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 F28 I1 R1
|
163 |
52.9 |
1786516 |
99.3% |
1774010 |
139.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,765,794 |
(C)7→9 |
intergenic (‑18/‑124) |
yfjM ← / → rnlA |
CP4‑57 prophage; protein YfjM/CP4‑57 prophage; RNase LS, toxin of the RnlAB toxin‑antitoxin system |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,765,787 | 1 | . | C | 100.0%
| 155.4
/ NA
| 46 | intergenic (‑11/‑131) | yfjM/rnlA | CP4‑57 prophage; protein YfjM/CP4‑57 prophage; RNase LS, toxin of the RnlAB toxin‑antitoxin system |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (16/30); total (16/30) |
| * | NC_000913 | 2,765,787 | 2 | . | C | 89.1%
| 137.1
/ 11.0
| 46 | intergenic (‑11/‑131) | yfjM/rnlA | CP4‑57 prophage; protein YfjM/CP4‑57 prophage; RNase LS, toxin of the RnlAB toxin‑antitoxin system |
| Reads supporting (aligned to +/- strand): ref base . (2/3); new base C (14/27); total (16/30) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.08e-01 |
TGGGCTCTCTGCTCGTTCTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑‑‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCC > NC_000913/2765648‑2765912
||
tGGGCTCTCTGCTCGTTCTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTg < 2:881346/140‑1 (MQ=255)
tctctGCTCGTTCTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑‑‑ccccc < 1:581339/140‑1 (MQ=255)
ctctGCTCGTTCTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑‑‑cccccc < 1:465799/140‑1 (MQ=255)
tctGCTCGTTCTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑‑‑ccccccc < 2:110206/140‑1 (MQ=255)
tctGCTCGTTCTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑‑‑ccccccc > 2:878729/1‑140 (MQ=255)
tctGCTCGTTCTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑‑‑ccccccc > 2:443093/1‑140 (MQ=255)
tctGCTCGTTCTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑‑‑ccccccc > 2:81425/1‑140 (MQ=255)
ctGCTCGTTCTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑‑‑cccccccc < 1:324752/140‑2 (MQ=255)
gCTCGTTCTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑‑‑cccccccccg > 2:804177/1‑137 (MQ=255)
cTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACg > 2:619585/1‑140 (MQ=255)
tttCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATTCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATc < 2:872093/140‑1 (MQ=255)
ttCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATcc > 1:499886/1‑140 (MQ=255)
tCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCt < 1:109054/140‑1 (MQ=255)
tCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGC‑‑CCCCCCCGGTAGACGATCCTg < 2:821409/140‑1 (MQ=255)
cGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTg < 2:779551/140‑1 (MQ=255)
gACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGc < 2:445170/140‑1 (MQ=255)
tCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTTCCGAAACGATGGACATCCTCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGt < 2:83888/140‑1 (MQ=255)
tCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGt < 2:498193/140‑1 (MQ=255)
ttGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGC‑‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGcc < 1:878729/140‑1 (MQ=255)
tGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGACGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGcc < 1:752868/140‑1 (MQ=255)
tCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGcccc < 1:90590/140‑1 (MQ=255)
gctgGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTa < 1:619585/140‑1 (MQ=255)
aCTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTaaa > 2:169173/1‑140 (MQ=255)
aCTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTaaa < 1:804177/140‑1 (MQ=255)
tATCGAGTTGGTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAg < 1:836443/140‑1 (MQ=255)
aTCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCa < 2:499886/140‑1 (MQ=255)
cGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCaaa > 2:313569/1‑140 (MQ=255)
gAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAAt < 1:81425/140‑1 (MQ=255)
gAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAAt < 1:242556/140‑1 (MQ=255)
aGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGC‑‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCa > 2:66678/1‑140 (MQ=255)
tgctgcTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGC‑‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa < 1:66678/140‑1 (MQ=255)
ctgctTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATac > 1:752932/1‑140 (MQ=255)
ctgctTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATac > 2:814369/1‑140 (MQ=255)
ctgctTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGC‑‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATaca > 1:728891/1‑140 (MQ=255)
gagaTCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCGCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAggg < 2:276055/140‑1 (MQ=255)
gagaTCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAggg < 2:203062/140‑1 (MQ=255)
agaTCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAgggg < 1:715128/140‑1 (MQ=255)
aTCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGCGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAgggggg > 1:32845/1‑140 (MQ=255)
aTCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAgggggg < 1:443093/140‑1 (MQ=255)
aTCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAgggggg < 1:106724/140‑1 (MQ=255)
tCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGt > 1:423214/1‑140 (MQ=255)
cAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGta < 1:449733/140‑1 (MQ=255)
aGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGtat < 2:451155/140‑1 (MQ=255)
aGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGtat < 2:242450/140‑1 (MQ=255)
gAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGtatta > 1:1797/1‑140 (MQ=255)
ggTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTg > 2:412634/1‑138 (MQ=255)
ggTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTg < 1:412634/138‑1 (MQ=255)
gTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTag < 2:423214/140‑1 (MQ=255)
gTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTag > 2:733534/1‑140 (MQ=255)
gTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTag > 1:102697/1‑140 (MQ=255)
aaaCGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTcc < 2:491983/140‑1 (MQ=255)
aaaCGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTcc < 2:1797/140‑1 (MQ=255)
aCGATGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTcccc > 1:267744/1‑140 (MQ=255)
aTGGACATCATCCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCata < 2:726730/140‑1 (MQ=255)
tcCCCCATTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATg < 2:267744/140‑1 (MQ=255)
aTTTTGTGGACTGCC‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATcc > 1:129745/1‑140 (MQ=255)
||
TGGGCTCTCTGCTCGTTCTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑‑‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCC > NC_000913/2765648‑2765912
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
