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 |
|
A14 F27 I0 R1
|
1573 |
67.6 |
2866070 |
96.6% |
2768623 |
147.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_000913 |
1,708,805 |
T→A |
45.0% |
R629R (CGT→CGA) |
rsxC → |
SoxR [2Fe‑2S] reducing system protein RsxC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,708,805 | 0 | T | A | 45.0%
| ‑2.6
/ 3.9
| 11 | R629R (CGT→CGA) | rsxC | SoxR [2Fe‑2S] reducing system protein RsxC |
| Reads supporting (aligned to +/- strand): ref base T (3/3); new base A (3/2); total (6/5) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAG > NC_000913/1708711‑1708950
|
ccAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGcc < 1:285299/98‑1 (MQ=33)
aGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCAc > 1:1304987/1‑93 (MQ=35)
aGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCAc < 2:1304987/93‑1 (MQ=35)
ggAACAGCAACAGGCTAATGCGGATCCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGcg < 2:455292/88‑2 (MQ=255)
ggAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGcg > 1:455292/1‑87 (MQ=17)
gCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGcc > 1:1017716/1‑76 (MQ=21)
gCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGcc < 2:1017716/76‑1 (MQ=21)
ggTCGATCCGCGCAAAGCCGCCGTAGAAGCCGCTATTGCCCGAGCAAAAGCACGCAAGCTCGAACAGCAACAGGCTAATGCCGAGCCAGAACAACAGTTCGATCAGCGCAAAGCCGCAGTAGCACCGGCTATTGCCAGAGCGCAAgccaa > 2:453783/1‑147 (MQ=14)
gccgccGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAATCTGGAACAGCAACAGGCTAATGCCGAGCCAGAACAACAGGTAGATCCGCGCAAAGCAGCCGTCGAAGCAGCTATTGCCCGAGCCAAAGCGCGCAAACGGGagcgggac > 2:1308125/1‑143 (MQ=17)
ctcccGTGCCAAAGCACGCAAGCTGTAATATCATCACGCTAATGCAGAGCCAGAACAACTTTTGGATCCTCTCTAAGCAGACGTCGATGTTGCTATTTCCCGTGCCAAAGCTCGCAATCGGGAACAGCAACCGGCTAATGCGGAGCCaga < 2:1242817/148‑1 (MQ=255)
cccGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCCAGAACAACAGGTCGCTCCGCGCAAGGCCGCCGTCGACGCCGCTATTGCCCGAGCCCACGCGCGCAACCGGGAACAGCACCCGGCGACTGCGGAGcccgcag > 1:1242817/1‑145 (MQ=17)
|
CCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAG > NC_000913/1708711‑1708950
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
