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 |
|
A5 F1 I1 R1
|
770 |
51.4 |
2439994 |
93.8% |
2288714 |
110.3 |
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 | 93.0%
| 130.2
/ 2.6
| 43 | 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 . (3/0); new base C (20/20); total (23/20) |
| Fisher's exact test for biased strand distribution p-value = 2.36e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAA‑C‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGG > NC_000913/2767305‑2767571
|
tctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAA‑c‑cc‑c > 1:736617/1‑138 (MQ=255)
tctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAA‑c‑cc‑c < 2:736617/138‑1 (MQ=255)
ctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAA‑c‑cc‑ccc > 1:792749/1‑139 (MQ=255)
tGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAA‑c‑cc‑cccc > 1:1045063/1‑139 (MQ=255)
gTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CC‑CCCCTcaca < 2:792749/139‑1 (MQ=255)
gTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CC‑CCCCTcaca < 2:1045063/139‑1 (MQ=255)
gCCAAGTCCTGTCAATGGATTTTTGAATCTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CC‑CCCCTCACAACGTCCTGCATAGGGa < 2:730640/138‑1 (MQ=255)
gCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCTAATAGCATTAACC‑CC‑CCCCTCACAACGTCCTGCATAGGGa > 1:730640/1‑138 (MQ=255)
gCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAA‑c‑cc‑c < 2:952872/113‑1 (MQ=255)
gCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAA‑c‑cc‑c > 1:952872/1‑113 (MQ=255)
ccAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAac < 2:1117868/139‑1 (MQ=255)
ccAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAac < 1:463971/139‑1 (MQ=255)
aGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACg > 1:689690/1‑139 (MQ=255)
gTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAA‑C‑CCTCCCCTCAAAAAGTACAGTATAGGGAACACga > 1:251424/1‑138 (MQ=255)
ccTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CC‑CCCCTcaca < 1:455270/115‑1 (MQ=255)
ccTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CC‑CCCCTcaca > 2:455270/1‑115 (MQ=255)
ccTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGttt > 1:810387/1‑139 (MQ=255)
tCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTTccc < 1:325329/139‑1 (MQ=255)
tCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTTccc < 1:1119537/139‑1 (MQ=255)
cAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTTcccc < 2:689690/139‑1 (MQ=255)
ttttGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCAcc < 2:810387/139‑1 (MQ=255)
gtataagagactggTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTccc < 2:598209/126‑1 (MQ=255)
ggTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACt < 2:558477/138‑1 (MQ=255)
taGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTTccc > 1:44848/1‑98 (MQ=255)
taGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTTccc < 2:44848/98‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CC‑CCCCTcaca < 1:335944/62‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CC‑CCCCTcaca > 2:335944/1‑62 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CC‑CCCCTCACAACGTCGTGGATAGGGAACACGTTTTCCCCTGTGGACCCACCACTAAATTCCCCCCCCGTTACATTTCTCAATAATgg > 2:772515/1‑138 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACC‑CC‑CCCCTCACAACGTCCTGCATCGGGTACACGATTCCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGt > 1:358663/1‑139 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAA‑CTCC‑CCCATCACAAAGTCCTGAATAAGGAACCCCTTTACCCCTGTGAAACCCCGACTAAAATTCACACCCTATAATCACCTCAATAATgc > 1:558477/1‑138 (MQ=255)
atatTAACTTGTCCAATATGATCAAATAGCATTAACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTgg < 2:782819/139‑1 (MQ=255)
aaCTTGTCCAATATGATCAAATAGCATTAA‑C‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCTTTGAAACTTCTATATAATTACACCAATTTTCTGGAACTcc > 1:767788/1‑139 (MQ=255)
cTTGTCCAATATGATCAAATAGCATTAACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCACTTTTCTGAAAATcca > 1:311759/1‑138 (MQ=255)
gTCCAATATGATCAAATAGCATTAACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAac < 2:336241/56‑1 (MQ=255)
gTCCAATATGATCAAATAGCATTAACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAac > 1:336241/1‑56 (MQ=255)
gTCCAATATGATCAAATAGCATTAACC‑CC‑CCCCTCACAACGTCCTACATAGGGAACACGTTTTCCCCTCTGCACCCACGACTAAATTTCACCACCTTTAAACTTCTCAATAATGTCACCACTTTTCTGGAAATCCTacg > 2:21188/1‑137 (MQ=255)
tCCAATATGATCAAATAGCATTAACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGtt > 2:14283/1‑60 (MQ=255)
tCCAATATGATCAAATAGCATTAACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGtt < 1:14283/60‑1 (MQ=255)
tCCAATATGATCAAATAGCATTAACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATTTCACCAATTTTCTGGAAATCCTatga > 1:656934/1‑139 (MQ=255)
tatGATCAAATAGCATTAACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCAcc < 1:1072110/69‑1 (MQ=255)
tatGATCAAATAGCATTAACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCAcc > 2:1072110/1‑69 (MQ=255)
tCAAATAGCATTAACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTCAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTccc > 1:668413/1‑139 (MQ=255)
tCAAATAGCATTAACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTCCCCCTGTGCACCCACGACTAAATTTCTCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAACTCCTATGTTGCCTTTccc > 1:548580/1‑139 (MQ=255)
tCAAATAGCATTAACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAACAAGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCAACAATTTTCTGGAAATCCTATGATGCCTTTccc > 1:372567/1‑139 (MQ=255)
cATTAACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCAcc < 2:632291/56‑1 (MQ=255)
cATTAACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCAcc > 1:632291/1‑56 (MQ=255)
aTTAACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACtt < 2:179915/84‑1 (MQ=255)
aTTAACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCACCCTTTAAACtt > 1:179915/1‑84 (MQ=255)
aTTAACC‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTGCTCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAAAAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATgg > 1:314711/1‑139 (MQ=255)
|
TCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAA‑C‑CC‑CCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGG > NC_000913/2767305‑2767571
|
| 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
