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 I175 R1
|
221 |
18.5 |
1047116 |
95.1% |
995807 |
84.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,596,032 |
(G)8→9 |
noncoding (72/87 nt) |
BW25113_RS22750 ← |
tRNA‑Leu |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,596,024 | 1 | . | G | 92.9%
| 41.1
/ ‑2.1
| 14 | noncoding (80/87 nt) | BW25113_RS22750 | tRNA‑Leu |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base G (5/8); total (6/8) |
| Fisher's exact test for biased strand distribution p-value = 4.29e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.05e-01 |
ACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑‑GGG‑GGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGC > NZ_CP009273/4595936‑4596094
|
acacTAACACCTGAAGCTAGCGCGTCTCCCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑‑g < 2:252074/90‑1 (MQ=255)
cacTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑‑gg < 2:509411/90‑1 (MQ=255)
tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑‑ggg‑ggggggact > 1:336866/1‑86 (MQ=255)
tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑‑ggg‑ggggggact > 1:40647/1‑86 (MQ=255)
gTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑‑ggg‑ggggg < 2:94185/74‑1 (MQ=255)
gTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑‑ggg‑ggggg > 1:94185/1‑74 (MQ=255)
ttCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAG‑GGG‑GGGGGACTTGAACCCCCACGTCCGTAAGa < 2:398763/90‑1 (MQ=255)
gCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGG‑GGGGGACTTGAACCCCCAc > 2:42751/1‑77 (MQ=38)
gCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGG‑GGGGGACTTGAACCCCCAc < 1:42751/77‑1 (MQ=38)
gCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAG‑GGG‑GGGGGACTTGAACCCCCACGTCCGTaa < 2:260389/84‑1 (MQ=255)
gCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAG‑GGG‑GGGGGACTTGAACCCCCACGTCCGTaa > 1:260389/1‑84 (MQ=255)
cACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAG‑GGG‑GGGGGACTTGAACCCCCACGTCCGTAAGAACACTa < 2:40647/90‑1 (MQ=255)
ccTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAG‑GGG‑GGGGGACTTGAACCCCCACGTCCGTAAGAACACTAac < 2:310142/90‑1 (MQ=255)
ttCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAG‑GGG‑GGGGGACTTGAACCCCCACGTCCGTAAGAACACTAacac > 2:360499/1‑90 (MQ=255)
cGCACAGTCATCTTACTTTTTTTGAAATCGCCTCGTTTGGTGCGAG‑GGG‑GGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCt < 2:268577/90‑1 (MQ=25)
gTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAG‑GGG‑GGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCt > 1:103992/1‑90 (MQ=255)
gTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑‑GGGTGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCt > 1:41389/1‑90 (MQ=255)
ttttGATATCGCCTCGTTTGGTGCGAG‑GGG‑GGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCa > 2:504390/1‑90 (MQ=255)
atCGCCTCGTTTGGTGCGAG‑GGG‑GGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGc < 2:103992/90‑1 (MQ=255)
atCGCCTCGTTTGGTGCGAG‑GGG‑GGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGc < 1:360499/90‑1 (MQ=255)
|
ACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑‑GGG‑GGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGC > NZ_CP009273/4595936‑4596094
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 29 ≤ 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
CACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑‑GGG‑GGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTG > NZ_CP009273/4595937‑4596126
|
CACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAG‑GGG‑GGGGGACT > SRR3722048.342091/1‑100 (MQ=60)
CACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAG‑GGG‑GGGGGACT > SRR3722048.41216/1‑100 (MQ=60)
ACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAG‑GGG‑GGGGGACTT > SRR3722048.314803/1‑100 (MQ=60)
AAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAG‑GGG‑GGGGGACTTGAACCCtgtct > SRR3722048.95531/1‑95 (MQ=60)
cagTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGG‑GGGGGACTTGAACCCCCACGTCCGTAAGA < SRR3722048.43356/97‑1 (MQ=60)
TACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAG‑GGG‑GGGGGACTTGAACCCCCACGTCCGTAAGAACAC > SRR3722048.264177/1‑100 (MQ=60)
CCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAG‑GGG‑GGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCT > SRR3722048.105520/1‑100 (MQ=60)
CCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑‑GGGTGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCT > SRR3722048.41968/1‑100 (MQ=60)
ATCGCCTCGTTTGGTGCGAG‑GGG‑GGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCC < SRR3722048.366249/100‑1 (MQ=36)
TCGCCTCGTTTGGTGCGAG‑GGG‑GGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCC < SRR3722048.429369/100‑1 (MQ=36)
CGTTTGGTGCGAG‑GGG‑GGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCG > SRR3722048.387280/1‑100 (MQ=36)
GGG‑GGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACG < SRR3722048.512713/100‑1 (MQ=60)
G‑GGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCActgtctcttat > SRR3722048.163847/1‑89 (MQ=46)
|
CACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑‑GGG‑GGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTG > NZ_CP009273/4595937‑4596126
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
