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
|
765 |
39.6 |
1867486 |
94.4% |
1762906 |
108.0 |
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 | 90.0%
| 89.8
/ 2.7
| 30 | 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 (11/16); total (14/16) |
| Fisher's exact test for biased strand distribution p-value = 8.97e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CCTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑C‑CCC‑CCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCG > NC_000913/2767303‑2767563
|
ccTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c‑cc < 2:485811/139‑1 (MQ=255)
ttGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c‑ccc‑cccctca < 1:221346/139‑5 (MQ=255)
gTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCC‑CCCTcaca < 1:891828/139‑1 (MQ=255)
cccGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑a‑cccactcaaacaacgt > 2:488085/1‑126 (MQ=255)
ccGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCC‑CCCTCACAACGTc < 1:264064/139‑1 (MQ=255)
ccGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCC‑CCCTCACAACGTc < 1:482311/139‑1 (MQ=255)
gatgatGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCC‑CCCTCACAACGTCCt < 2:358375/139‑1 (MQ=255)
aGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAAA‑C‑CAC‑TCCCCACAACGCCATCTATCGGGAACTCg > 1:812030/1‑139 (MQ=255)
tCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c‑ccc‑cccctca < 2:800722/109‑5 (MQ=255)
tCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c‑ccc‑cccctca > 1:800722/1‑105 (MQ=255)
ttctAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCC‑CCCTcaca < 2:43429/87‑1 (MQ=255)
ttctAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCC‑CCCTcaca > 1:43429/1‑87 (MQ=255)
ccAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAAA‑C‑CCC‑CCCTCACAACGTCCTCCATAGGGAACACGTTTTCCCCTGTTCACCCACGACTAAATTTCCCCCCCTTTaaa > 2:483734/1‑139 (MQ=255)
caggtgtaGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCC‑CCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTaaa < 1:579133/133‑1 (MQ=255)
ttCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCC‑CCCTCACAACGTCCTGCATa > 2:735984/1‑77 (MQ=255)
ttCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCC‑CCCTCACAACGTCCTGCATa < 1:735984/77‑1 (MQ=255)
ttCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCC‑CCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCaataa < 1:488085/139‑1 (MQ=255)
tcccTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCC‑CCCTCACAACGTCCTGCAt > 1:571745/2‑73 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCC‑CCCTCACATCGTCCTCCATAGGGAACACGTTTTCCCCTGTGCACCAACGACAAAAGTTCCCCCACTTTAAACCTCTCaatagcgg > 2:579133/1‑135 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCC‑CCCTCACAACGTCCTGCAt < 2:571745/73‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCC‑CCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCAcc < 2:802205/99‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCC‑CCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCAcc > 1:802205/1‑99 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCC‑CCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGt > 2:244718/1‑139 (MQ=255)
tttGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AC‑C‑CCCACCCCCCCAACGTCCTACATAACGAACACGTTTTCCCCTTTTCGCTCTCTACTAAAATTATACCCCTTTAAACATCACAAGAATgataaaa > 1:463915/1‑133 (MQ=255)
atTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCC‑CCCTCACAAAGTCCTGCATAGTGAAAACGTTTTACCCTGTGCACCCACGACCAAATTTCCCCCCCTCTAAACATCTCAATACTGTCCACAATTCTCTgtta > 1:256705/1‑136 (MQ=255)
ttAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCC‑CCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGaaa < 1:483734/139‑1 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACC‑CCC‑CCCTcaca < 2:337165/37‑1 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACC‑CCC‑CCCTcaca > 1:337165/1‑37 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACC‑CCC‑CCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTaaa < 2:650950/100‑1 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACC‑CCC‑CCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATTTCACCAATTTTCTGGAAATCCTatga > 2:804091/1‑139 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACC‑CCC‑CCCTCACAACGTCCTGCATAGGGAAAACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCCCCATAATGTCACCAATTTACTGGAAATCCTatga > 2:701926/1‑139 (MQ=255)
tCCAATATGATCAAATAGCATT‑AA‑CACCC‑CCCTCACAACGTCCTGCATAGGGAACCCGTTTTCCCCTTTGCACCCACGACTAAATTTCCCCCCCTTTaaa > 1:650950/1‑100 (MQ=255)
ccAATATGATCAAATAGCATT‑AACC‑CCC‑CCCTcaca > 1:829141/1‑36 (MQ=255)
ccAATATGATCAAATAGCATT‑AACC‑CCC‑CCCTcaca < 2:829141/36‑1 (MQ=255)
gATCAAATAGCATT‑AACC‑CCC‑CCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTc < 2:812030/139‑1 (MQ=255)
cAAATAGCATT‑AACC‑CCC‑CCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCg < 1:804091/139‑1 (MQ=255)
|
CCTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑C‑CCC‑CCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCG > NC_000913/2767303‑2767563
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
