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 I195 R1
|
222 |
27.1 |
1551108 |
96.0% |
1489063 |
86.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,900,885 |
A→G |
S145P (TCC→CCC) |
rlmA ← |
23S rRNA (guanine(745)‑N(1))‑methyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,900,885 | 0 | A | G | 100.0%
| 49.4
/ NA
| 15 | S145P (TCC→CCC) | rlmA | 23S rRNA (guanine(745)‑N(1))‑methyltransferase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (12/3); total (12/3) |
AGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGAAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGA > NZ_CP009273/1900801‑1900966
|
aGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACg > 1:372819/1‑90 (MQ=255)
ttACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGc > 1:344834/1‑90 (MQ=255)
gcgcGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGc > 1:401038/1‑90 (MQ=255)
gcgcGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGc > 2:723069/1‑90 (MQ=255)
cgTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGtt > 2:527525/1‑90 (MQ=255)
aCGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTcgccgc > 2:175403/1‑90 (MQ=255)
ttatGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCtt < 2:461116/90‑1 (MQ=255)
gCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATc > 1:251352/1‑90 (MQ=255)
gCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATc > 2:368984/1‑90 (MQ=255)
gCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATc > 2:90895/1‑90 (MQ=255)
cGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCg > 1:761882/1‑90 (MQ=255)
gTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGc > 2:63550/1‑90 (MQ=255)
ccATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTa < 2:325009/90‑1 (MQ=255)
ccATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTa < 2:383926/90‑1 (MQ=255)
ggTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGa > 1:363697/1‑90 (MQ=255)
|
AGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGAAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGA > NZ_CP009273/1900801‑1900966
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GTAATGACCCAGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGAAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGAAACATCCAGA > NZ_CP009273/1900791‑1900976
|
GTAATGACCCAGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACG > SRR3722073.380721/1‑100 (MQ=60)
TTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGC > SRR3722073.352136/1‑100 (MQ=60)
GCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGC > SRR3722073.409577/1‑100 (MQ=60)
ACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATC > SRR3722073.256635/1‑100 (MQ=60)
CGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCG > SRR3722073.777265/1‑100 (MQ=60)
CGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGA > SRR3722073.371413/1‑100 (MQ=60)
GGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGAAACATCCAGA > SRR3722073.775597/1‑100 (MQ=60)
|
GTAATGACCCAGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGAAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGAAACATCCAGA > NZ_CP009273/1900791‑1900976
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
