGGTACAGGCGCTACGTGAGAAGATGGGCGAg < 1:110842/65‑1 (MQ=255)
tgcgtgcgCAGTTAGAAACTGTCGATAGTGCACCGGTACAGGCGCTACGTGAGAAGATGGGCGAg < 1:922108/65‑1 (MQ=255)
tgcgtgcgCAGTTAGAAACTGTCGATAGTGCACCGGTACAGGCGCTACGTGAGAAGATGGGCGAg < 1:2537169/65‑1 (MQ=255)
cgtgcgCAGTTAGAAACTGTCGATAGTGCACCGGTACAGGCGCTACGTGAGAAGATGGGCGAGTTTGCCg < 1:3715013/70‑1 (MQ=255)
cgtgcgCAGTTAGAAACTGTCGATAGTGCACCGGTACAGGCGCTACGTGAGAAGATGGGCGAATTTGcc < 1:3109641/69‑1 (MQ=255)
cgcAGTTAGAAACTGTCGATAGTGCACCGGTACAGGTGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCTg > 1:739541/1‑71 (MQ=255)
cgcAGTTAGAAACTGTCGATAGTGCACCGGTACAGGTGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCTg > 1:816812/1‑71 (MQ=255)
cgcAGTTAGAAACTGTCGATAGTGCACCGGTACAGGTGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCTg > 1:4054400/1‑71 (MQ=255)
cgcAGTTAGAAACTGTCGATAGTGCACCGGTACAGGTGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCTg > 1:1735579/1‑71 (MQ=255)
aGTTAGAAACTGTCGATAGTGCACCGGTACAGGTGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCTgcgc < 1:939419/71‑1 (MQ=255)
aGTTAGAAACTGTCGATAGTGCACCGGTACAGGTGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCTgcgc < 1:3735729/71‑1 (MQ=255)
aGTTAGAAACTGTCGATAGTGCACCGGTACAGGTGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCTgcgc < 1:3045995/71‑1 (MQ=255)
aGTTAGAAACTGTCGATAGTGCACCGGTACAGGTGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCTgcgc < 1:428666/71‑1 (MQ=255)
gTTAGAAACTGTCGATAGTGCACCGGTACAGGCGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCTgcgc > 1:2964426/1‑70 (MQ=255)
ttAGAAACTTTAGATAGTGCACCGGTACAGGTGCTACGTGAGAAGATGGGCGAGTTTGCCGAg < 1:2516490/63‑1 (MQ=255)
ttAGAAACTGTCGATAGTGCACCGGTACAGGTGCTACGTGAGAAGATGGGCGAGTTTGCCGAg < 1:889232/63‑1 (MQ=255)
ttAGAAACTGTCGATAGTGCACCGGTACAGGTGCTACGTGAGAAGATGGGCGAGTTTGCCGAg < 1:3177042/63‑1 (MQ=255)
ttAGAAACTGTCGATAGTGCACCGGTACAGGCGCTACGTGagaa < 1:1344940/44‑1 (MQ=255)
ttAGAAACTGTCGATAGTGCACCGGTACAGGCGCTACGTGagaa < 1:1927832/44‑1 (MQ=255)
ttAGAAACTGTCGATAGTGCACCGGTACAGGCGCTACGTGagaa < 1:2837715/44‑1 (MQ=255)
tAGAAACTGTCGATAGTGCACCGGTACAGGTGCTACGTGagaaga > 1:2391891/1‑45 (MQ=255)
tAGAAACTGTCGATAGTGCACCGGTACAGGTGCTACGTGagaaga > 1:2232676/1‑45 (MQ=255)
tAGAAACTGTCGATAGTGCACCGGTACAGGTGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCTGCGCGAt > 1:2875851/1‑71 (MQ=255)
tAGAAACTGTCGATAGTGCACCGGTACAGGTGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCTGCGCGAt > 1:1516391/1‑71 (MQ=255)
tAGAAACTGTCGATAGTGCACCGGTACAGGTGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCTGAGCGAt > 1:1065021/1‑71 (MQ=255)
aGAAACTGTCGATAGTGCACCGGTACAGGTGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCt > 1:2534333/1‑63 (MQ=255)
aGAAACTGTCGATAGTGCACCGGTACAGGTGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCt > 1:46724/1‑63 (MQ=255)
aGAAACTGTCGATAGTGCACCGGTACAGGTGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCt > 1:1408354/1‑63 (MQ=255)
aGAAACTGTCGATAGTGCACCGGTACAGGTGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCt > 1:4043517/1‑63 (MQ=255)
aGAAACTGTCGATAGTGCACCGGTACAGGTGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCt > 1:3789118/1‑63 (MQ=255)
aGAAACTGTCGATAGTGCACCGGTACAGGTGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCt > 1:3499672/1‑63 (MQ=255)
aGAAACTGTCGATAGTGCACCGGTACAGGCGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCTGCGCGATc > 1:190557/1‑71 (MQ=255)
aGAAACTGTCGATAGTGCACCGGTACAGGCGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCTGCGCGATc > 1:3053458/1‑71 (MQ=255)
gAAACTGTCGATAGTGCACCGGTACAGGCGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCTGCGCGATct > 1:3177558/1‑71 (MQ=255)
aTAGTGCACCGGTACAGGCGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCTGcgcg < 1:1240361/57‑1 (MQ=255)
gTGCACCGGTACAGGCGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCTGCGCGATc > 1:2309640/1‑57 (MQ=255)
gTGCACCGGTACAGGCGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCTGCGCGATc > 1:869544/1‑57 (MQ=255)
gTGCACCGGTACAGGCGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCTGCGCGATCTGCTGGAGCGAGCa < 1:2539026/71‑1 (MQ=255)
cGGTACAGGCGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCTGCGCGATCTGCTGGAGCGAGCAatcatc < 1:1983141/71‑1 (MQ=255)
cGGTACAGGCGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCTGCGCGATCTGCTGGAGCGAGCAatcatc < 1:1816234/71‑1 (MQ=255)
ggTACAGGCGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCTGCGCGATCTGCTGGAGCGAGCAATCATCg < 1:647482/71‑1 (MQ=255)
tACAGGCGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCTGCGCGATCTGCTGGAGCGAGCa < 1:2078130/62‑1 (MQ=255)
tACAGGCGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCTGCGCGATCTGCTGGAGCGAGCa < 1:865607/62‑1 (MQ=255)
tACAGGCGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCTGCGCGATCTGCTGGAGCGAGCa < 1:2372903/62‑1 (MQ=255)
tACAGGCGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCTGCGCGATCTGCTGGAGCGAGCa < 1:2160766/62‑1 (MQ=255)
cAGGCGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCTGCGCGATCTGCTGGAGCGAGCAATCATCGacac < 1:1023125/71‑1 (MQ=255)
cAGGCGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCTGCGCGATCTGCTGGAGCGAGCAATCATCGaca > 1:1039389/1‑70 (MQ=255)
|
TCCAGCAACTGCCGGAGCTGCGTGCGCAGTTAGAAACTGTCGATAGTGCACCGGTACAGGCGCTACGTGAGAAGATGGGCGAGTTTGCCGAGCTGCGCGATCTGCTGGAGCGAGCAATCATCGACAC > minE/1827872‑1827998
|
| 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
