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 I230 R1
|
226 |
18.8 |
1048726 |
96.7% |
1014118 |
86.4 |
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%
| 56.2
/ NA
| 18 | S145P (TCC→CCC) | rlmA | 23S rRNA (guanine(745)‑N(1))‑methyltransferase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (12/6); total (12/6) |
GGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGAAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGAAA > NZ_CP009273/1900809‑1900968
|
ggCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACgg < 2:496305/90‑1 (MQ=255)
ggCTTCACTACTCGTGCAAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACgg < 1:423795/90‑1 (MQ=255)
cGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCg > 1:148564/1‑90 (MQ=255)
cGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCg > 2:186379/1‑90 (MQ=255)
tGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGac > 2:47002/1‑90 (MQ=255)
tctGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTg > 1:263914/1‑90 (MQ=255)
gCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGAcc < 1:247832/90‑1 (MQ=255)
ttACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGc > 1:102927/1‑90 (MQ=255)
cGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATa > 1:53986/1‑90 (MQ=255)
gcgcGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGc > 1:22360/1‑90 (MQ=255)
aCGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAg > 1:193222/1‑65 (MQ=255)
aCGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAg < 2:193222/65‑1 (MQ=255)
cGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCg > 1:57622/1‑90 (MQ=255)
cGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCg > 1:85053/1‑90 (MQ=255)
cGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGGGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCg > 2:364166/1‑90 (MQ=255)
gTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGc > 1:449668/1‑90 (MQ=255)
gTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGc < 2:412718/90‑1 (MQ=255)
tATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGaaa < 1:96842/90‑1 (MQ=255)
|
GGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGAAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGAAA > NZ_CP009273/1900809‑1900968
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ 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
GGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGAAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGAAACATCCAGACC > NZ_CP009273/1900809‑1900978
|
GGCTTCACTACTCGTGCAAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAG < SRR3722114.428990/100‑1 (MQ=60)
CTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCG > SRR3722114.150075/1‑100 (MQ=60)
TGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTG > SRR3722114.266607/1‑100 (MQ=60)
TTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGC > SRR3722114.104014/1‑100 (MQ=60)
CTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATA > SRR3722114.54521/1‑100 (MQ=60)
GCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGC > SRR3722114.22582/1‑100 (MQ=60)
GCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGC < SRR3722114.250249/100‑1 (MQ=60)
GCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGctgtctcttatacac > SRR3722114.195111/1‑85 (MQ=60)
CGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCG > SRR3722114.58190/1‑100 (MQ=60)
CGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCG > SRR3722114.85959/1‑100 (MQ=60)
GTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGC > SRR3722114.455258/1‑100 (MQ=60)
ATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGAAACAT > SRR3722114.487536/1‑100 (MQ=60)
GGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGAAACATCCAGA > SRR3722114.493097/1‑100 (MQ=60)
TATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGAAACATCCAGACC < SRR3722114.97860/100‑1 (MQ=60)
|
GGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGAAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGAAACATCCAGACC > NZ_CP009273/1900809‑1900978
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
