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 |
|
A6 F21 I0 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,513,018 |
T→C |
21.4% |
intergenic (+141/+291) |
pta → / ← ubiX |
phosphate acetyltransferase/3‑octaprenyl‑4‑hydroxybenzoate carboxy‑lyase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,513,018 | 0 | T | C | 21.4%
| 106.7
/ 26.1
| 56 | intergenic (+141/+291) | pta/ubiX | phosphate acetyltransferase/3‑octaprenyl‑4‑hydroxybenzoate carboxy‑lyase |
| Reads supporting (aligned to +/- strand): ref base T (22/22); new base C (8/4); total (30/26) |
| Fisher's exact test for biased strand distribution p-value = 3.47e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.90e-01 |
CTTAATTTGCATTAATCCTTTCTGATTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTATGTTGTGTAT > minE/1512952‑1513084
|
ctTAATTTGCATTAATCCTTTCTGATTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCCCACt > 1:2078111/1‑71 (MQ=255)
ttAATTTGCATTAATCCTTTCTGATTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACtt > 1:583963/1‑71 (MQ=255)
aaTTTGCATTAATCCTTTCTGATTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACttt < 1:3339297/70‑1 (MQ=255)
aaTTTGCATTAATCCTTTCTGATTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACttt < 1:1543880/70‑1 (MQ=255)
aTTTGCATTAATCCTTTCTGATTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTg < 1:317096/70‑1 (MQ=255)
tttGCATTAATCCTTTCTGATTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCCCACTTTGCa < 1:3438293/71‑1 (MQ=255)
tGCATTAATCCTTTCTGATTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATa > 1:1221119/1‑71 (MQ=255)
tGCATTAATCCTTTCTGATTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATa > 1:1560243/1‑71 (MQ=255)
gCATTAATCCTTTCTGATTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCCCACTTTGCATAc > 1:1288176/1‑71 (MQ=255)
cATTAATCCTTTCTGATTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACt < 1:420565/71‑1 (MQ=255)
ttAATCCTTTCTGATTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTc < 1:313807/71‑1 (MQ=255)
tAATCCTTTCTGATTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACttt > 1:1568517/1‑61 (MQ=255)
tAATCCTTTCTGATTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCCCACTTTGCATACttac > 1:890272/1‑69 (MQ=255)
aaTCCTTTCTGATTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCCCACTTTGCATACttac > 1:1826536/1‑68 (MQ=255)
aTCCTTTCTGATTATCTTGCTTAACTGCGCTGCATCAATGAATTGAGCCATCCCACTTTGCATACTTACCa > 1:2780713/1‑71 (MQ=255)
tCCTTTCTGATTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCAc > 1:1620607/1‑71 (MQ=255)
tttCTGATTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCCCACTTTGCATACTTACCACttt > 1:1063585/1‑71 (MQ=255)
cTGATTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCCCACTTTGCATACTTACCACt < 1:86305/66‑1 (MQ=255)
tGATTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCCCACTTTg < 1:3321386/52‑1 (MQ=255)
tGATTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCCCACTTTg < 1:3231668/52‑1 (MQ=255)
gATTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCAt < 1:600866/54‑1 (MQ=255)
gATTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCCCACTTTGCATACTTACCACttt > 1:2442505/1‑66 (MQ=255)
aTTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTg < 1:3447466/50‑1 (MQ=255)
aTTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACt < 1:2178333/63‑1 (MQ=255)
aTTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTACa > 1:3884080/1‑71 (MQ=255)
aTCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTACATaa > 1:1989703/1‑71 (MQ=255)
tCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTg < 1:1056442/46‑1 (MQ=255)
tCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCa > 1:943068/1‑48 (MQ=255)
tCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTa > 1:1412050/1‑65 (MQ=255)
cTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACtt < 1:1274920/59‑1 (MQ=255)
tGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTACATAACCCt > 1:922039/1‑71 (MQ=255)
gCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTccc > 1:1668442/1‑52 (MQ=255)
gCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTccc > 1:1323435/1‑52 (MQ=255)
gCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTACATAACCCt > 1:2249481/1‑70 (MQ=255)
cTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTACATAACCCTc < 1:2778936/70‑1 (MQ=255)
cTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTACATAACCCTCa < 1:3801586/71‑1 (MQ=255)
cTTAACTGCGCTGCATCAATGAATTGCGCCATCCCACTTTGCATAc > 1:2454610/1‑46 (MQ=255)
aaCTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTACATAACCCTCAAGt > 1:289583/1‑71 (MQ=255)
aaCTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTACATAACCCTCAAGt > 1:157099/1‑71 (MQ=255)
tGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTACATAACCCTc > 1:1820529/1‑64 (MQ=255)
gcTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTACATAACCCTCAAGTGAAAAt < 1:2198801/71‑1 (MQ=255)
tGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATgg > 1:1426430/1‑71 (MQ=255)
tGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATg > 1:140645/1‑70 (MQ=255)
gCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTACATAAcc > 1:3365218/1‑55 (MQ=255)
aaTGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGtt < 1:242317/42‑1 (MQ=255)
aaTGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGt < 1:691328/41‑1 (MQ=255)
aaTGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGt < 1:991445/41‑1 (MQ=255)
tGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTa > 1:1230194/1‑41 (MQ=255)
tGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTa < 1:1579425/71‑1 (MQ=255)
tGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTACATAACCCTCAAGTG‑AAATGGCTTTTTTAt < 1:2121785/71‑1 (MQ=255)
aaTTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTAtg > 1:2142166/1‑71 (MQ=255)
aaTTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTAt < 1:2576565/70‑1 (MQ=255)
ttGCGCCATCTCACTTTGCATACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTAtgtt < 1:813573/71‑1 (MQ=255)
ttGCGCCATCTCACTTTGCATACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGCCTTTTTTAtgtt < 1:2690014/71‑1 (MQ=255)
cgcCATCTCACTTTGCATACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTAtgttgt < 1:149284/70‑1 (MQ=255)
cATCTCACTTTGCATACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTATGTTGTGTAt > 1:1322456/1‑71 (MQ=255)
tctcACTTTGCATACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTAtg < 1:3524969/61‑1 (MQ=255)
|
CTTAATTTGCATTAATCCTTTCTGATTATCTTGCTTAACTGCGCTGCATCAATGAATTGCGCCATCTCACTTTGCATACTTCCCACTTTGTTACATAACCCTCAAGTGAAAATGGCTTTTTTATGTTGTGTAT > minE/1512952‑1513084
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
