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 F5 I102 R1
|
278 |
39.1 |
2251254 |
95.8% |
2156701 |
87.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
977,344 |
A→G |
D281G (GAC→GGC) |
ldtD → |
L,D‑transpeptidase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 977,344 | 0 | A | G | 100.0%
| 123.7
/ NA
| 34 | D281G (GAC→GGC) | ldtD | L,D‑transpeptidase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (18/16); total (18/16) |
TACCGGCGTTGCGCGAAATATTGCAACGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGACGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGTCTCGTAGTAA > NZ_CP009273/977257‑977425
|
tACCGGCGTTGCGCGAAATATTGCAACGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGgcgc < 1:367089/91‑1 (MQ=255)
tACCGGCGTTGCGCGAAATATTGCAACGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGgcgc < 2:621878/91‑1 (MQ=255)
gTTGCGCGAAATATTGCAACGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTc > 1:398100/1‑91 (MQ=255)
ttGCGCGAAATATTGCAACGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCa < 2:1006189/91‑1 (MQ=255)
ttGCGCGAAATATTGCAACGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCa < 2:343451/91‑1 (MQ=255)
gcgcGAAATATTGCAACGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGc > 1:973755/1‑91 (MQ=255)
gAAATATTGCAACGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCAt < 2:1125440/91‑1 (MQ=255)
aaTATTGCACCGCACAGGCATGTTGGACGCGGGGCCGAAAATTCCTCTACCTGGCGATGACCCGCCAACTGGCGCGGAAGCCAACCCATcc < 2:395816/91‑1 (MQ=255)
aaTATTGCAACGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATcc < 1:1091628/91‑1 (MQ=255)
ttGCAACGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTg > 2:1037783/1‑91 (MQ=255)
gCAACGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGtt < 2:742391/91‑1 (MQ=255)
aCGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACt > 1:262410/1‑91 (MQ=255)
aCGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACt > 2:1046703/1‑91 (MQ=255)
ggCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGaaa > 2:581215/1‑91 (MQ=255)
gCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAAc < 2:638256/91‑1 (MQ=255)
gCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAAc < 1:725608/91‑1 (MQ=255)
gCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAAc < 2:77278/91‑1 (MQ=255)
gTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAAcagca > 2:456591/1‑91 (MQ=255)
gTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAAcagca < 2:936287/91‑1 (MQ=255)
ggggCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAg > 1:627809/1‑91 (MQ=255)
ggggCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAg > 1:657006/1‑91 (MQ=255)
gggCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGc > 1:112392/1‑91 (MQ=255)
gggCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGc > 1:91609/1‑91 (MQ=255)
ggCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGcc > 2:767987/1‑91 (MQ=255)
ggCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGcc > 2:221855/1‑91 (MQ=255)
aaTTACTCTCCCTGGCGATGTCACTCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTCCTGTTTAAACAGCAGAAACTAACCCGATGTAt < 2:548712/91‑1 (MQ=255)
aaTTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGAt < 1:385638/91‑1 (MQ=255)
aaTTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGAt < 2:91609/91‑1 (MQ=255)
aCCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAacg > 1:717908/1‑91 (MQ=255)
ccTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAacga < 2:364036/91‑1 (MQ=255)
gATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGtctc < 1:469094/91‑1 (MQ=255)
gATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGtctc < 2:112392/91‑1 (MQ=255)
gATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGtctc < 1:135926/91‑1 (MQ=255)
aTGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGTCTCg > 1:805984/1‑91 (MQ=255)
gACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGTCTCgta > 2:68934/1‑91 (MQ=255)
gACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGTCTCgta > 1:317346/1‑91 (MQ=255)
gACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGTCTCgta > 1:838727/1‑91 (MQ=255)
acGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGTCTCgtagta < 1:581215/91‑1 (MQ=255)
cGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGTCTCGTAGTaa > 2:420701/1‑91 (MQ=255)
|
TACCGGCGTTGCGCGAAATATTGCAACGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGACGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGTCTCGTAGTAA > NZ_CP009273/977257‑977425
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ACGTACCGGCGTTGCGCGAAATATTGCAACGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGACGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGTCTCGTAGTAAACCTGCGCC > NZ_CP009273/977254‑977434
|
ACGTACCGGCGTTGCGCGAAATATTGCAACGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTC > SRR3722125.406464/1‑101 (MQ=60)
TACCGGCGTTGCGCGAAATATTGCAACGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGC > SRR3722125.995488/1‑101 (MQ=60)
TACCGGCGTTGCGCGAAATATTGCAACGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGC < SRR3722125.374786/101‑1 (MQ=60)
AAATATTGCAACGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACT > SRR3722125.267692/1‑101 (MQ=60)
AATATTGCAACGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTG < SRR3722125.1116189/101‑1 (MQ=60)
GCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACT < SRR3722125.741246/101‑1 (MQ=60)
TGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAG > SRR3722125.671173/1‑101 (MQ=60)
TGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAG > SRR3722125.641338/1‑101 (MQ=60)
GTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGC > SRR3722125.114500/1‑101 (MQ=60)
GTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGC > SRR3722125.93340/1‑101 (MQ=60)
AAATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACG > SRR3722125.733404/1‑101 (MQ=60)
AATTACTCTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGA < SRR3722125.393727/101‑1 (MQ=60)
CTACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGTCTCG > SRR3722125.823636/1‑101 (MQ=60)
ACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGTCTCGTA > SRR3722125.857192/1‑101 (MQ=60)
ACCTGGCGATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGTCTCGTA > SRR3722125.323873/1‑101 (MQ=60)
GATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGTCTCGTAGTAAACC < SRR3722125.478995/101‑1 (MQ=60)
GATGACACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGTCTCGTAGTAAACC < SRR3722125.138511/101‑1 (MQ=60)
ACGCCAACTGGCGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGTCTCGTAGTAAACCTGCGCC < SRR3722125.593691/101‑1 (MQ=60)
|
ACGTACCGGCGTTGCGCGAAATATTGCAACGCACAGGCATGTTGGACGGGGGGCCGAAAATTACTCTACCTGGCGATGACACGCCAACTGACGCGGTAGTCAGCCCATCCGCTGTTACTGTTGAAACAGCAGAAACTAAGCCGATGGATAAGCAAACGACGTCTCGTAGTAAACCTGCGCC > NZ_CP009273/977254‑977434
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
