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 |
413,643 |
A→G |
46.3% |
S180S (AGT→AGC) |
lnt ← |
apolipoprotein N‑acyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 413,643 | 0 | A | G | 46.3%
| 1.4
/ 44.8
| 54 | S180S (AGT→AGC) | lnt | apolipoprotein N‑acyltransferase |
| Reads supporting (aligned to +/- strand): ref base A (17/12); new base G (5/20); total (22/32) |
| Fisher's exact test for biased strand distribution p-value = 5.58e-03 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.24e-01 |
CAAACAGCACGACGGCCACCACCAGCGGACGCCAGTTGCGTTTGACCAACGCCAGTGCCAGCAGGCCACTAACCATCATCAGCAGGAAGTTAATGGCTTCCACGCCCATTATCGGTGCCAGCCCTTTT > minE/413576‑413703
|
cAAACAGCACGACGGCCACCACCAGCGGACGCCAGTTGCGTTTGACCAACGCCAGTGCCAGCAGGCCa > 1:1058472/1‑68 (MQ=255)
cAAACAGCACGACGGCCACCACCAGCGGACGCCAGTTGCGTTTGACCAACGCCAGTGCCAGCAGGCCa > 1:3043821/1‑68 (MQ=255)
cAAACAGCACGACGGCCACCACCAGCGGACGCCAGTTGCGTTTGACCAACGCCAGTGCCAGCAGGCCa > 1:2965384/1‑68 (MQ=255)
cAAACAGCACGACGGCCACCACCAGCGGACGCCAGTTGCGTTTGACCAACGCCAGTGCCAGCAGGCCa > 1:1448977/1‑68 (MQ=255)
aGCACGACGGCCACCACCAGCGGACGCCAGTTGCGTTTGACCAACGCCAGTGCCAGCAGGCCACTAAcc < 1:614824/69‑1 (MQ=255)
cgacgGCCACCACCAGCGGACGCCAGTTGCGTTTGACCAACGCCAGTGCCAGCAGGCCGCTAACcatc > 1:2519818/1‑68 (MQ=255)
cgacgGCCACCACCAGCGGACGCCAGTTGCGTTTGACCAACGCCAGTGCCAGCAGGCCGCTAACcatc > 1:2439247/1‑68 (MQ=255)
cgacgGCCACCACCAGCGGACGCCAGTTGCGTTTGACCAACGCCAGTGCCAGCAGGCCGCTAACcatc > 1:2120301/1‑68 (MQ=255)
cgacgGCCACCACCAGCGGACGCCAGTTGCGTTTGACCAACGCCAGTGCCAGCAGGCCGCTAACcatc > 1:2088683/1‑68 (MQ=255)
cgacgGACACCACCAGCGGACGCCAGTTGCGTTTGACCAACGCCAGTGCCAGCAGGCCGCTAACcat > 1:1527152/1‑67 (MQ=255)
accaccaGCGGACGCCAGTTGCGTTTGACCAACGCCAGTGCCAGCAGGCCACTAACCATCATCAGCAgg < 1:377876/69‑1 (MQ=255)
gCGTTTTACCAACGCCAGTGCCAGCAGGCCAGTAACCATCATCAGCAGGAAGTTAATGGCTTCCACGcc < 1:927519/69‑1 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCGCTAACCATCATCAGCAGGAAGtt < 1:2845314/54‑1 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCGCTAACCATCATCAGCAGGAAGtt < 1:2550437/54‑1 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCGCTAACCATCATCAGCAGGAAGtt < 1:1150441/54‑1 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCGCTAACCATCATCAGCAGGAAGtt < 1:3136010/54‑1 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCGCTAACCATCATCAGCAGGAAGtt < 1:2421495/54‑1 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCGCTAACCATCATCAGCAGGAAGtt < 1:3153651/54‑1 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCGCTAACCATCATCAGCAGGAAGtt < 1:3269193/54‑1 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCGCTAACCATCATCAGCAGGAAGtt < 1:2254270/54‑1 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCGCTAACCATCATCAGCAGGAAGtt < 1:398074/54‑1 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCGCTAACCATCATCAGCAGGAAGtt < 1:2091657/54‑1 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCGCTAACCATCATCAGCAGGAAGtt < 1:547764/54‑1 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCGCTAACCATCATCAGCAGGAAGtt < 1:708282/54‑1 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCGCTAACCATCATCAGCAGGAAGtt < 1:88720/54‑1 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCGCTAACCATCATCAGCAGGAAGtt < 1:917531/54‑1 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCGCTAACCATCATCAGCAGGAAGtt < 1:1827039/54‑1 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCGCTAACCATCATCAGCAGGAAGtt < 1:1678349/54‑1 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCGCTAACCATCATCAGCAGGAAGtt < 1:1668282/54‑1 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCGCTAACCATCATCAGCAGGAAGtt < 1:1612979/54‑1 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCGCTAACCATCATCAGCAGGAAGtt < 1:96838/54‑1 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCACTAACCATCATcagca > 1:1611005/1‑47 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCACTAACCATCATCAGCAGGAAGTTAATg > 1:2676594/1‑58 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCACTAACCATCATCAGCAGGAAGTTAATg > 1:821998/1‑58 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCACTAACCATCATCAGCAGGAAGTTAATg > 1:1939538/1‑58 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCACTAACCATCATCAGCAGGAAGTTAATg > 1:2058311/1‑58 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCACTAACCATCATCAGCAGGAAGTTAATg > 1:476207/1‑58 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCACTAACCATCATCAGCAGGAAGTTAATg > 1:460056/1‑58 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCACTAACCATCATCAGCAGGAAGTTAATg > 1:1510261/1‑58 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCACTAACCATCATCAGCAGGAAGTTAATg > 1:3345992/1‑58 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCACTAACCATCATCAGCAGGAAGTTAATg > 1:332200/1‑58 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCACTAACCATCATCAGCAGGAAGTTAATg > 1:2413979/1‑58 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCACTAACCATCATCAGCAGGAAGTTAATg > 1:1155997/1‑58 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCACTAACCATCATCAGCAGGAAGTTAATg > 1:2945463/1‑58 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCACTAACCATCATCAGCAGGAAGTTAATGGCTTCCACGcc < 1:3106544/69‑1 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCACTAACCATCATCAGCAGGAAGTTAATGGCTTCCACGcc < 1:2285922/69‑1 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCACTAACCATCATCAGCAGGAAGTTAATGGCTTCCACGcc < 1:3040954/69‑1 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCACTAACCATCATCAGCAGGAAGTTAATGGCTTCCACGcc < 1:2587176/69‑1 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCACTAACCATCATCAGCAGGAAGTTAATGGCTTCCACGcc < 1:1870050/69‑1 (MQ=255)
gCGTTTGACCAACGCCAGTGCCAGCAGGCCACTAACCATCATCAGCAGGAAGTTAATGGCTTCCACGcc < 1:1605571/69‑1 (MQ=255)
aGTGCCAGCAGGCCGCTAACCATCATCAGCAGGAAGtt < 1:1087662/38‑1 (MQ=255)
aGTGCCAGCAGGCCACTAACCATCATCAGCAGGAAGTTAATGGCTTCCACGCCCATTATCGGTGCCAGc < 1:1055143/69‑1 (MQ=255)
aGTGCCAGCAGGCCACTAACCATCATCAGCAGGAAGTTAATGGCTTCCACGCCCATTATCGGTGCCAGc < 1:2627399/69‑1 (MQ=255)
tGCCAGCAGGCCACTAACCATCATCAGCAGGAAGTTAATGGCTTCCACGcc < 1:2879955/51‑1 (MQ=255)
agcagGCCACTAACCATCATCAGCAGGAAGTTAATGGCTTCCACGCCCATTATCGGTGCCAGCCCtttt > 1:1244800/1‑69 (MQ=255)
agcagGCCACTAACCATCATCAGCAGGAAGTTAATGGCTTCCACGCCCATTATCGGTGCCAGCCCtttt > 1:2313997/1‑69 (MQ=255)
agcagGCCACTAACCATCATCAGCAGGAAGTTAATGGCTTCCACGCCCATTATCGGTGCCAGCCCtttt > 1:1832272/1‑69 (MQ=255)
agcagGCCACTAACCATCATCAGCAGGAAGTTAATGGCTTCCACGCCCATTATCGGTGCCAGCCCtttt > 1:179460/1‑69 (MQ=255)
|
CAAACAGCACGACGGCCACCACCAGCGGACGCCAGTTGCGTTTGACCAACGCCAGTGCCAGCAGGCCACTAACCATCATCAGCAGGAAGTTAATGGCTTCCACGCCCATTATCGGTGCCAGCCCTTTT > minE/413576‑413703
|
| 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
