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 I199 R1
|
220 |
57.5 |
3163680 |
97.0% |
3068769 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
RA |
NZ_CP009273 |
2,122,267 |
A→C |
S35A (TCG→GCG) |
wcaF ← |
colanic acid biosynthesis acetyltransferase WcaF |
|
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
* | NZ_CP009273 | 2,122,267 | 0 | A | C | 93.8%
| 149.8
/ 1.9
| 48 | S35A (TCG→GCG) | wcaF | colanic acid biosynthesis acetyltransferase WcaF |
Reads supporting (aligned to +/- strand): ref base A (0/3); new base C (17/28); total (17/31) |
Fisher's exact test for biased strand distribution p-value = 5.43e-01 |
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.05e-01 |
CTGACGGACGAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGAAA > NZ_CP009273/2122180‑2122352
|
ctaacggacgAATACTTACGTTTTTTCCTATTTTTGCCCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGccc < 2:1024164/87‑1 (MQ=255)
cTGACGGACGAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGccc < 2:617081/90‑1 (MQ=255)
cTGACGGACGAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGccc < 2:434064/90‑1 (MQ=255)
cTGACGGACGAATAACTACGTTTTTTCCTATTTTTGCCCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGccc < 1:1493794/90‑1 (MQ=255)
acggacgAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAACCGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAgg < 1:1191050/90‑1 (MQ=255)
aaTAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAatat > 1:980693/1‑90 (MQ=255)
tAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATAttg < 2:982781/90‑1 (MQ=255)
tAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATAttg < 2:980693/90‑1 (MQ=255)
tAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATAttg < 2:311935/90‑1 (MQ=255)
tAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATAttg < 1:571685/90‑1 (MQ=255)
tAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATAttg < 1:562898/90‑1 (MQ=255)
tAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATAttg < 1:554326/90‑1 (MQ=255)
tAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGACCAGGCAAATAttg < 2:978278/90‑1 (MQ=255)
aCGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGcc < 1:69681/90‑1 (MQ=255)
aCGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGcc < 1:28907/90‑1 (MQ=255)
ttttttCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGt > 2:985621/1‑90 (MQ=255)
ttttCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTAc < 1:542578/90‑1 (MQ=255)
ttttCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTAc < 2:429524/90‑1 (MQ=255)
ttttCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTAc < 1:466281/90‑1 (MQ=255)
ttttCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTAc < 2:432322/90‑1 (MQ=255)
ttttCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTAc > 2:246501/1‑90 (MQ=255)
ttttCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTAc < 1:1534320/90‑1 (MQ=255)
tCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGc < 1:1326867/90‑1 (MQ=255)
cTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGccc < 2:1120981/90‑1 (MQ=255)
cTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGccc < 1:979941/90‑1 (MQ=255)
cTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGccc < 1:598041/90‑1 (MQ=255)
tttttGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCccacc < 1:994520/90‑1 (MQ=255)
tttttGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCccacc < 2:615951/90‑1 (MQ=255)
cTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCCCACCATAAtt < 2:472602/90‑1 (MQ=255)
ccGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGc < 1:10484/90‑1 (MQ=255)
ccGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGc < 1:330650/90‑1 (MQ=255)
ccGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGc < 2:1214356/90‑1 (MQ=255)
gAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCAc < 2:42506/90‑1 (MQ=255)
gAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCAc < 1:1531275/90‑1 (MQ=255)
gAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCAc < 1:784400/90‑1 (MQ=255)
aataaAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGc > 2:1477434/1‑78 (MQ=255)
aataaAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGc < 1:1477434/78‑1 (MQ=255)
aataaAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCg > 1:440832/1‑90 (MQ=255)
aataaAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCg > 2:845218/1‑90 (MQ=255)
aaaaGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTgcc < 1:471649/90‑1 (MQ=255)
gCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGccc > 1:319203/1‑90 (MQ=255)
gCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGa > 2:265056/1‑90 (MQ=255)
aTACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCa > 2:731968/1‑90 (MQ=255)
tgtgGCGCTCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCgag > 1:1016426/1‑90 (MQ=255)
tgtgGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCgag > 1:667724/1‑90 (MQ=255)
tgtgGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCgag > 2:483819/1‑90 (MQ=255)
tgtgGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCgag > 2:10738/1‑90 (MQ=255)
tgtgGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCgag > 1:654611/1‑90 (MQ=255)
tgtgGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCgag > 1:692668/1‑90 (MQ=255)
tgtgGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCgag > 1:1237982/1‑90 (MQ=255)
ggCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGaaa > 2:1145380/1‑90 (MQ=255)
ggCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGaaa < 1:631214/90‑1 (MQ=255)
|
CTGACGGACGAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGAAA > NZ_CP009273/2122180‑2122352
|
Alignment Legend |
---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 31 ≤ 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
CTGACGGACGAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGAAACCGCTTAAAT > NZ_CP009273/2122180‑2122362
|
CTGACGGACGAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATAT > SRR3722078.994830/1‑100 (MQ=60)
CTGACGGACGAATAACTACGTTTTTTCCTATTTTTGCCCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAGTAT < SRR3722078.1518145/100‑1 (MQ=60)
ACGGACGAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAACCGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGT < SRR3722078.1209685/100‑1 (MQ=60)
acccccgagatctacacgaccgccatcgtcggcagcgtcagatgtgtataagagacaGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTAC < SRR3722078.616019/43‑1 (MQ=60)
TAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTAC < SRR3722078.578374/100‑1 (MQ=60)
TAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTAC < SRR3722078.569505/100‑1 (MQ=60)
TAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTAC < SRR3722078.560865/100‑1 (MQ=60)
ACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCC < SRR3722078.70496/100‑1 (MQ=60)
ACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCC < SRR3722078.29264/100‑1 (MQ=60)
TTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCAT < SRR3722078.471842/100‑1 (MQ=60)
TTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCAT < SRR3722078.548986/100‑1 (MQ=60)
TTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCAT < SRR3722078.1559333/100‑1 (MQ=60)
TCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAAT < SRR3722078.1348084/100‑1 (MQ=60)
CTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTG < SRR3722078.994061/100‑1 (MQ=60)
CTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTG < SRR3722078.604970/100‑1 (MQ=60)
TTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCAC < SRR3722078.1008989/100‑1 (MQ=60)
agGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAG < SRR3722078.1501535/98‑1 (MQ=60)
CCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAG < SRR3722078.334694/100‑1 (MQ=60)
CCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAG < SRR3722078.10600/100‑1 (MQ=60)
GAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCG > SRR3722078.446120/1‑100 (MQ=60)
GAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCG < SRR3722078.1556230/100‑1 (MQ=60)
GAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCG < SRR3722078.794621/100‑1 (MQ=60)
TAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCC > SRR3722078.323114/1‑100 (MQ=60)
AAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAAC < SRR3722078.477244/100‑1 (MQ=60)
ATACAATACTTGTGGCGCTCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAG > SRR3722078.1031418/1‑100 (MQ=60)
ATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAG > SRR3722078.662109/1‑100 (MQ=60)
ATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAG > SRR3722078.675361/1‑100 (MQ=60)
ATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAG > SRR3722078.700897/1‑100 (MQ=60)
ATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAG > SRR3722078.1257526/1‑100 (MQ=60)
ATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGAAACC > SRR3722078.112884/1‑100 (MQ=60)
ATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGAAACC > SRR3722078.1580476/1‑100 (MQ=60)
GGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGAAACCGCTTAAAT < SRR3722078.638476/100‑1 (MQ=60)
|
CTGACGGACGAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGAAACCGCTTAAAT > NZ_CP009273/2122180‑2122362
|
Alignment Legend |
---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |