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 |
|
A1 F21 I0 R1
|
476 |
35.3 |
2812105 |
96.7% |
2719305 |
61.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,714,423 |
C→T |
100% |
H61Y (CAC→TAC) |
atpI → |
ATP synthase, membrane‑bound accesory subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,714,423 | 0 | C | T | 87.0%
| 115.8
/ 10.7
| 46 | H61Y (CAC→TAC) | atpI | ATP synthase, membrane‑bound accesory subunit |
| Reads supporting (aligned to +/- strand): ref base C (5/1); new base T (25/15); total (30/16) |
| Fisher's exact test for biased strand distribution p-value = 6.49e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.74e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
TCTGCAATAAGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCATTTGGCGAAGCTTTCAAAGT > W3110S.gb/3714357‑3714490
|
tctGCAATAAGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTAc > 1:1175372/1‑69 (MQ=255)
tctGCAATAAGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTAc > 1:1581638/1‑69 (MQ=255)
tctGCAATAAGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTAc > 1:222658/1‑69 (MQ=255)
cAATAAGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGgcg < 1:2431433/71‑1 (MQ=255)
aTAAGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCa > 1:801969/1‑71 (MQ=255)
aTAAGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCa < 1:2242807/71‑1 (MQ=255)
aGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAg > 1:987298/1‑63 (MQ=255)
aGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATac < 1:1218446/71‑1 (MQ=255)
aGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTATATGATATTTGCCTGGCGTTACCAGGCGCATa > 1:2789880/1‑70 (MQ=255)
cTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATa < 1:2342588/61‑1 (MQ=255)
tGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATa < 1:818542/60‑1 (MQ=255)
gCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTAc > 1:2757824/1‑48 (MQ=255)
gCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTAc > 1:1133601/1‑48 (MQ=255)
gCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCa < 1:2188436/56‑1 (MQ=255)
gCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAgg > 1:1166083/1‑71 (MQ=255)
tCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCgg < 1:85085/71‑1 (MQ=255)
tCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCgg < 1:266774/71‑1 (MQ=255)
cTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATa > 1:1193387/1‑53 (MQ=255)
cTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCggg > 1:815700/1‑71 (MQ=255)
cTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCa > 1:2138153/1‑51 (MQ=255)
cTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCa > 1:2761270/1‑51 (MQ=255)
cTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCa > 1:2064562/1‑51 (MQ=255)
tttCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGt > 1:120470/1‑71 (MQ=255)
tttCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGt > 1:1964936/1‑71 (MQ=255)
tttCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGt > 1:514743/1‑71 (MQ=255)
tttCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGt > 1:265014/1‑71 (MQ=255)
tCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTAc > 1:2335345/1‑40 (MQ=255)
tCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTgg > 1:61649/1‑71 (MQ=255)
tCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCATATACCAGCGAAAGGCCGGGt < 1:486556/69‑1 (MQ=255)
cTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTgg < 1:291207/70‑1 (MQ=255)
ttttGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCg < 1:2001457/55‑1 (MQ=255)
ttGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCggg > 1:1884801/1‑55 (MQ=255)
ttGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCggg > 1:2469523/1‑55 (MQ=255)
ttGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCgg > 1:2319341/1‑54 (MQ=255)
ttGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCg > 1:54149/1‑70 (MQ=255)
ttGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCg > 1:445710/1‑70 (MQ=255)
ttGTTTATGATATTTGCCTGGCGTCACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCg > 1:2143821/1‑70 (MQ=255)
tGTTTATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGc < 1:1804745/70‑1 (MQ=255)
tttATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCgg < 1:2272402/51‑1 (MQ=255)
tATGATATTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGt > 1:594563/1‑51 (MQ=255)
tatTTGCCTGGCGTCACCAGGCGCATACACCAGCGAAAGGCCggg > 1:6040/1‑45 (MQ=255)
atTTGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCATTTGGCGAAg > 1:1379039/1‑71 (MQ=255)
tttGCCTGGCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCATTTGGCGAAGc > 1:2299468/1‑71 (MQ=255)
gCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCATTTGGCGAAGCTTTCaa < 1:430841/69‑1 (MQ=255)
gCGTTACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCATTTGGCGAAGCTTTCaa < 1:170993/69‑1 (MQ=255)
cGTTACCAGGCGCATACACCAGCGAAAGGCCAGGTGGCCTGGACATTCGCATTTGGCGAAGCTTTCAAAGt < 1:643292/71‑1 (MQ=255)
|
TCTGCAATAAGCGGGGGCCTGGCAGTCTTTCTGCCTAACGTTTTGTTTATGATATTTGCCTGGCGTCACCAGGCGCATACACCAGCGAAAGGCCGGGTGGCCTGGACATTCGCATTTGGCGAAGCTTTCAAAGT > W3110S.gb/3714357‑3714490
|
| 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
