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 F4 I88 R1
|
217 |
30.5 |
1742422 |
95.9% |
1670982 |
87.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
870,468 |
A→G |
Q678Q (CAA→CAG) |
pdeI → |
EAL domain‑containing protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 870,468 | 0 | A | G | 100.0%
| 89.5
/ NA
| 24 | Q678Q (CAA→CAG) | pdeI | EAL domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (19/5); total (19/5) |
TGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAAGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGT > NZ_CP009273/870396‑870554
|
tGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGAtt > 1:375853/1‑91 (MQ=255)
gagaTCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATtg > 1:178601/1‑91 (MQ=255)
aTCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATtgatg < 1:209750/91‑1 (MQ=255)
cACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGAc > 2:632171/1‑91 (MQ=255)
cACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGAc > 1:785017/1‑91 (MQ=255)
cACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGAc > 1:59712/1‑91 (MQ=255)
gAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGt > 2:720565/1‑91 (MQ=255)
tttttATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGtttt > 1:444799/1‑91 (MQ=255)
tcAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAAt > 2:559775/1‑91 (MQ=255)
tcAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAAt > 1:604379/1‑91 (MQ=255)
tcAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAAt > 1:334973/1‑91 (MQ=255)
atatTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTaa > 1:802029/1‑91 (MQ=255)
atTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATc < 2:49183/91‑1 (MQ=255)
gAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTGTGAAATTAATCCAg > 2:648075/1‑91 (MQ=255)
gAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAg > 1:304537/1‑91 (MQ=255)
acaacTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGAc < 1:720565/91‑1 (MQ=255)
acaacTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGAc < 2:785017/91‑1 (MQ=255)
acaacTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGAc < 2:334973/91‑1 (MQ=255)
acTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGc > 2:799366/1‑91 (MQ=255)
acTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGc > 1:653996/1‑91 (MQ=255)
acTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGc > 2:515717/1‑91 (MQ=255)
acTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGc > 1:217538/1‑91 (MQ=255)
gCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATa > 1:111235/1‑91 (MQ=255)
gCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATa > 1:147664/1‑91 (MQ=255)
aaCAGGGGGGACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGt < 1:451940/91‑1 (MQ=255)
|
TGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAAGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGT > NZ_CP009273/870396‑870554
|
| 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
ATGGCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAAGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAA > NZ_CP009273/870368‑870564
|
ATGGCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAG < SRR3722118.86820/101‑1 (MQ=60)
CCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGG < SRR3722118.227685/101‑1 (MQ=60)
GCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATT > SRR3722118.383706/1‑101 (MQ=60)
CCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTG > SRR3722118.182120/1‑101 (MQ=60)
GTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGAC > SRR3722118.802242/1‑101 (MQ=60)
GTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGAC > SRR3722118.60817/1‑101 (MQ=60)
ATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCAC < SRR3722118.213949/101‑1 (MQ=60)
TTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTT > SRR3722118.454170/1‑101 (MQ=60)
CATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAAT > SRR3722118.341874/1‑101 (MQ=60)
CATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAAT > SRR3722118.617276/1‑101 (MQ=60)
TTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAA > SRR3722118.819646/1‑101 (MQ=60)
TCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAG > SRR3722118.310798/1‑101 (MQ=60)
ATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGC > SRR3722118.668127/1‑101 (MQ=60)
ATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGC > SRR3722118.221911/1‑101 (MQ=60)
TTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCtgtctcttatacacatctccgagcccacgagacggactcctatctcgt > SRR3722118.696493/1‑53 (MQ=60)
TTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATA > SRR3722118.113291/1‑101 (MQ=60)
TTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATA > SRR3722118.150503/1‑101 (MQ=60)
ACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGG < SRR3722118.736388/101‑1 (MQ=60)
AACAGGGGGGACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAA < SRR3722118.461463/101‑1 (MQ=60)
|
ATGGCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAAGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAA > NZ_CP009273/870368‑870564
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
