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 I1 R1
|
748 |
32.0 |
1685426 |
92.6% |
1560704 |
103.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,767,445 |
(C)7→8 |
intergenic (+90/‑265) |
rnlB → / → yfjP |
CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, 50S ribosome‑binding GTPase family protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,767,438 | 1 | . | C | 93.8%
| 44.1
/ ‑2.9
| 16 | intergenic (+83/‑272) | rnlB/yfjP | CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, 50S ribosome‑binding GTPase family protein |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base C (6/9); total (7/9) |
| Fisher's exact test for biased strand distribution p-value = 4.38e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.28e-01 |
TCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑CC‑CCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCC > NC_000913/2767305‑2767561
|
tctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑cc‑ccc > 1:839365/1‑139 (MQ=255)
tctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑cc‑ccc > 1:702971/1‑139 (MQ=255)
tctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c > 2:39499/1‑135 (MQ=255)
tctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c < 1:39499/135‑1 (MQ=255)
gTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCCTcaca < 2:839365/139‑1 (MQ=255)
gTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCCTcaca < 2:702971/139‑1 (MQ=255)
gTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑cc‑ccccc > 1:671501/1‑111 (MQ=255)
gTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑cc‑ccccc < 2:671501/111‑1 (MQ=255)
gTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑CCACCCACTCACAACGTTTTGCATAGTGTACACGTGTTct > 2:171250/1‑138 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCCTcaca < 1:530293/62‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCCTcaca > 2:530293/1‑62 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCCTCACAACGTCCTGCATAGGGAac < 1:710810/80‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCCTCACAACGTCCTGCATAGGGAac > 2:710810/1‑80 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCCTCACAACGTCCTGCATAGGGAACACGTTTTccc < 1:348115/90‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCCTCACAACGTCCTGCATAGGGAACACGTTTTccc > 2:348115/1‑90 (MQ=255)
tttGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAAA‑AT‑CCCCCTCACAACCTCCTTCAAAGGGAACACGTTTTCCCCTGTGCACCCACTACTAAATTTCCCCCCCATCACACTACTCAATAATATCACCa > 2:324447/1‑139 (MQ=255)
atatTAACTAGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCCTCACAACGTCCTGCATAGGGAACTCGTTTTCCCCTGTGCACCCACGACTAAATCTCCCCCCCTGCAAACTTCTCAATGATATCACCAAATTTCTgg < 2:539124/139‑1 (MQ=255)
aCTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCCTCACAACGTCCTGCATAGGGAACACGTTTTccc < 2:273647/70‑1 (MQ=255)
aCTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCCTCACAACGTCCTGCATAGGGAACACGTTTTccc > 1:273647/1‑70 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACCC‑CCCCCTCACAACGTCCTTCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTatga > 1:120020/1‑139 (MQ=255)
atGATCAAATAGCATT‑AACCC‑CCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCtt < 2:17800/139‑1 (MQ=255)
gATCAAATAGCATT‑AACCC‑CCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTc < 1:324447/139‑1 (MQ=255)
aTCAAATAGCATT‑AACCC‑CCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAAATTCCCCCCCTTTAAACTTCTCAATAATTTCACCAATTTTCTGGAAATCATATGATCCCTTTcc > 2:276667/1‑139 (MQ=255)
aTCAAATAGCATT‑AACCC‑CCCCCTCACAACGTCCTGCATAGGGAACACGTGTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTcc < 2:445787/139‑1 (MQ=255)
|
TCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑CC‑CCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCC > NC_000913/2767305‑2767561
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
