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 |
2,790,638 |
C→T |
13.2% |
intergenic (+33/‑742) |
pgi → / → ubiC |
glucosephosphate isomerase/chorismate pyruvate lyase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,790,638 | 0 | C | T | 13.2%
| 148.0
/ 11.1
| 53 | intergenic (+33/‑742) | pgi/ubiC | glucosephosphate isomerase/chorismate pyruvate lyase |
| Reads supporting (aligned to +/- strand): ref base C (25/21); new base T (5/2); total (30/23) |
| Fisher's exact test for biased strand distribution p-value = 6.85e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.35e-01 |
TGGTCTGATTAACCGCTATAAAGCGTGGCGCGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCC > minE/2790569‑2790706
|
tGGTCTGATTAACCGCTATAAAGCGTGGCGCGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCa > 1:2505344/1‑71 (MQ=255)
tGGTCTGATTAACCGCTATAAAGCGTGGCGCGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCa > 1:1585350/1‑71 (MQ=255)
ggTCTGATTAACCGCTATAAAGCGTGGCGCGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCa > 1:1536010/1‑70 (MQ=255)
gTCTGATTAACCGCTATAAAGCGTGGCGCGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCAc < 1:2842301/70‑1 (MQ=255)
gTCTGATTAACCGCTATAAAGCGTGGCGCGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCAc < 1:210972/70‑1 (MQ=255)
aTTAACCGCTATAAAGCGTGGCGCGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCAcgccgc < 1:2523028/70‑1 (MQ=255)
ttAACCGCTATAAAGCGTGGCGCGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCAt < 1:3554798/71‑1 (MQ=255)
tAACCGCTATAAAGCGTGGCGCGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATc > 1:1344852/1‑71 (MQ=255)
aaCCGCTATAAAGCGTGGCGCGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATcc > 1:94173/1‑71 (MQ=255)
aaCCGCTATAAAGCGTGGCGCGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATc < 1:680092/70‑1 (MQ=255)
aaCCGCTATAAAGCGTGGCGCGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATc < 1:2380976/70‑1 (MQ=255)
gCTATAAAGCGTGGCGCGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGc > 1:1508970/1‑70 (MQ=255)
cTATAAAGCGTGGCGCGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCaa > 1:3767946/1‑71 (MQ=255)
cTATAAAGCGTGGCGCGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCaa > 1:3377727/1‑71 (MQ=255)
taAAGCGTGGCGCGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAAcc > 1:279988/1‑70 (MQ=255)
taAAGCGTGGCGCGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAAc > 1:3302448/1‑69 (MQ=255)
taAAGCGTGGCGCGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCg < 1:1988246/71‑1 (MQ=255)
aaGCGTGGCGCGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGAt > 1:150484/1‑71 (MQ=255)
aGCGTGGCGCGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATg > 1:3244876/1‑71 (MQ=255)
gCGTGGCGCGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCAcgc < 1:3910258/52‑1 (MQ=255)
gCGTGGCGCGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGc > 1:1368499/1‑71 (MQ=255)
gCGTGGCGCGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGc > 1:3815276/1‑71 (MQ=255)
cGTGGCGCGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCAcgc < 1:2047637/51‑1 (MQ=255)
cGTGGCGCGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCg < 1:1822452/59‑1 (MQ=255)
gTGGCGCGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCt < 1:2609538/71‑1 (MQ=255)
cgcgGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCa > 1:1467790/1‑43 (MQ=255)
gTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGAc < 1:2660733/71‑1 (MQ=255)
aaTCATCGTCGATATGTAGGCCGGATAAGGCGTTCAcgcc > 1:3708286/1‑40 (MQ=255)
cgtcgATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGTTGCGACGCGGTc < 1:1892250/68‑1 (MQ=255)
gtcgATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTcgcg > 1:2580379/1‑70 (MQ=255)
gATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCt > 1:447588/1‑70 (MQ=255)
ttcgTAGGACGGATAAGGCGTTTACGCCGCATCCGGCAACAGATGCCTGATGCGACGCTACCGCGTCTTAt < 1:382514/68‑1 (MQ=11)
tatGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTAt < 1:3247193/71‑1 (MQ=255)
tGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATc < 1:1509578/70‑1 (MQ=255)
tAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAgg < 1:380818/71‑1 (MQ=255)
tAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAg > 1:1369066/1‑70 (MQ=255)
aGGACGGATAAGGCGTTTACGCCGCATCCGGCAACAGATGCCTGATGCGACGCTACCGCGTATTATCa > 1:2394589/1‑68 (MQ=14)
ggCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGAcgcg < 1:2896853/53‑1 (MQ=255)
gacGGATAAGGCGTTTACGCTGCATCCGGCAACCTATGCCTGATGCGACGCTGAAGCGTCTTATCATGcc > 1:1671754/3‑70 (MQ=11)
gCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGcc > 1:1719234/1‑70 (MQ=255)
gCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCt < 1:612785/71‑1 (MQ=255)
ccGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTcgc > 1:661493/1‑56 (MQ=255)
acGGATAAGGCGTTTACGCTGCATCCGGCAACCTATGCCTGATGCGACGCTGAAGCGTCTTATCATGCCTa > 1:3894761/2‑71 (MQ=11)
acGGATAAGGCGTTTACGCTGCATCCGGCAACCTATGCCTGATGCGACGCTGAAGCGTCTTATCATGCCTa < 1:1830808/70‑1 (MQ=11)
cGGATAAGGCGTTTACGCTGCATCCGGCAACCTATGCCTGATGCGACGCTGAAGCGTCTTATCATGCCTa > 1:2182873/1‑70 (MQ=11)
ggATAAGGCGTTTACGCTGCATCCGGCAACCTATGCCTGATGCGACGCTGAAGCGTCTTATCATGCCTACa > 1:1131528/1‑71 (MQ=11)
tAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGa < 1:1557150/42‑1 (MQ=255)
tAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGt > 1:2354780/1‑71 (MQ=255)
aGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTc < 1:1910216/70‑1 (MQ=255)
cGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGa > 1:219223/1‑69 (MQ=255)
cGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGAt > 1:1458042/1‑70 (MQ=255)
ttCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTc < 1:2689770/65‑1 (MQ=255)
ttCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGcc > 1:3530579/1‑71 (MQ=255)
|
TGGTCTGATTAACCGCTATAAAGCGTGGCGCGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCC > minE/2790569‑2790706
|
| 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
