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 |
|
A1 F1 I1 R1
|
66 |
20.9 |
912876 |
97.7% |
891879 |
114.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,765,794 |
(C)7→6 |
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 | 2,765,788 | 0 | C | . | 84.6%
| 78.3
/ 12.8
| 26 | intergenic (‑12/‑130) | yfjM/rnlA | CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, RNase LS |
| Reads supporting (aligned to +/- strand): ref base C (2/2); new base . (9/13); total (11/15) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.05e-01 |
GCTCTCTGCTCGTTCTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATC > NC_000913/2765651‑2765911
|
gCTCTCTGCTCGTTCTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGcc < 2:198947/139‑1 (MQ=255)
ctctGCTCGTTCTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGccccc < 1:149668/139‑1 (MQ=255)
ctctGCTCGTTCTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGccccc < 1:381962/139‑1 (MQ=255)
tctGCTCGTTCTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGccccc > 2:39280/1‑138 (MQ=255)
tctGCTCGTTCTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGccccc < 1:39280/138‑1 (MQ=255)
cGTTCTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CCCCCCGGTAGa < 1:347955/139‑1 (MQ=255)
cTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CCCCCCGGTAGACGAt > 2:249085/1‑139 (MQ=255)
ttCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CCCCCCGGTAGACGATCCTg < 2:85433/139‑1 (MQ=255)
gACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGGTCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CCCCCCGGTAGACGATCCTGccc < 1:249085/139‑1 (MQ=255)
gACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CCCCCCGGTAGACGATCCTGccc < 1:40415/139‑1 (MQ=255)
gTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CCCCCCGGTAGACGATCCTGCCCtat < 1:158040/139‑1 (MQ=255)
gAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CCCCCCGGTAGACGATCCTGCCCTATAGt > 2:254269/1‑139 (MQ=255)
tCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTGTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTg > 2:212260/1‑139 (MQ=255)
cTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGcc < 1:405794/139‑1 (MQ=255)
taatTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CCCCCCGGTAGACGATc < 2:286280/102‑1 (MQ=255)
taatTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CCCCCCGGTAGACGATc > 1:286280/1‑102 (MQ=255)
aGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGt < 1:382507/112‑1 (MQ=255)
aGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGt > 2:382507/1‑112 (MQ=255)
tgctgcTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa < 1:212260/139‑1 (MQ=255)
ctgctTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATacac > 2:316580/1‑139 (MQ=255)
gTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAggg < 1:316580/139‑1 (MQ=255)
aagagacagTTACCGAAACGATGGACCTCATCCCCCATTTTGTGGACTG‑CCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGtatta < 2:290139/131‑1 (MQ=255)
ggTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CCCCCCGGTAGa < 1:153855/54‑1 (MQ=255)
ggTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CCCCCCGGTAGa > 2:153855/1‑54 (MQ=255)
aTGGACATCATCCCCCATTTTGTGGACTG‑CCCCCCGATAGACGATCCCGCCCTATAGTTGGAGAGCCCCCTATTCAGGTGGCTAAATGTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTctgtctctt > 1:290139/1‑131 (MQ=255)
atcatcCCCCATTTTGTGGACTG‑CCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTa < 1:254269/139‑1 (MQ=255)
catcCCCCATTTTGTGGACTG‑CCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATg < 2:406613/139‑1 (MQ=255)
atcCCCCATTTTGTGGACTG‑CCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATgg > 2:183874/1‑139 (MQ=255)
atcCCCCATTTTGTGGACTG‑CCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCCAAATTTAGCAAATCAATACACTTCAGGGGGGta > 2:95076/1‑107 (MQ=255)
atcCCCCATTTTGTGGACTG‑CCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCCAAATTTAGCAAATCAATACACTTCAGGGGGGta < 1:95076/107‑1 (MQ=255)
cccATTTTGTGGACTG‑CCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATc > 2:218842/1‑139 (MQ=255)
|
GCTCTCTGCTCGTTCTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATC > NC_000913/2765651‑2765911
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
