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 F2 I228 R1
|
214 |
26.5 |
1448192 |
97.1% |
1406194 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,172,868 |
G→C |
G190A (GGC→GCC) |
yegT → |
nucleoside permease |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,172,868 | 0 | G | C | 96.0%
| 77.7
/ ‑4.5
| 25 | G190A (GGC→GCC) | yegT | nucleoside permease |
| Reads supporting (aligned to +/- strand): ref base G (1/0); new base C (17/7); total (18/7) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TCCCGCTGCTGATTACCGCCGGAAGTTCTGCTCTGCTCGGTGTGTTTGCGTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGGCAAAATGGATATTAAAGTCATGCTCGGCCTGGATGCGCTGATCCTGCTGCGCGATAAAAACTTCCTCGTCTTTTTCTTCTGTT > NZ_CP009273/2172784‑2172951
|
tCCCGCTGCTGATTACCGCCGGAAGTTCTGCTCTGCTCGGTGTGTTTGCGTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGCCaaaa < 2:661702/90‑1 (MQ=255)
ccGCTGCTGATTACCGCCGGAAGTTCTGCTCTGCTCGGTGTGTTTGCGTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGCCAAAATg > 1:695394/1‑90 (MQ=255)
ccgccgGAAGTTCTGCTCTGCTCGGTGTGTTTGCGTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGCCAAAATGGATATTAAAGTCa < 1:115294/90‑1 (MQ=255)
gccgGAAGTTCTGCTCTGCTCGGTGTGTTTGCGTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGCCAAAATGGATATTAAAGTCATg > 2:266764/1‑90 (MQ=255)
cgGAAGTTCTGCTCTGCTCGGTGTGTTTGCGTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGCCAAAATGGATATTAAAGTCATGCt < 2:347962/90‑1 (MQ=255)
ggAAGTTCTGCTCTGCTCGGTGTGTTTGCGTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGCCAAAATGGATATTAAAGTCATGCTc < 1:179801/90‑1 (MQ=255)
ggAAGTTCTGCTCTGCTCGGTGTGTTTGCGTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGCCAAAATGGATATTAAAGTCATGCTc < 2:202155/90‑1 (MQ=255)
gctcGGTGTGTTTGCGTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGGCAAAATGGATATTAAAGTCATGCTCGGCCTGGATGCGCt > 1:232091/1‑90 (MQ=255)
gctcGGTGTGTTTGCGTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGCCAAAATGGATATTAAAGTCATGCTCGGCCTGGATGCGCt > 1:53492/1‑90 (MQ=255)
gctcGGTGTGTTTGCGTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGCCAAAATGGATATTAAAGTCATGCTCGGCCTGGATGCGCt > 1:58160/1‑90 (MQ=255)
gctcGGTGTGTTTGCGTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGCCAAAATGGATATTAAAGTCATGCTCGGCCTGGATGCGCt > 2:19699/1‑90 (MQ=255)
gctcGGTGTGTTTGCGTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGCCAAAATGGATATTAAAGTCATGCTCGGCCTGGATGCGCt > 1:421760/1‑90 (MQ=255)
gtgtgtTTGCGTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGCCAAAATGGATATTAAAGTCATGCTCGGCCTGGATGCGCTGATcc > 1:389775/1‑90 (MQ=255)
gtgtgtTTGCGTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGCCAAAATGGATATTAAAGTCATGCTCGGCCTGGATGCGCTGATcc > 2:350307/1‑90 (MQ=255)
tttGCGTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGCCAAAATGGATATTAAAGTCATGCTCGGCCTGGATGCGCTGATCctgctg > 1:429390/1‑90 (MQ=255)
gTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGCCAAAATGGATATTAAAGTCATGCTCGGCCTGGATGCGCTGATCCTGCTGCGCGa > 1:64240/1‑90 (MQ=255)
gTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGCCAAAATGGATATTAAAGTCATGCTCGGCCTGGATGCGCTGATCCTGCTGCGCGa > 1:448955/1‑90 (MQ=255)
gTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGCCAAAATGGATATTAAAGTCATGCTCGGCCTGGATGCGCTGATCCTGCTGCGCGa < 1:700958/90‑1 (MQ=255)
gTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGCCAAAATGGATATTAAAGTCATGCTCGGCCTGGATGCGCTGATCCTGCTGCGCGa > 2:604625/1‑90 (MQ=255)
gCCCGACACGCCACCAAAAAGCACCGCCAAAATGGATATTAAAGTCATGCTCGGCCTGGATGCGCTGATCCTGCTGCGCGATAAAAACtt > 1:556168/1‑90 (MQ=255)
aaaaaGCACCGCCAAAATGGATATTAAAGTCATGCTCGGCCTGGATGCGCTGATCCTGCTGCGCGATAAAAACTTCCTCGTCTTTttctt > 2:659459/1‑90 (MQ=255)
aaGCACCGCCAAAATGGATATTAAAGTCATGCTCGGCCTGGATGCGCTGATCCTGCTGCGCGATAAAAACTTCCTCGTCTTTTTCTTCTg > 2:485056/1‑90 (MQ=255)
gCACCGCCAAAATGGATATTAAAGTCATGCTCGGCCTGGATGCGCTGATCCTGCTGCGCGATAAAAACTTCCTCGTCTTTTTCTTCTGtt > 1:595081/1‑90 (MQ=255)
cACCGCCAAAATGGATATTAAAGTCATGCTCGGCCt > 1:707561/1‑36 (MQ=38)
cACCGCCAAAATGGATATTAAAGTCATGCTCGGCCt < 2:707561/36‑1 (MQ=38)
|
TCCCGCTGCTGATTACCGCCGGAAGTTCTGCTCTGCTCGGTGTGTTTGCGTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGGCAAAATGGATATTAAAGTCATGCTCGGCCTGGATGCGCTGATCCTGCTGCGCGATAAAAACTTCCTCGTCTTTTTCTTCTGTT > NZ_CP009273/2172784‑2172951
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GACTAACATCCCGCTGCTGATTACCGCCGGAAGTTCTGCTCTGCTCGGTGTGTTTGCGTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGGCAAAATGGATATTAAAGTCATGCTCGGCCTGGATGCGCTGATCCTGCTGCGCGATAAAAACTTCCTCGTCTTTTTCTTCTGTTC > NZ_CP009273/2172776‑2172952
|
GACTAACATCCCGCTGCTGATTACCGCCGGAAGTTCTGCTCTGCTCGGTGTGTTTGCGTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGCCAAAATG > SRR3722112.706252/1‑100 (MQ=60)
CCGCCGGAAGTTCTGCTCTGCTCGGTGTGTTTGCGTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGCCAAAATGGATATTAAAGTCATGCTCGGCCT < SRR3722112.116727/100‑1 (MQ=60)
GGAAGTTCTGCTCTGCTCGGTGTGTTTGCGTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGCCAAAATGGATATTAAAGTCATGCTCGGCCTGGATG < SRR3722112.181996/100‑1 (MQ=60)
GTTCTGCTCTGCTCGGTGTGTTTGCGTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGGCAAAATGGATATTAAAGTCATGCTCGGCCTGGATGCGCT > SRR3722112.234875/1‑100 (MQ=60)
GTTCTGCTCTGCTCGGTGTGTTTGCGTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGCCAAAATGGATATTAAAGTCATGCTCGGCCTGGATGCGCT > SRR3722112.427369/1‑100 (MQ=60)
GTTCTGCTCTGCTCGGTGTGTTTGCGTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGCCAAAATGGATATTAAAGTCATGCTCGGCCTGGATGCGCT > SRR3722112.54154/1‑100 (MQ=60)
GTTCTGCTCTGCTCGGTGTGTTTGCGTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGCCAAAATGGATATTAAAGTCATGCTCGGCCTGGATGCGCT > SRR3722112.58868/1‑100 (MQ=60)
GCTCTGCTCGGTGTGTTTGCGTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGCCAAAATGGATATTAAAGTCATGCTCGGCCTGGATGCGCTGATCC > SRR3722112.394869/1‑100 (MQ=60)
GCTCGGTGTGTTTGCGTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGCCAAAATGGATATTAAAGTCATGCTCGGCCTGGATGCGCTGATCCTGCTG > SRR3722112.435195/1‑100 (MQ=60)
GTGTGTTTGCGTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGCCAAAATGGATATTAAAGTCATGCTCGGCCTGGATGCGCTGATCCTGCTGCGCGA > SRR3722112.455213/1‑100 (MQ=60)
GTGTGTTTGCGTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGCCAAAATGGATATTAAAGTCATGCTCGGCCTGGATGCGCTGATCCTGCTGCGCGA > SRR3722112.65014/1‑100 (MQ=60)
CGTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGCCAAAATGGATATTAAAGTCATGCTCGGCCTGGATGCGCTGATCCTGCTGCGCGATAAAAACTT > SRR3722112.564597/1‑100 (MQ=60)
GTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGCCAAAATGGATATTAAAGTCATGCTCGGCCTGGATGCGCTGATCCTGCTGCGCGATAAAAACTTC < SRR3722112.711909/100‑1 (MQ=60)
CCACCAAAAAGCACCGCCAAAATGGATATTAAAGTCATGCTCGGCCTGGATGCGCTGATCCTGCTGCGCGATAAAAACTTCCTCGTCTTTTTCTTCTGTT > SRR3722112.604185/1‑100 (MQ=60)
CACCAAAAAGCACCGCCAAAATGGATATTAAAGTCATGCTCGGCCTGGATGCGCTGctgtctcttatacacatctgacgctgccgacgaatgtcaatgtg > SRR3722112.718616/1‑56 (MQ=60)
|
GACTAACATCCCGCTGCTGATTACCGCCGGAAGTTCTGCTCTGCTCGGTGTGTTTGCGTTTTTCCTGCCCGACACGCCACCAAAAAGCACCGGCAAAATGGATATTAAAGTCATGCTCGGCCTGGATGCGCTGATCCTGCTGCGCGATAAAAACTTCCTCGTCTTTTTCTTCTGTTC > NZ_CP009273/2172776‑2172952
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
