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 I2 R1
|
67 |
32.5 |
1435938 |
95.9% |
1377064 |
112.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
3,350,675 |
Δ1 bp |
noncoding (99/121 nt) |
arcZ → |
sRNA positive antisense regulator of rpoS, binds Hfq |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 3,350,672 | 0 | C | . | 96.2%
| 105.4
/ ‑1.6
| 26 | noncoding (96/121 nt) | arcZ | sRNA positive antisense regulator of rpoS, binds Hfq |
| Reads supporting (aligned to +/- strand): ref base C (0/1); new base . (14/11); total (14/12) |
| Fisher's exact test for biased strand distribution p-value = 4.62e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.95e-01 |
TGATTCATGTAACAAATCATTTAAGTTTTGCTATCTTAACTGCGTGCGGCCTGAAAAACAGTGCTGTGCCCTTGTAACTCATCATAATAATTTACGGCGCAGCCAAGATTTCCCTGGTGTTGGCGCAGTATTCGCGCACCCCGGTCTAGCCGGGGTCATTTTTTAGTGGCTTTTGCCACCCACGCTTTCAGCACTTCTACGTCGTGACGCCACTCTTCTTTCATCTCTTCAATCCATTCACCGACGTTATCTTCCCAGGCCGGAAGGTCA > NC_000913/3350534‑3350803
|
tGATTCATGTAACAAATCATTTAAGTTTTGCTATCTTAACTGCGTGCGGCCTGAAAAACAGTGCTGTGCCCTTGTAACTCATCATAATAATTTACGGCGCAGCCAAGATTTCCCTGGTGTTGGCGCAGTATTCGCGCAc < 2:198634/139‑1 (MQ=255)
cAAATCATTTAAGTTTTGCTATCTTAACTGCGTGCGGCCTGAAAAACAGTGCTGTGCCCTTGTAACTCATCATAATAATTTACGGCGCAGCCAAGATTTCCCTGGTGTTGGCGCAGTATTCGCGCA‑CCCGGTCTAGCCg < 2:451564/139‑1 (MQ=255)
ttGCTATCTTAACTGCGTGCGGCCTGAAAAACAGTGCTGTGCCCTTGTAACTCATCATAATAATTTACGGCGCAGCCAAGATTTCCCTGGTGTTGGCGCAGTATTCGCGCA‑CCCGGTCTAGCCGGGGTCATTTTTTAGt < 1:189007/139‑1 (MQ=255)
ttGCTATCTTAACTGCGTGCGGCCTGAAAAACAGTGCTGTGCCCTTGTAACTCATCATAATAATTTACGGCGCAGCCAAGATTTCCCTGGTGTTGGCGCAGTATTCGCGCA‑CCCGGTCTAGCCGGGGTCATTTTTTAGt > 2:189007/1‑139 (MQ=255)
gtgcgGCCTGAAAAACAGTGCTGTGCCCTTGTAACTCATCATAATAATTTACGGCGCAGCCAAGATTTCCCTGGTGTTGGCGCAGTATTCGCGCAcc > 2:355889/1‑97 (MQ=255)
gtgcgGCCTGAAAAACAGTGCTGTGCCCTTGTAACTCATCATAATAATTTACGGCGCAGCCAAGATTTCCCTGGTGTTGGCGCAGTATTCGCGCAcc < 1:355889/97‑1 (MQ=255)
tgcgGCCTGAAAAACAGTGCTGTGCCCTTGTAACTCATCATAATAATTTACGGCGCAGCCAAGATTTCCCTGGTGTTGGCGCAGTATTCGCGCA‑CCCGGTCTAGCCGGGGTCATTTTTTAGTGGCTTTTGCCACCCACg > 1:222720/1‑139 (MQ=255)
tgcgGCCTGAAAAACAGTGCTGTGCCCTTGTAACTCATCATAATAATTTACGGCGCAGCCAAGATTTCCCTGGTGTTGGCGCAGTATTCGCGCA‑CCCGGTCTAGCCGGGGTCATTTTTTAGTGGCTTTTGCCACCCACg > 2:35751/1‑139 (MQ=255)
cTGAAAAACAGTGCTGTGCCCTTGTAACTCATCATAATAATTTACGGCGCAGCCAAGATTTCCCTGGTGTTGGCGCAGCATTCGCGCA‑CCCGGTCTAGCCGGGGTCATTTTTTAGTGGCTTTTGCCACCCACGCTTTCa < 1:405265/139‑1 (MQ=255)
tGAAAAACAGTGCTGTGCCCTTGTAACTCATCATAATAATTTACGGCGCAGCCAAGATTTCCCTGGTGTTGGCGCAGTATTCGCGCA‑CCCGGTCTAGCCGGGGTCATTTTTTAGTGGCTTTTGCCACCCACGCTTTCAg < 1:404296/139‑1 (MQ=255)
gTGCTGTGCCCTTGTAACTCATCATAATAATTTACGGCGCAGCCAAGATTTCCCTGGTGTTGGCGCAGTATTCGCGCACCCCGGTCTAGCCGGGGTCATTTTTTAGTGGCTTTTGCCACCCACGCTTTCAGCACTTCTa < 2:610856/139‑1 (MQ=255)
cTGTGCCCTTGTAACTCATCATAATAATTTACGGCGCAGCCAAGATTTCCCTGGTGTTGGCGCAGTATTCGCGCA‑CCCGGTCTAGCCGGGGTCATTTTTTCGTGGCTTTTGCCACCCACGCTTTCAGCACTTCTAcgtc > 2:493616/1‑139 (MQ=255)
aCTCATCATAATAATTTACGGCGCAGCCAAGATTTCCCTGGTGTTGGCGCAGTATTCGCGCA‑CCCGGTCTAGCCGGGGTCATTTTTTAGTGGCTTTTGCCACCCACGCTTTCAGCACTTCTACGTCGTGACGCCActct > 2:653754/1‑139 (MQ=255)
taatgaTTTACGGCGTAGCCAAGATTTCCCTGGTGTTGGCGCAGTATTCGCGCA‑CCCGGTCTAGCCGGGGTCATTTTTTAGTGGCTTTTGCCACCCACGCTTTCAGCACTTCTACGTCGTGACGCCACTCTTCTTTCAt < 1:240789/139‑1 (MQ=255)
taataaTTTACGGCGCAGCCAAGATTTCCCTGGTGTTGGCGCAGTATTCGCGCA‑CCCGGTCTAGCCGGGGTCATTTTTTAGTGGCTTTTGCCACCCACGCTTTCAGCACTTCTACGTCGTGACGCCACTCTTCTTTCAt < 1:653754/139‑1 (MQ=255)
tACGGCGCAGCCAAGATTTCCCTGGTGTTGGCGCAGTATTCGCGCA‑CCCGGTCTAGCCGGGGTCATTTTTTAGTGGCTTTTGCCACCCACGCTTTCAGCACTTCTACGTCGTGACGCCACTCTTCTTTCATCTCTTCaa > 2:255651/1‑139 (MQ=255)
tACGGCGCAGCCAAGATTTCCCTGGTGTTGGCGCAGTATTCGCGCA‑CCCGGTCTAGCCGGGGTCATTTTTTAGTGGCTTTTGCCACCCACGCTTTCAGCACTTCTACGTCGTGACGCCACTCTTCTTTCATCTCTTCaa > 1:120680/1‑139 (MQ=255)
ggCGCAGCCAAGATTTCCCTGGTGTTGGCGCAGTATTCGCGCAc > 1:60143/1‑44 (MQ=255)
ggCGCAGCCAAGATTTCCCTGGTGTTGGCGCAGTATTCGCGCAc < 2:60143/44‑1 (MQ=255)
cgcAGCCAAGATTTCCCTGGTGTTGGCGCAGTATTCGCGCA‑CCCGGTCTAGCCGGGGTCATTTTTTAGTGGCTTTTGccaccc < 2:662588/83‑1 (MQ=255)
cgcAGCCAAGATTTCCCTGGTGTTGGCGCAGTATTCGCGCA‑CCCGGTCTAGCCGGGGTCATTTTTTAGTGGCTTTTGccaccc > 1:662588/1‑83 (MQ=255)
cgcAGCCAAGATTTCCCTGGTGTTGGCGCAGTATTCGCGCA‑CCCGGTCTAGCCGGGGTCATTTTTTAGTGGCTTTTGccac < 2:488283/81‑1 (MQ=255)
cgcAGCCAAGATTTCCCTGGTGTTGGCGCAGTATTCGCGCA‑CCCGGTCTAGCCGGGGTCATTTTTTAGTGGCTTTTGccac > 1:488283/1‑81 (MQ=255)
ccAAGATTTCCCTGGTGTTGGCGCAGTATTCGCGCA‑CCCGGTCTAGCCGGGGTCATTTTTTAGTGGCTTTTGCCACCCACGCTTTCAGCACTTCTAcg < 2:35750/98‑1 (MQ=255)
ccAAGATTTCCCTGGTGTTGGCGCAGTATTCGCGCA‑CCCGGTCTAGCCGGGGTCATTTTTTAGTGGCTTTTGCCACCCACGCTTTCAGCACTTCTAcg > 1:35750/1‑98 (MQ=255)
tgtTGGCGCAGTATTCGCGCA‑CCCGGTCTAGCCGGGGTCAt < 1:641790/41‑1 (MQ=255)
tgtTGGCGCAGTATTCGCGCA‑CCCGGTCTAGCCGGGGTCAt > 2:641790/1‑41 (MQ=255)
tgtTGGCGCAGTATTCGCGCA‑CCCGGTCTAGCCGGGGTCATTTTTTAGTGGCTTTTGCCACCCACGCTTTCAGCACTTCTACGTCGTGACGCCACTCTTCTTTCATCTCTTCAATCCATTCACCGACGTTATCTTCCCa > 1:663241/1‑139 (MQ=255)
tGGCGCAGTATTCGCGCA‑CCCGGTCTAGCCGGGGTCATTTTTTAGTGGCTTTTGCCACCCACGCTTTCAGCACTTCTACGTCGTGACGCCACtcttct < 2:208284/98‑1 (MQ=255)
tGGCGCAGTATTCGCGCA‑CCCGGTCTAGCCGGGGTCATTTTTTAGTGGCTTTTGCCACCCACGCTTTCAGCACTTCTACGTCGTGACGCCACtcttct > 1:208284/1‑98 (MQ=255)
ttCGCGCA‑CCCGGTCTAGCCGGGGTCATTTTTTAGTGGCTTTTGCCACCCACGCTTTCAGCACTTCTACGTCGTGACGCCACTCTTCTTTCATCTCTTCAATCCATTCACCGACGTTATCTTCCCAGGCCGGAAGGTCa > 1:264507/1‑139 (MQ=255)
|
TGATTCATGTAACAAATCATTTAAGTTTTGCTATCTTAACTGCGTGCGGCCTGAAAAACAGTGCTGTGCCCTTGTAACTCATCATAATAATTTACGGCGCAGCCAAGATTTCCCTGGTGTTGGCGCAGTATTCGCGCACCCCGGTCTAGCCGGGGTCATTTTTTAGTGGCTTTTGCCACCCACGCTTTCAGCACTTCTACGTCGTGACGCCACTCTTCTTTCATCTCTTCAATCCATTCACCGACGTTATCTTCCCAGGCCGGAAGGTCA > NC_000913/3350534‑3350803
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
