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 I75 R1
|
71 |
32.8 |
2150506 |
93.3% |
2006422 |
83.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,749,862 |
A→C |
H37P (CAC→CCC) |
BW25113_RS26160 → |
protein YnhH |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,749,862 | 0 | A | C | 100.0%
| 69.8
/ NA
| 21 | H37P (CAC→CCC) | BW25113_RS26160 | protein YnhH |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (11/10); total (11/10) |
ACAGGCACTCACGTTGGGCTGAGACACAAGCACACATTCCTCTGCACGCTTTTTCGATGTCACCTATCCTTAGAGCGAGGCACCACCACTTTCGTAATACCGGATTCGCTTTCCGGCAGTGCGCCCAGAAAGCAAGTTTCTCCCATCCTTCTCAACTTAAAGACTA > NZ_CP009273/1749781‑1749946
|
aCAGGCACTCACGTTGGGCTGAGACACAAGCACACATTCCTCTGCACGCTTTTTCGATGTCACCTATCCTTAGAGCGAGGCCCCACCACt < 2:717793/90‑1 (MQ=255)
aCAGGCACTCACGTTGGGCTGAGACACAAGCACACATTCCTCTGCACGCTTTTTCGATGTCACCTATCCTTAGAGCGAGGCCCCACCACt < 2:422721/90‑1 (MQ=255)
aGCACACCTTCCTCTGCACGCTTTTTCGATGTCACCTATCCTTAGAGCGAGGCCCCACCACTTTCGTAATACCGGATTCGCTTTCCGGCa < 2:414861/90‑1 (MQ=255)
ttCCTCTGCACGCTTTTTCGATGTCACCTATCCTTAGAGCGAGGccccacc > 2:734493/1‑51 (MQ=255)
ttCCTCTGCACGCTTTTTCGATGTCACCTATCCTTAGAGCGAGGccccacc < 1:734493/51‑1 (MQ=255)
ttCCTCTGCACGCTTTTTCGATGTCACCTATCCTTAGAGCGAGGCCCCACCACTTTCGTAATACCGGATTCGCTTTCCGGCAGTGCGccc > 1:497749/1‑90 (MQ=255)
gCACGCTTTTTCGATGTCACCTATCCTTAGAGCGAGGCCCCACCACTTTCGTAATACCGGATTCGCTTTCCGGCAGTGCGCCCAGAAAGc < 2:774820/90‑1 (MQ=255)
cACGCTTTTTCGATGTCACCTATCCTTAGAGCGAGGCCCCACCACTTTCGTAATACCGGATTCGCTTTCCGGCAGTGCGCCCAGAAAGCa > 2:728272/1‑90 (MQ=255)
tttttCGATGTCACCTATCCTTAGAGCGAGGCCCCACCACTTTCGTAATACCGGATTCGCTTTCCGGCAGTGCGCCCAGAAAGCAAGttt < 1:728272/90‑1 (MQ=255)
tATCCTTAGAGCGAGGCCCCACCACTTTCGTAATACCGGATTCGCTTTCCGGCAGTGCGCCCAGAAAGCAAGTTTCTCCCATCCTTCTCa < 2:730834/90‑1 (MQ=255)
tAGAGCGAGTCCCCACCACGTTCGTAATACCGGCTTCGCTTTCCGGCAGTGCGCCCAGAAAGCAAGTTCCTCCCATCCTTCTCCACTTaa < 2:379842/90‑1 (MQ=255)
tAGAGCGAGGCCCCACCACTTTCGTAATACCGGATTCGCTTTCCGGCAGTGCGCCCAGAAAGCAAGTTTCTCCCATCCTTCTCAACTTaa > 1:202379/1‑90 (MQ=255)
tAGAGCGAGGCCCCACCACTTTCGTAATACCGGATTCGCTTTCCGGCAGTGCGCCCAGAAAGCAAGTTTCTCCCATCCTTCTCAACTTaa < 2:583203/90‑1 (MQ=255)
tAGAGCGAGGCCCCACCACTTTCGTAATACCGGATTCGCTTTCCGGCAGTGCGCCCAGAAAGCAAGTTTCTCCCATCCTTCTCAACTTaa < 2:495725/90‑1 (MQ=255)
tAGAGCGAGGCCCCACCACTTTCGTAATACCGGATTCGCTTTCCGGCAGTGCGCCCAGAAAGCAAGTTTCTCCCATCCTTCTCAACTTaa > 1:495725/1‑90 (MQ=255)
cGAGGCCCCACCACTTTCGTAATACCGGATTCGCTTTCCGGCAGTGCGCCCAGAAAGCAAGTTTCTCCCATCCTTCTCAACTTAaagact > 1:968318/1‑90 (MQ=255)
gAGGCCCCACCACTTTCGTAATACCGGATTCGCTTTCCGGCAGTGCGCCCAGAAAGCAAGTTTCTCCCATCCTTCTCAACTTAaagacta > 2:193170/1‑90 (MQ=255)
gAGGCCCCACCACTTTCGTAATACCGGATTCGCTTTCCGGCAGTGCGCCCAGAAAGCAAGTTTCTCCCATCCTTCTCAACTTAaagacta > 2:709669/1‑90 (MQ=255)
gAGGCCCCACCACTTTCGTAATACCGGATTCGCTTTCCGGCAGTGCGCCCAGAAAGCAAGTTTCTCCCATCCTTCTCAACTTAaagacta > 1:374570/1‑90 (MQ=255)
gAGGCCCCACCACTTTCGTAATACCGGATTCGCTTTCCGGCAGTGCGCCCAGAAAGCAAGTTTCTCCCATCCTTCTCAACTTAaagacta > 1:340964/1‑90 (MQ=255)
gAGGCCCCACCACTTTCGTAATACCGGATTCGCTTTCCGGCAGTGCGCCCAGAAAGCAAGTTTCTCCCATCCTTCTCAACTTAaagacta > 2:818798/1‑90 (MQ=255)
aGGCCCCACCACTTTCGTAATACCGGATTCGCTTTCCGGCAGTGCGCCCa < 2:1636/50‑1 (MQ=255)
aGGCCCCACCACTTTCGTAATACCGGATTCGCTTTCCGGCAGTGCGCCCa > 1:1636/1‑50 (MQ=255)
|
ACAGGCACTCACGTTGGGCTGAGACACAAGCACACATTCCTCTGCACGCTTTTTCGATGTCACCTATCCTTAGAGCGAGGCACCACCACTTTCGTAATACCGGATTCGCTTTCCGGCAGTGCGCCCAGAAAGCAAGTTTCTCCCATCCTTCTCAACTTAAAGACTA > NZ_CP009273/1749781‑1749946
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ 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
AAAACAGGCACTCACGTTGGGCTGAGACACAAGCACACATTCCTCTGCACGCTTTTTCGATGTCACCTATCCTTAGAGCGAGGCACCACCACTTTCGTAATACCGGATTCGCTTTCCGGCAGTGCGCCCAGAAAGCAAGTTTCTCCCATCCTTCTCAACTTAAAGACTAAGACTGTCATGAA > NZ_CP009273/1749778‑1749959
|
gtgggctcggagatgtgtataagagacagCAAGCACACATTCCTCTGCACGCTTTTTCGATGTCACCTATCCTTAGAGCGAGGCCCCACCACTTTCGTAA < SRR3722213.751011/71‑1 (MQ=60)
acgagataataacgggtctcgtgggctcggagatgtgtataagagacagTCCTTAGAGCGAGGCCCCACCACTTTCGTAATACCTGATTCGCTTTCCGGC < SRR3722213.56482/51‑1 (MQ=60)
CAAGCACACATTCCTCTGCACGCTTTTTCGATGTCACCTATCCTTAGAGCGAGGCCCCACCACTTTCGTAATACCGGATTCGCTTTCCGGCAGTGCGCCC > SRR3722213.508985/1‑100 (MQ=60)
TTTTTCGATGTCACCTATCCTTAGAGCGAGGCCCCACCACTTTCGTAATACCGGATTCGCTTTCCGGCAGTGCGCCCAGAAAGCAAGTTTCTCCCATCCT < SRR3722213.744655/100‑1 (MQ=60)
CACCTATCCTTAGAGCGAGGCCCCACCACTTTCGTAATACCGGATTCGCTTTCCGGCAGTGCGCCCAGAAAGCAAGTTTCTCCCATCCTTCTCAACTTAA > SRR3722213.206822/1‑100 (MQ=60)
CACCTATCCTTAGAGCGAGGCCCCACCACTTTCGTAATACCGGATTCGCTTTCCGGCAGTGCGCCCAGAAAGCAAGTTTCTCCCATCCTTCTCAACTTAA > SRR3722213.506910/1‑100 (MQ=60)
ATCCTTAGAGCGAGGCCCCACCACTTTCGTAATACCGGATTCGCTTTCCGGCAGTGCGCCCAGAAAGCAAGTTTCTCCCATCCTTCTCAACTTAAAGACT > SRR3722213.989471/1‑100 (MQ=60)
TCCTTAGAGCGAGGCCCCACCACTTTCGTAATACCGGATTCGCTTTCCGGCAGTGCGCCCAGAAAGCAAGTTTCTCCCATCCTTCTCAACTTAAAGACTA > SRR3722213.348479/1‑100 (MQ=60)
TCCTTAGAGCGAGGCCCCACCACTTTCGTAATACCGGATTCGCTTTCCGGCAGTGCGCCCAGAAAGCAAGTTTCTCCCATCCTTCTCAACTTAAAGACTA > SRR3722213.382930/1‑100 (MQ=60)
CCTTAGAGCGAGGCCCCACCACTTTCGTAATACCGGATTCGCTTTCCGGCAGTGCGCCCAGAAAGCAAGTctgtctcttatacacatctccgagcccacg > SRR3722213.1684/1‑70 (MQ=60)
GCCCCACCACTTTCGTAATACCGGATTCGCTTTCCGGCAGTGCGCCCAGAAAGCAAGTTTCTCCCATCCTTCTCAACTTAAAGACTAAGACTGTCATGAA > SRR3722213.351407/1‑100 (MQ=60)
|
AAAACAGGCACTCACGTTGGGCTGAGACACAAGCACACATTCCTCTGCACGCTTTTTCGATGTCACCTATCCTTAGAGCGAGGCACCACCACTTTCGTAATACCGGATTCGCTTTCCGGCAGTGCGCCCAGAAAGCAAGTTTCTCCCATCCTTCTCAACTTAAAGACTAAGACTGTCATGAA > NZ_CP009273/1749778‑1749959
|
| 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: ‑ |
