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 |
|
A8 F1 I1 R1
|
82 |
28.6 |
1225488 |
97.4% |
1193625 |
116.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,765,794 |
(C)7→8 |
intergenic (‑18/‑124) |
yfjM ← / → rnlA |
CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, RNase LS |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,765,787 | 1 | . | C | 93.3%
| 97.8
/ 0.4
| 30 | intergenic (‑11/‑131) | yfjM/rnlA | CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, RNase LS |
| Reads supporting (aligned to +/- strand): ref base . (2/0); new base C (9/19); total (11/19) |
| Fisher's exact test for biased strand distribution p-value = 1.26e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.42e-01 |
GGCTCTCTGCTCGTTCTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑C‑CCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATG > NC_000913/2765650‑2765906
|
ggCTCTCTGCTCGTTCTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑c > 2:92395/1‑139 (MQ=255)
ctGCTCGTTCTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑c‑cccccc < 2:489595/139‑1 (MQ=255)
ttCTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCGGTAGa < 1:95916/139‑1 (MQ=255)
tttCGATGTAGAATTTTTTCTTGTCTGCTAGCGAATAATTACTGAGTGTCGAGTTGCTGCTTGGGGAGATCGGGAAGGGGTTGTAGAAGCGATGGCTGTCATCCCCCATTTTTTGGACAG‑c‑cccccccgctagattatc < 1:445172/139‑13 (MQ=255)
tttCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCGGTAGACGATc < 2:297247/139‑1 (MQ=255)
aCGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCGGTAGACGATCCTGcc < 1:194750/139‑1 (MQ=255)
cGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCGGTAGACGATCCTGccc < 1:508773/139‑1 (MQ=255)
gAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTT‑c‑cc > 1:34041/1‑113 (MQ=255)
gAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑c‑cc < 2:34041/113‑1 (MQ=255)
tCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGt < 1:23820/139‑1 (MQ=255)
tCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGt < 2:121608/139‑1 (MQ=255)
tCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCGGTAGa < 1:582400/111‑1 (MQ=255)
tCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCGGTAGa > 2:582400/1‑111 (MQ=255)
tATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑C‑CCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCa > 2:585604/1‑139 (MQ=255)
tATCGAGTTGCTGCTTGGTGAGATAAGGAAGAGGTTACCGAAACGATGGACATCATACACCATTTTGTGGACTGCC‑CCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGc > 1:227275/1‑139 (MQ=255)
tCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑c‑cccc > 2:334469/1‑77 (MQ=255)
tCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑c‑cccc < 1:334469/77‑1 (MQ=255)
gAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAAt < 1:255394/139‑1 (MQ=255)
aGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATc > 1:336672/1‑139 (MQ=255)
gctgctTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa < 1:92395/139‑1 (MQ=255)
ctgctTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCGGTAGACGATc > 1:164804/1‑83 (MQ=255)
ctgctTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCGGTAGACGATc < 2:164804/83‑1 (MQ=255)
ctgctTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGcc < 1:340735/104‑1 (MQ=255)
ctgctTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATac > 2:322345/1‑139 (MQ=255)
ctgctTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑c‑cccccccg < 1:504554/73‑3 (MQ=255)
ctgctTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑c‑cccccccg > 2:504554/1‑71 (MQ=255)
ctgctTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CTCCCCCCGGTAGACGATCCAGCCCTATCGTTGGAGTGcc > 2:340735/1‑104 (MQ=255)
tGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAgg < 2:136400/139‑1 (MQ=255)
tGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAgg > 1:136400/1‑139 (MQ=255)
agaTCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAgggg < 1:461934/139‑1 (MQ=255)
aTCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAgggggg < 2:336672/139‑1 (MQ=255)
gTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAggg < 2:152430/125‑1 (MQ=255)
gTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAggg > 1:152430/1‑125 (MQ=255)
aaaCGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTcc < 2:44488/139‑1 (MQ=255)
tGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCGGTAGACGATCCTGCCCTATAGTTg < 1:359637/61‑1 (MQ=255)
tGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCGGTAGACGATCCTGCCCTATAGTTg > 2:359637/1‑61 (MQ=255)
tcCCCCATTTTGTGGACTGCC‑CCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATg < 1:322345/139‑1 (MQ=255)
tgGACTGCC‑CCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGcc < 2:322012/47‑1 (MQ=255)
tgGACTGCC‑CCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGcc > 1:322012/1‑47 (MQ=255)
|
GGCTCTCTGCTCGTTCTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑C‑CCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATG > NC_000913/2765650‑2765906
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
