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 |
3,736,824 |
A→G |
A244A (GCA→GCG) |
yiaK → |
3‑dehydro‑L‑gulonate 2‑dehydrogenase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,736,824 | 0 | A | G | 97.9%
| 166.4
/ ‑4.2
| 48 | A244A (GCA→GCG) | yiaK | 3‑dehydro‑L‑gulonate 2‑dehydrogenase |
| Reads supporting (aligned to +/- strand): ref base A (0/1); new base G (27/20); total (27/21) |
| Fisher's exact test for biased strand distribution p-value = 4.38e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.75e-01 |
CCGCATTTTGCCGATGGGCTACTGGAAAGGTTCTGGCATGTCGATTGTGCTGGATATGATCGCTACTCTCCTTTCCGACGGCGCATCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACAAATTTTTATTGCCATTGAAGTGGACAAGCTTA > NZ_CP009273/3736740‑3736906
|
ccgcATTTTGCCGATGGGCTACTGGAAAGGTTCTGGCATGTCGATTGTGCTGGATATGATCGCTACTCTCCTTTCCGACGGCGCGTCCGt < 2:969417/90‑1 (MQ=255)
aTTTTGCCGATGGGCTACTGGAAAGGTTCTGGCATGTCGATTGTGCTGGATATGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGcc < 2:448881/90‑1 (MQ=255)
aTTTTGCCGATGGGCTACTGGAAAGGTTCTGGCATGTCGATTGTGCTGGATATGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGcc < 1:986329/90‑1 (MQ=255)
ttGCCGATGGGCTACTGGAAAGGTTCTGGCATGTCGATTGTGCTGGATATGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGaa > 1:624299/1‑90 (MQ=255)
gATGGGCTACTGGAAAGGTTCTGGCATGTCGATTGTGCTGGATATGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCAc < 1:595895/90‑1 (MQ=255)
tACTGGAAAGGTTCTGGCATGTCGATTGTGCTGGATATGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGac > 1:369309/1‑90 (MQ=255)
tGGAACGGTTCTGGCATGTCGATTGTGCTGGATATGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGacaac < 2:498258/90‑1 (MQ=255)
aGGTTCTGGCATGTCGATTGTGCTGGATATGATCGCTACTCTCCTTTCCGACGGCGCATCCGTTGCCGAAGTCACCCAGGACAACAGcga < 1:1060360/90‑1 (MQ=255)
ttCTGGCATGTCGATTGTGCTGGATATGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGcgacga > 1:347637/1‑90 (MQ=255)
tGTCGATTGTGCTGGATATGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAgg < 2:981727/69‑1 (MQ=255)
tGTCGATTGTGCTGGATATGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAgg > 1:981727/1‑69 (MQ=255)
tGTCGATTGTGCTGGATATGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCa > 2:905260/1‑90 (MQ=255)
tGTCGATTGTGCTGGATATGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCa > 2:222441/1‑90 (MQ=255)
gTCGATTGTGCTGGATATGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCAt > 1:504174/1‑90 (MQ=255)
gTCGATTGTGCTGGATATGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCAt > 2:959165/1‑90 (MQ=255)
gTCGATTGTGCTGGATATGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCAt > 1:809620/1‑90 (MQ=255)
gTCGATTGTGCTGGATATGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCAt > 1:92220/1‑90 (MQ=255)
gTCGATTGTGCTGGATATGATCGCTACACTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCAccc < 1:210301/65‑1 (MQ=255)
gTCGATTGTGCTGGATATGATCGCTACACTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCAccc > 2:210301/1‑65 (MQ=255)
atGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACAAATTTTTAtt < 2:809620/90‑1 (MQ=255)
tGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCAccc < 2:217222/48‑1 (MQ=255)
tGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCAccc > 1:217222/1‑48 (MQ=255)
tGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGTCATTTCACAAATTTTTATTg < 2:369309/90‑1 (MQ=255)
tGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACAAATTTTTATTg > 1:364686/1‑90 (MQ=255)
tGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACAAATTTTTATTg > 1:948906/1‑90 (MQ=255)
tGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACAAATTTTTATTg > 2:457554/1‑90 (MQ=255)
tGATCGCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACAAATTTTTATTg > 2:813972/1‑90 (MQ=255)
gCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGt < 1:973244/38‑1 (MQ=38)
gCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGt > 2:973244/1‑38 (MQ=38)
gCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGt < 1:868396/38‑1 (MQ=38)
gCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGt > 2:868396/1‑38 (MQ=38)
gCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACAAATTTTTATTGCCAtt > 1:601772/1‑90 (MQ=255)
gCTACTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACAAATTTTTATTGCCAtt > 1:251778/1‑90 (MQ=255)
aCTCTCCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACAAATTTTTATTGCCATTGaa < 1:959165/90‑1 (MQ=255)
ctcCTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACAAATTTTTATTGCCATTGAAGTg < 1:376736/90‑1 (MQ=255)
cTTTCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACAAATTTTTATTGCCATTGAAGTGGAc < 2:9540/90‑1 (MQ=255)
ttCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATAc > 1:698524/1‑52 (MQ=255)
ttCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATAc < 2:698524/52‑1 (MQ=255)
ttCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACAAATTTTTATTGCCATTGAAGTGGACaa > 1:396116/1‑90 (MQ=255)
ttCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACAAATTTTTATTGCCATTGAAGTGGACaa > 1:621311/1‑90 (MQ=255)
ttCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACAAATTTTTATTGCCATTGAAGTGGACaa < 1:610821/90‑1 (MQ=255)
ttCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACAAATTTTTATTGCCATTGAAGTGGACaa > 1:973746/1‑90 (MQ=255)
ttCCGACGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACAAATTTTTATTGCCATTGAAGTGGACaa < 1:1005324/90‑1 (MQ=255)
ttCCGAAGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACAAATTTTTATTGCCATTGAAGTGGACaa > 1:575201/1‑90 (MQ=255)
aCGGCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCGTTTCACAAATTTTTATTGCCATTGAAGTGGACAAGCTTa < 2:93992/90‑1 (MQ=255)
aCGGCGCGTACGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACAAATTTTTATTGCCATTGAAGTGGACAAGCTTa > 2:36804/1‑90 (MQ=255)
ggCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACaa > 1:976344/1‑57 (MQ=255)
ggCGCGTCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACaa < 2:976344/57‑1 (MQ=255)
|
CCGCATTTTGCCGATGGGCTACTGGAAAGGTTCTGGCATGTCGATTGTGCTGGATATGATCGCTACTCTCCTTTCCGACGGCGCATCCGTTGCCGAAGTCACCCAGGACAACAGCGACGAATACGGCATTTCACAAATTTTTATTGCCATTGAAGTGGACAAGCTTA > NZ_CP009273/3736740‑3736906
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 33 ≤ 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
GCGACCGGCTGACCACAATACAGAACGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCGCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGT > NZ_CP009273/3758634‑3758823
|
GCGACCGGCTGACCACAATACATAACGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGG < SRR3722213.782053/100‑1 (MQ=35)
CGGCTGACCACAATACAGAACGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGC < SRR3722213.315125/100‑1 (MQ=32)
CCACAATACAGAACGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAA > SRR3722213.1031166/1‑100 (MQ=25)
CCACAATACAGAACGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAA > SRR3722213.878007/1‑100 (MQ=25)
CCACAATACAGAACGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAA > SRR3722213.61400/1‑100 (MQ=25)
CAATACAGAACGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAAC > SRR3722213.803640/1‑100 (MQ=12)
CAATACAGAACGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAAC > SRR3722213.524412/1‑100 (MQ=12)
ATACAGAACGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGC > SRR3722213.992516/1‑100 (MQ=7)
ATACAGAACGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGC > SRR3722213.48493/1‑100 (MQ=7)
GAACGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTTGCGAAAACGCAGCGC > SRR3722213.617814/1‑100 (MQ=7)
GACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCA > SRR3722213.25156/1‑100 (MQ=7)
ACAGAACCCGCATCCAGACGATTTATCAGCCGAGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAG < SRR3722213.32523/100‑1 (MQ=7)
GAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCT > SRR3722213.560476/1‑100 (MQ=7)
CGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGG < SRR3722213.277226/100‑1 (MQ=7)
CATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGAT > SRR3722213.747966/1‑100 (MQ=7)
TCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGTCGAAAACGCAGCGCCGCAGCCTGGCGGATGC > SRR3722213.722512/1‑100 (MQ=11)
CGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCA > SRR3722213.885162/1‑100 (MQ=32)
ATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGC > SRR3722213.1095951/1‑100 (MQ=37)
TTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAG < SRR3722213.615277/100‑1 (MQ=37)
TATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGT > SRR3722213.922773/1‑100 (MQ=37)
GCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCGCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGC > SRR3722213.805494/1‑100 (MQ=38)
GGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCG > SRR3722213.367199/1‑100 (MQ=49)
TCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGAAGACGG > SRR3722213.641854/1‑100 (MQ=49)
TCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGAGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGAAGACGG < SRR3722213.592047/100‑1 (MQ=35)
agacagCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGAAGACGGTGGC < SRR3722213.1030765/94‑1 (MQ=38)
CCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGAAGACGGTGGCA > SRR3722213.432023/1‑100 (MQ=49)
ACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGT > SRR3722213.961567/1‑100 (MQ=37)
CATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCctgtctcttatacacatctccgagcccacgagacc > SRR3722213.142901/1‑65 (MQ=26)
agagacagTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTNG < SRR3722213.450524/92‑1 (MQ=20)
GAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTT > SRR3722213.243498/1‑100 (MQ=29)
GAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTT > SRR3722213.975434/1‑100 (MQ=29)
CCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGT > SRR3722213.47786/1‑100 (MQ=9)
CCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGT > SRR3722213.382649/1‑100 (MQ=9)
|
GCGACCGGCTGACCACAATACAGAACGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCGCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGT > NZ_CP009273/3758634‑3758823
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
