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 I227 R1
|
223 |
21.3 |
1167702 |
97.0% |
1132670 |
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%
| 62.7
/ NA
| 20 | S145P (TCC→CCC) | rlmA | 23S rRNA (guanine(745)‑N(1))‑methyltransferase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (16/4); total (16/4) |
CCCAGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGAAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGC > NZ_CP009273/1900798‑1900957
|
cccAGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGgaa > 1:74930/1‑90 (MQ=255)
gccgGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCaa < 1:251718/90‑1 (MQ=255)
ttCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTgg > 1:56508/1‑90 (MQ=255)
actCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGaa > 1:102935/1‑90 (MQ=255)
cGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCg > 2:471851/1‑90 (MQ=255)
tGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGac > 2:57639/1‑90 (MQ=255)
gCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGaca > 1:568825/1‑90 (MQ=255)
tAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGAcaca < 2:2174/90‑1 (MQ=255)
tctGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTg > 1:206622/1‑90 (MQ=255)
gcgcGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGc > 1:80617/1‑90 (MQ=255)
gcgcGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGc > 2:14622/1‑90 (MQ=255)
gcgcGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGc > 2:155199/1‑90 (MQ=255)
gcgcGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGc > 2:397685/1‑90 (MQ=255)
gcgTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGAcaca < 1:550871/68‑1 (MQ=255)
gcgTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGAcaca > 2:550871/1‑68 (MQ=255)
ttatGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCtt > 2:142396/1‑90 (MQ=255)
ttatGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCtt > 2:212107/1‑90 (MQ=255)
gTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTcgccgc > 2:289447/1‑78 (MQ=255)
gTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTcgccgc < 1:289447/78‑1 (MQ=255)
gTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGc > 2:103943/1‑90 (MQ=255)
gTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGc > 1:488136/1‑90 (MQ=255)
|
CCCAGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGAAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGC > NZ_CP009273/1900798‑1900957
|
| 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
TGGCAGTAATGACCCAGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGAAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGAAACATCCAGA > NZ_CP009273/1900786‑1900976
|
TGGCAGTAATGACCCAGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGG > SRR3722111.191441/1‑100 (MQ=60)
TGGCAGTAATGACCCAGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGG < SRR3722111.357543/100‑1 (MQ=60)
GCAGTAATGACCCAGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAA > SRR3722111.75835/1‑100 (MQ=60)
GCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGG > SRR3722111.57182/1‑100 (MQ=60)
GCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTG < SRR3722111.254676/100‑1 (MQ=60)
GGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAA > SRR3722111.104219/1‑100 (MQ=60)
CACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACA > SRR3722111.577772/1‑100 (MQ=60)
TGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTG > SRR3722111.209163/1‑100 (MQ=60)
tataagagacagTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACC < SRR3722111.559523/88‑1 (MQ=60)
GCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGC > SRR3722111.81600/1‑100 (MQ=60)
AGGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATC < SRR3722111.293136/100‑1 (MQ=60)
GTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGC > SRR3722111.495635/1‑100 (MQ=60)
GGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGAAACATCCAGA > SRR3722111.252987/1‑100 (MQ=60)
|
TGGCAGTAATGACCCAGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGAAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGAAACATCCAGA > NZ_CP009273/1900786‑1900976
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
