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 |
|
A4 F1 I1 R1
|
73 |
24.7 |
1166784 |
93.9% |
1095610 |
107.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
1,927,241 |
(C)6→7 |
coding (1599/2061 nt) |
ptrB ← |
protease II |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,927,235 | 1 | . | C | 91.7%
| 78.7
/ 1.0
| 24 | coding (1605/2061 nt) | ptrB | protease II |
| Reads supporting (aligned to +/- strand): ref base . (1/1); new base C (11/11); total (12/12) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.92e-01 |
AGAGGAATTGATTCATCAAGCATCGTTGTTACAACATCAACAAACGGTACCTGGGCGATAACGCCGTGGAATAATTCCGGGCGTTGATTAATTGCAACGCCCATCAACATG‑CCCCCCGCACTCCCGCCCATCGCATAACAAAGCGAAGGAGAGCCATAGCCCAGTTTTAACAATGCATCGCAGGCATCAAGATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGT > NC_000913/1927125‑1927362
|
agagGAATTGATTCATCAAGCATCGTTGTTACAACATCAACAAACGGTACCTGGGCGATAACGCCGTGGAATAATTCCGGGCGTTGATTAATTGCAACGCCCATCAACATG‑CCCCCCGCACTCCCGCCCATCGCATAAc > 2:83763/1‑139 (MQ=255)
tcatcaAGCATCGTTGTTACAACATCAACAAACGGTACCTGGGCGATAACGCCGTGGAATAATTCCGGGCGTTGATTAATTGCAACGCCCATCAACATGCCCCCCCGCACTCCCGCCCATCGCATAACAAAGCGAAGga < 1:52861/139‑1 (MQ=255)
atcaAGCATCGTTGTTACAACATCAACAAACGGTACCTGGGCGATAACGCCGTGGAATAATTCCGGGCGTTGATTAATTGCAACGCCCATCAACATGCCCCCCCGCACTc < 1:214687/110‑1 (MQ=255)
atcaAGCATCGTTGTTACAACATCAACAAACGGTACCTGGGCGATAACGCCGTGGAATAATTCCGGGCGTTGATTAATTGCAACGCCCATCAACATGCCCCCCCGCACTc > 2:214687/1‑110 (MQ=255)
gttgttACAACATCAACAAACGGTACCTGGGCGATAACGCCGTGGAATAATTCCGGGCGTTGATTAATTGCAACGCCCATCAACATGCCCCCCCGCACTCCCGCCCATCGCATAACAAAGCGAAGGAGAGCCATAGccc > 2:487078/1‑139 (MQ=255)
caacaTCAACAAACGGTACCTGGGCGATAACGCCGTGGAATAATTCCGGGCGTTGATTAATTGCAACGCCCATCAACATG‑CCCCCCGCACTCCCGCCCATCGCATAACAAAGCGAAGGAGAGCCATAGCCCAGTTTTaa < 1:83763/139‑1 (MQ=255)
caTCAACAAACGGTACCTGGGCGATAACGCCGTGGAATAATTCCGGGCGTTGATTAATTGCAACGCCCATCAACATGCCCCCCCGCACTCCCGCCCATCGCATAACAAAGCGAAGGAGAGCCATAGCCCAGTTTTAACa > 2:288051/1‑139 (MQ=255)
aTCAACAAACGGTACCTGGGCGATAACGCCGTGGAATAATTCCGGGCGTTGATTAATTGCAACGCCCATCAACATGCCCCCCCGCACTCCCGCCCATCGCATAACAAAGCGAAGGAGAGCCATAGCCCAGTTTTAACaa > 1:89463/1‑139 (MQ=255)
ggTACCTGGGCGATAACGCCGTGGAATAATTCCGGGCGTTGATTAATTGCAACGCCCATCAACATGCCCCCCCGCACTCCCGCCCATCGCATAACAAAGCGAAGGAGAGCCATAGCCCAGTTTTAACAATGCATCGCAg > 1:582973/1‑139 (MQ=255)
aCCTGGGCGATAACGCCGTGGAATAATTCCGGGCGTTGATTAATTGCAACGCCCATCAACATGCCCCCCCGCACTCCCGCCCATCGCATAACAAAGCGAAGGAGAGCCATAGCCCAGTTTTAACAATGCATCGCAGGCa < 2:582973/139‑1 (MQ=255)
cTGGGCGATAACGCCGTGGAATAATTCCGGGCGTTGATTAATTGCAACGCCCATCAACATGCCCCCCCGCACTCCCGCCCATCGCATAACAAAGCGAAGGAGAGCCATAGCCCAGTTTTAACAATGCATCGCAGGCATc < 1:487078/139‑1 (MQ=255)
cGATAACGCCGTGGAATAATTCCGGGCGTTGATTAATTGCAACGCCCATCAACATGCCCCCCCGCACTCCCGcc > 1:343259/1‑74 (MQ=255)
cGATAACGCCGTGGAATAATTCCGGGCGTTGATTAATTGCAACGCCCATCAACATGCCCCCCCGCACTCCCGcc < 2:343259/74‑1 (MQ=255)
cGATAACGCCGTGGAATAATTCCGGGCGTTGATTAATTGCAACGCCCATCAACATGCCCCCCCGCACTCCCGCCCATCGCATAACAAAGCGAAGGAGAGCCCTAGc > 2:479268/1‑106 (MQ=255)
cGATAACGCCGTGGAATAATTCCGGGCGTTGATTAATTGCAACGCCCATCAACATGCCCCCCCGCACTCCCGCCCATCGCATAACAAAGCGAAGGAGAGCCATAGc < 1:479268/106‑1 (MQ=255)
cGATAACGCCGTGGAATAATTCCGGGCGTTGATTAATTGCAACGCCCATCAACATGCCCCCCCGCACTCCCGCCCATCGCATAACAAAGCGAAGGAGAGCCATAGCCCAGTTTTAACAATGCATCGCAGGCATCAAGAt < 2:89463/139‑1 (MQ=255)
gAATAATTCCGGGCGTTGATTAATTGCAACGCCCATCAACATGCCCCCCCGCACTCCCGCCCATCGCATAACAAAGCGAAGGAGAGCCATAGCCCAGTTTTAACAATGCATCGCAGGCATCAAGATAATCATTAAACGt > 1:239998/1‑139 (MQ=255)
ttGATTAATTGCAACGCCCATCAACATGCCCCCCCGCACTCCCGCCCATCGCATAACAAAGCGAAGGAGAGCCATAGCCCAGTTTTAACAATg > 2:193308/1‑93 (MQ=255)
ttGATTAATTGCAACGCCCATCAACATGCCCCCCCGCACTCCCGCCCATCGCATAACAAAGCGAAGGAGAGCCATAGCCCAGTTTTAACAATg < 1:193308/93‑1 (MQ=255)
aCGCCCATCAACATGCCCCCCCGCACTCCCGCCCATCGCATAACAAAGCGAAGGAGAGCCATAGCCCAGTTTTAACAATGCATCGCAGGCATCAAGATa > 2:218027/1‑99 (MQ=255)
aCGCCCATCAACATGCCCCCCCGCACTCCCGCCCATCGCATAACAAAGCGAAGGAGAGCCATAGCCCAGTTTTAACAATGCATCGCAGGCATCAAGATa < 1:218027/99‑1 (MQ=255)
ccATCAACATGCCCCCCCGCACTCCCGCCCATCGCATAACAAAGCGAAGGAGAGCCATAGCCCAGTTTTAACAATGCATCGCAGGCATCAAGATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGt < 1:17039/139‑1 (MQ=255)
atgaaCATGCCCCCCCGCACTCCCGCCCATCGCATAACAAAGCGAAGGAGAGCCATAGCCCAGTTTTAACAATGCATCGCAGGCATCAAGATAATCATTAAACGTATTTttc < 2:393642/109‑1 (MQ=255)
aTCAACATGCCCCCCCGCACTCCCACCCATCGCATAACAAAGCGAAGGAGAGCCATAGCCCAGTTTTAACAATGCATCGCAGGCATCAAGATAATCATTAAACGTATTTttc > 1:393642/1‑112 (MQ=255)
|
AGAGGAATTGATTCATCAAGCATCGTTGTTACAACATCAACAAACGGTACCTGGGCGATAACGCCGTGGAATAATTCCGGGCGTTGATTAATTGCAACGCCCATCAACATG‑CCCCCCGCACTCCCGCCCATCGCATAACAAAGCGAAGGAGAGCCATAGCCCAGTTTTAACAATGCATCGCAGGCATCAAGATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGT > NC_000913/1927125‑1927362
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
