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 I2 R1
|
764 |
42.0 |
2018750 |
95.5% |
1927906 |
109.2 |
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 | 92.6%
| 74.6
/ 0.2
| 28 | 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 . (1/1); new base C (12/13); total (14/14) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.62e-01 |
CTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑A‑CCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCC > NC_000913/2767306‑2767561
|
ctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAATCGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑A‑caccac > 1:688995/1‑137 (MQ=255)
cccGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑ACCCCCCCCTCACAACGt > 2:920065/1‑139 (MQ=255)
cccGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑A‑cccccccaccacacgcc > 2:836009/1‑129 (MQ=255)
ccAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑ACCCCCCCCTCACAACGTCCTGCATAGGGAac < 1:920065/139‑1 (MQ=255)
aGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑ACCCCCCCCTCACAACGTCCTGCATAGGGAac < 2:189435/136‑1 (MQ=255)
aGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑ACCCCCCCCTCACAACGTCCTGCATAGGGAac > 1:189435/1‑136 (MQ=255)
tctatgtatgtctGAAACTCTTCTTTCTAAACGAACCAGTATAGACTTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑ATC‑CCCCCCCTCACGGCGTCCTGTATAGGGAACACGTTTTccc < 1:760930/127‑1 (MQ=255)
ggATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑A‑cccccccctca > 2:505456/1‑100 (MQ=255)
ggATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑A‑cccccccctca < 1:505456/104‑5 (MQ=255)
gtataagagacaggTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑ACCCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTccc < 2:522117/126‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAA‑A‑CACCCAATCAAAACGTCATACATAGGGAACACGTTTAACCCTGTGCACCACAGAATAAATTTCCACCCCTTTAAACTTATCaataatat > 2:706026/1‑137 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑ATCCCCCCCTCACAACGTCCTGCTTAGAGAACACGTTTTCCGCTGTTTAGACACCACTGAATATCCCCCCCGTCAAACTTCTCACTAATGt > 1:710968/1‑139 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑ACCCCCCCCTCTCAACTTCCTGCATAGGGAACAACTTTTCCCCTGTGCACACACGACTAAATTTCCCCCACTTCAAAccagacacttatca > 1:522117/1‑126 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑ACCCCCCCCTCACAACGt < 2:227866/66‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑ACCCCCCCCTCACAACGt > 1:227866/1‑66 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑ACCCCCCCCTCACAACGTCCTGCATAGGGAac < 1:65422/80‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑ACCCCCCCCTCACAACGTCCTGCATAGGGAac > 2:65422/1‑80 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑ACCCCCCCCTCACAACGTCCTGCAAAGGGAACTAGTTTTCCCTTGTGCACCCACGACTAAATTTCCTCCCCTTTAAACTTCCCAATAATga > 1:883918/1‑138 (MQ=255)
tGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑ACCCCCCCCTCCCAACGTCCTGCATAGGGAACACGGTTGCGCCTCTGCACCCAAGACTAAATTACTCACCCTTTAAAATTCTGAATAATATCACCATTTTTCt > 2:757195/1‑139 (MQ=255)
atatTAACTTGTCCAATATGATCAAATAGCATT‑A‑ACCCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTgg < 2:710968/139‑1 (MQ=255)
atatTAACTTGTCCAATATGATCAAATAGCATT‑A‑ACCCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTgg < 2:377948/139‑1 (MQ=255)
atatTAACTTGTCCAATATGATCAAATAGCATT‑A‑ACCCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTgg < 2:883918/139‑1 (MQ=255)
atTAACTTGTCCAATATGATCAAATAGCATT‑A‑ACCCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGaa < 1:706026/139‑1 (MQ=255)
tatGATCAAATAGCATT‑A‑ACCCCCCCCTCACAACGt > 2:213368/1‑36 (MQ=255)
tatGATCAAATAGCATT‑A‑ACCCCCCCCTCACAACGt < 1:213368/36‑1 (MQ=255)
tGATCAAATAGCATT‑A‑ACCCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTACACCCAAGACTAAATTTCCCCCCCTTTAAACTTCTCAAAAATGACACCAATTTTCTGGAAATCCTATGATGTCttt > 2:173043/1‑139 (MQ=255)
gaccAAATAGCATT‑A‑C‑CCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTcc < 1:836009/136‑1 (MQ=255)
aTT‑A‑ACCCCCCCCTCACAACGTCCTGCATAGGGAac < 2:324550/36‑1 (MQ=255)
aTT‑A‑ACCCCCCCCTCACAACGTCCTGCATAGGGAac > 1:324550/1‑36 (MQ=255)
aTT‑A‑ACCCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCTCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCCCCAATTTTCTGGAAATCCTATGATGCCTTTc > 2:355706/1‑128 (MQ=255)
aTT‑A‑ACCCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTcc < 1:986128/129‑1 (MQ=255)
aTT‑A‑ACCCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTc < 1:355706/128‑1 (MQ=255)
aTT‑A‑ACCCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTCAAATTTCTCAATAATGTCACCAATTCTCTGGAAATCCTATGATGCCTTTcc > 2:986128/1‑129 (MQ=255)
|
CTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑A‑CCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCC > NC_000913/2767306‑2767561
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
