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 I220 R1
|
9 |
22.2 |
1497724 |
96.2% |
1440810 |
85.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,206,635 |
C→G |
A77G (GCC→GGC) |
rpoD → |
RNA polymerase sigma factor RpoD |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,206,635 | 0 | C | G | 100.0%
| 82.3
/ NA
| 25 | A77G (GCC→GGC) | rpoD | RNA polymerase sigma factor RpoD |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base G (11/14); total (11/14) |
TGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGCCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGGCGCACGACTGACCCGGTACGCATGTA > NZ_CP009273/3206557‑3206707
|
tGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGGCGAAGccgccg > 1:664393/1‑90 (MQ=255)
ttCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAgg < 1:634459/90‑1 (MQ=255)
aTGGAAGAAGCACCGGATGCCGATGATCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTcc < 2:489800/90‑1 (MQ=255)
tGGAAGAAGCACCGGATGCCGATGATCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCa > 1:641213/1‑90 (MQ=255)
agaagCACCGGATGCCGATGATCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCCGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGt < 1:324248/90‑1 (MQ=255)
gaagCACCGGATGCCGATGATCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTg > 1:87554/1‑90 (MQ=255)
gCACCGGATGCCGATGATCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGaa > 1:296388/1‑90 (MQ=255)
ccGATGATCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCg > 2:226095/1‑90 (MQ=255)
gatCTGATGCTGGCTGAAAACCCCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGgcgc < 2:388257/90‑1 (MQ=255)
gatCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGgcgc < 1:442417/90‑1 (MQ=255)
gatCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGgcgc < 2:159929/90‑1 (MQ=255)
atCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGGCGCa < 2:87554/90‑1 (MQ=255)
atCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGGCGCa > 2:475800/1‑90 (MQ=255)
aTGCTGGCTGAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGGCGCACGACt < 1:636770/90‑1 (MQ=255)
tggctgAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGGCGCACGACTGAcc > 1:137873/1‑90 (MQ=255)
ggctgAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCa < 1:472009/45‑1 (MQ=255)
ggctgAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCa > 2:472009/1‑45 (MQ=255)
ggctgAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGc > 1:588261/1‑50 (MQ=255)
ggctgAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGc < 2:588261/50‑1 (MQ=255)
ggctgAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGGCGCACGACTGAccc < 2:664393/90‑1 (MQ=255)
tgAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGGCGCCCGACTGACCCGGt < 1:431183/90‑1 (MQ=255)
gAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGGCGCACGACTGACCCGGTa < 2:594467/90‑1 (MQ=255)
aaaCACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGGCGCACGACTGACCCGGTACg < 2:367696/90‑1 (MQ=255)
ccGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGGCGCACGACTGACCCGGTACGCATGt > 2:232290/1‑90 (MQ=255)
cgcgGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGGCGCCCGACTGACCCGGTACGCATGTa > 1:208676/1‑90 (MQ=255)
|
TGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGCCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGGCGCACGACTGACCCGGTACGCATGTA > NZ_CP009273/3206557‑3206707
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 30 ≤ 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
TCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGCCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGGCGCACGACTGACCCGGTACGCATGTACATGCGTGAAATGGGCACCGTTGAAC > NZ_CP009273/3206536‑3206733
|
TCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGG > SRR3722103.421494/1‑100 (MQ=60)
TCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGG > SRR3722103.62790/1‑100 (MQ=60)
ATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCG > SRR3722103.676009/1‑100 (MQ=60)
attcgtcggcagcgtcagatgtgtataagagacaGATCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCC < SRR3722103.479564/66‑1 (MQ=60)
ATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCA > SRR3722103.652379/1‑100 (MQ=60)
TTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAG < SRR3722103.645487/100‑1 (MQ=60)
GGTGATGGAAGAAGCACCGGATGCCGATGATCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTG > SRR3722103.88806/1‑100 (MQ=60)
GATGGAAGAAGCACCGGATGCCGATGATCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAA > SRR3722103.300583/1‑100 (MQ=60)
AGAAGCACCGGATGCCGATGATCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCCGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAA < SRR3722103.328783/100‑1 (MQ=60)
GATCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGGCGCACGACTGACC > SRR3722103.139908/1‑100 (MQ=60)
GATCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGGCGCACGACTGACC < SRR3722103.449210/100‑1 (MQ=60)
ATCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTctgtctcttatacacatctgacgctgccga > SRR3722103.598380/1‑70 (MQ=60)
ATGCTGGCTGAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGGCGCACGACTGACCCGGTAC < SRR3722103.647844/100‑1 (MQ=60)
CTGAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGGCGCCCGACTGACCCGGTACGCATGTA > SRR3722103.211721/1‑100 (MQ=60)
TGAAAACACCGCGGACGAAGATGCTGGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGGCGCCCGACTGACCCGGTACGCATGTAC < SRR3722103.437797/100‑1 (MQ=60)
GGCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGGCGCACGACTGACCCGGTACGCATGTACATGCGTGAAATGGGCACCGTTGAAC < SRR3722103.141850/100‑1 (MQ=60)
|
TCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTGATGCTGGCTGAAAACACCGCGGACGAAGATGCTGCCGAAGCCGCCGCGCAGGTGCTTTCCAGCGTGGAATCTGAAATCGGGCGCACGACTGACCCGGTACGCATGTACATGCGTGAAATGGGCACCGTTGAAC > NZ_CP009273/3206536‑3206733
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
