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 I211 R1
|
223 |
18.0 |
1007644 |
96.3% |
970361 |
85.7 |
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%
| 56.4
/ 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 (14/4); total (14/4) |
AGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGAAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGAAA > NZ_CP009273/1900801‑1900968
|
aGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACg > 2:94663/1‑90 (MQ=255)
aGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACg > 1:381669/1‑90 (MQ=255)
aGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACg > 1:94110/1‑90 (MQ=255)
aGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACg > 2:273400/1‑90 (MQ=255)
aGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACg > 2:292956/1‑90 (MQ=255)
ctCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAg > 2:104920/1‑90 (MQ=255)
cGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCg > 1:427295/1‑90 (MQ=255)
cGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCg > 1:467512/1‑90 (MQ=255)
cTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCt < 2:427295/90‑1 (MQ=255)
ttACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGc > 1:65525/1‑90 (MQ=255)
gcgcGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGc > 1:229227/1‑90 (MQ=255)
gcgcGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGc > 2:495943/1‑90 (MQ=255)
ttatGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCtt > 2:211095/1‑90 (MQ=255)
tGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTa > 2:339309/1‑90 (MQ=255)
gCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATc > 1:119643/1‑90 (MQ=255)
ccATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTa < 1:211095/90‑1 (MQ=255)
gTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGaa < 2:54048/90‑1 (MQ=255)
tATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGaaa < 2:2216/90‑1 (MQ=255)
|
AGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGAAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGAAA > NZ_CP009273/1900801‑1900968
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ 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
GTAATGACCCAGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGAAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGAAACAT > NZ_CP009273/1900791‑1900971
|
GTAATGACCCAGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACG > SRR3722094.388174/1‑100 (MQ=60)
GTAATGACCCAGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACG > SRR3722094.95478/1‑100 (MQ=60)
CTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCG > SRR3722094.475766/1‑100 (MQ=60)
CTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACAGCAAACGGTGGCTGGAAGCG > SRR3722094.434758/1‑100 (MQ=60)
TTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGC > SRR3722094.66445/1‑100 (MQ=60)
GCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGC > SRR3722094.232385/1‑100 (MQ=60)
ACGTATTATGGCGTCCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATC > SRR3722094.121369/1‑100 (MQ=60)
CCATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGAAAC < SRR3722094.213941/100‑1 (MQ=60)
ATACTGGTATCGGGAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGAAACAT > SRR3722094.337103/1‑100 (MQ=60)
|
GTAATGACCCAGCCGCCGGGCTTCACTACTCGTGCTAATTCTTCTGCTTTACACGGCGCGTAAATACGTATTATGGCGTCCATACTGGTATCGGAAAACGGCAAACGGTGGCTGGAAGCGACACAAAAAGTGACCTGCGGATAGCGTTTCGCCGCCGCTTTTATCGCTACCTTCGAAACAT > NZ_CP009273/1900791‑1900971
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
