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 |
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%
| 162.5
/ NA
| 43 | Q678Q (CAA→CAG) | pdeI | EAL domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (27/16); total (27/16) |
GAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAAGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAA > NZ_CP009273/870381‑870550
|
gAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAgggg > 1:601420/1‑91 (MQ=255)
aGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTAc < 2:753079/91‑1 (MQ=255)
gCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACg > 1:976375/1‑91 (MQ=255)
gCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACg > 2:22522/1‑91 (MQ=255)
gtgtTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATc < 2:601420/91‑1 (MQ=255)
tGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGAtt > 1:134420/1‑91 (MQ=255)
tGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGAtt > 2:266150/1‑91 (MQ=255)
gaTCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTGCGGATATCGATtgat > 1:186321/1‑91 (MQ=255)
gaTCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATtgat > 1:767178/1‑91 (MQ=255)
aTCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATtgatg < 1:687336/91‑1 (MQ=255)
cACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTAc > 1:865480/1‑74 (MQ=255)
cACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTAc < 2:865480/74‑1 (MQ=255)
cACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGAc > 1:510874/1‑91 (MQ=255)
cACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGAc > 1:50452/1‑91 (MQ=255)
cACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGAc > 2:564398/1‑91 (MQ=255)
cACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGAc > 1:360803/1‑91 (MQ=255)
aCTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACt < 1:125616/91‑1 (MQ=255)
cTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACtt > 1:618649/1‑91 (MQ=255)
tGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACttt < 2:709616/91‑1 (MQ=255)
gAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTg > 2:522314/1‑91 (MQ=255)
gTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCg > 1:619660/1‑91 (MQ=255)
gTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCg > 1:1031107/1‑91 (MQ=255)
gAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGt > 2:688292/1‑91 (MQ=255)
aCATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGt > 1:716291/1‑91 (MQ=255)
aCATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGt > 2:717425/1‑91 (MQ=255)
cATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGtt > 2:10610/1‑91 (MQ=255)
tttttATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGtttt > 1:499505/1‑91 (MQ=255)
tATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATg < 1:463791/91‑1 (MQ=255)
tcAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAAt < 1:522314/91‑1 (MQ=255)
tcAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAAt < 2:618649/91‑1 (MQ=255)
aaTATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTa > 1:1090573/1‑91 (MQ=255)
atTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATc < 2:334683/91‑1 (MQ=255)
ttGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATcc > 1:272417/1‑91 (MQ=255)
gAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAg > 2:1064520/1‑91 (MQ=255)
aacaacTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGa > 2:281492/1‑91 (MQ=255)
acaacTGCGTAAACAGGGGGTGCGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGAc < 2:186321/91‑1 (MQ=255)
acaacTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGAc < 1:10610/91‑1 (MQ=255)
acaacTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGAc < 2:50452/91‑1 (MQ=255)
acaacTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGAc < 1:816347/91‑1 (MQ=255)
acTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGc > 2:577345/1‑91 (MQ=255)
acTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGc > 1:205380/1‑91 (MQ=255)
acTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGc > 2:976876/1‑91 (MQ=255)
tGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCAt < 1:797664/91‑1 (MQ=255)
cGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATaa < 2:767178/91‑1 (MQ=255)
|
GAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAAGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAA > NZ_CP009273/870381‑870550
|
| 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
GCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAAGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGAC > NZ_CP009273/870371‑870558
|
GCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGG > SRR3722125.614367/1‑101 (MQ=60)
AAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACG > SRR3722125.998169/1‑101 (MQ=60)
tataagagacagTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGG < SRR3722125.688440/89‑1 (MQ=60)
AGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGG < SRR3722125.663241/101‑1 (MQ=60)
GGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGA < SRR3722125.652312/101‑1 (MQ=60)
GCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATT > SRR3722125.136971/1‑101 (MQ=60)
TCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTGCGGATATCGATTGAT > SRR3722125.189938/1‑101 (MQ=60)
TCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGAT > SRR3722125.783828/1‑101 (MQ=60)
GTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGAC > SRR3722125.368375/1‑101 (MQ=60)
GTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGAC > SRR3722125.51389/1‑101 (MQ=60)
GTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGAC > SRR3722125.521715/1‑101 (MQ=60)
GTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAAGATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATctgtctc > SRR3722125.884576/1‑94 (MQ=60)
GTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTT > SRR3722125.631987/1‑101 (MQ=60)
ATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCAC < SRR3722125.702161/101‑1 (MQ=60)
CACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCG > SRR3722125.1054227/1‑101 (MQ=60)
CACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCG > SRR3722125.633020/1‑101 (MQ=60)
ACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGG < SRR3722125.127976/101‑1 (MQ=60)
GAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGT > SRR3722125.731734/1‑101 (MQ=60)
TTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTT > SRR3722125.510072/1‑101 (MQ=60)
TTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTA > SRR3722125.1115104/1‑101 (MQ=60)
TATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCC < SRR3722125.473574/101‑1 (MQ=60)
TATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCC > SRR3722125.277909/1‑101 (MQ=60)
TCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGAC < SRR3722125.533410/101‑1 (MQ=60)
ATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGC > SRR3722125.209429/1‑101 (MQ=60)
ACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGG < SRR3722125.10814/101‑1 (MQ=60)
ACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGG < SRR3722125.834232/101‑1 (MQ=60)
ACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGG < SRR3722125.970819/101‑1 (MQ=60)
TGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGAC < SRR3722125.815080/101‑1 (MQ=60)
|
GCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAAGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGAC > NZ_CP009273/870371‑870558
|
| 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: ‑ |
