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 F8 I0 R2
|
422 |
46.8 |
3726540 |
94.7% |
3529033 |
61.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
4,501,608 |
A→G |
100% |
K59K (AAA→AAG) |
intB → |
predicted integrase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 4,501,608 | 0 | A | G | 83.0%
| 114.7
/ 15.8
| 47 | K59K (AAA→AAG) | intB | predicted integrase |
| Reads supporting (aligned to +/- strand): ref base A (7/1); new base G (14/25); total (21/26) |
| Fisher's exact test for biased strand distribution p-value = 1.52e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.70e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CCAGAGTACGTCGTGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTGAGTGG > W3110S.gb/4501547‑4501671
|
ccAGAGTACGTCGTGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGaaaaa > 1:385396/1‑70 (MQ=255)
ccAGAGTACGTCGTGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAAt > 1:3380283/1‑71 (MQ=255)
ccAGAGTACGTCGTGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAAt > 1:201826/1‑71 (MQ=255)
ccAGAGTACGTCGTGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAAt > 1:1941345/1‑71 (MQ=255)
cgtGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTg < 1:2076394/70‑1 (MQ=255)
tAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAAt < 1:2846934/46‑1 (MQ=255)
tAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAAt < 1:2872879/46‑1 (MQ=255)
tAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTaa < 1:2218985/66‑1 (MQ=255)
tAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTaa < 1:206448/66‑1 (MQ=255)
tAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTaa < 1:1351701/66‑1 (MQ=255)
tAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTaa < 1:3108696/66‑1 (MQ=255)
tAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTaa < 1:763186/66‑1 (MQ=255)
tAAGCTGCTTGCGAATGGCGGCGATCCGGGAGACAAGAAGTAAAAt < 1:1153960/46‑1 (MQ=38)
aaGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAAt < 1:3066025/45‑1 (MQ=255)
agatgctTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACg > 1:2288700/4‑70 (MQ=255)
aGCTGCTTGCGAATGGCGTCGCTCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACg > 1:2075422/1‑70 (MQ=255)
aGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACg > 1:2956298/1‑70 (MQ=255)
aGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACg > 1:1005608/1‑70 (MQ=255)
aGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACg > 1:140225/1‑70 (MQ=255)
aGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACg > 1:124640/1‑70 (MQ=255)
aGCTGCTTGCGAATGGCGGCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGa < 1:557449/71‑1 (MQ=255)
tgctTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAAcc > 1:38314/1‑71 (MQ=255)
tgctTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAAcc > 1:3416264/1‑71 (MQ=255)
tgctTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAAcc > 1:493353/1‑71 (MQ=255)
tgctTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAAcc > 1:1000400/1‑71 (MQ=255)
ctTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCtt < 1:538155/71‑1 (MQ=255)
ctTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCtt < 1:1987187/71‑1 (MQ=255)
gCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGaa > 1:1319502/1‑41 (MQ=255)
gCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAG‑ACGAACCTTTAAAGAAGTcg > 1:1679926/1‑71 (MQ=255)
gTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTcgc < 1:79516/71‑1 (MQ=255)
tCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTcgcg < 1:3126915/71‑1 (MQ=255)
tCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTcgcg < 1:2441509/71‑1 (MQ=255)
tCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTcgcg < 1:3440677/71‑1 (MQ=255)
tCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTcgcg < 1:3712513/71‑1 (MQ=255)
gATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGa > 1:2168437/1‑70 (MQ=255)
tCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGAtt > 1:1089311/1‑70 (MQ=255)
ccGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGAtt > 1:958612/1‑69 (MQ=255)
ccGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGAtt > 1:3036540/1‑69 (MQ=255)
ccGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGAtt > 1:2135326/1‑69 (MQ=255)
gagaCAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTGAGtgg < 1:3509547/71‑1 (MQ=255)
gagaCAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTGAGtgg < 1:3335034/71‑1 (MQ=255)
gagaCAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTGAGtgg < 1:1319887/71‑1 (MQ=255)
gagaCAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTGAGtgg < 1:1853449/71‑1 (MQ=255)
gagaCAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTGAGtgg < 1:2350919/71‑1 (MQ=255)
gagaCAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTGAGtgg < 1:871809/71‑1 (MQ=255)
gagaCAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTGAGtgg < 1:592342/71‑1 (MQ=255)
agaCAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTGAGtgg < 1:499298/70‑1 (MQ=255)
|
CCAGAGTACGTCGTGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTGAGTGG > W3110S.gb/4501547‑4501671
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
