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 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,345,414 |
T→G |
H147P (CAC→CCC) |
glpT ← |
glycerol‑3‑phosphate transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,345,414 | 0 | T | G | 89.5%
| 111.5
/ 5.5
| 38 | H147P (CAC→CCC) | glpT | glycerol‑3‑phosphate transporter |
| Reads supporting (aligned to +/- strand): ref base T (1/3); new base G (13/21); total (14/24) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.76e-01 |
AACAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATC > NZ_CP009273/2345327‑2345488
|
aaCAGCAGCGGCGGAATACCCCCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGc < 2:61003/90‑1 (MQ=255)
aaCAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTTCGACCACCAGGGc < 2:534548/90‑1 (MQ=255)
aaCAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGc < 2:397193/90‑1 (MQ=255)
aaCAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGc < 2:19063/90‑1 (MQ=255)
aaCAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGc < 2:775580/90‑1 (MQ=255)
agcagcGGCGGAATACCACCCCCGCCGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCAcc < 1:582668/90‑1 (MQ=255)
agcagcGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCAcc < 2:381269/90‑1 (MQ=255)
agcagcGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCAcc < 1:255182/90‑1 (MQ=255)
agcagcGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCAcc < 1:521787/90‑1 (MQ=255)
agcGGCGGAATACCACCCCCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATa < 2:467816/90‑1 (MQ=255)
gtgCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCAt < 2:685657/90‑1 (MQ=255)
aGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGa > 2:85378/1‑90 (MQ=255)
tGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCa < 2:503451/90‑1 (MQ=255)
tGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCa < 1:748240/90‑1 (MQ=255)
gACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGc < 1:726479/39‑1 (MQ=255)
gACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGc > 2:726479/1‑39 (MQ=255)
gACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCAcc > 1:551702/1‑42 (MQ=255)
gACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCAcc < 2:551702/42‑1 (MQ=255)
gACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCAt > 2:227124/1‑44 (MQ=255)
gACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCAt < 1:227124/44‑1 (MQ=255)
gACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGt < 2:611709/47‑1 (MQ=255)
gACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGt > 1:611709/1‑47 (MQ=255)
gACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATc > 2:23423/1‑72 (MQ=255)
gACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATc < 1:23423/72‑1 (MQ=255)
gACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCag > 2:250835/1‑90 (MQ=255)
gACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCag > 2:587333/1‑90 (MQ=255)
gACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCag > 2:825775/1‑90 (MQ=255)
aTGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGaac < 2:331151/90‑1 (MQ=255)
aTGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGaac > 2:156807/1‑90 (MQ=255)
ccgccACGTTCTTTCTGCGACCACCAGTGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGaacaac < 1:137328/90‑1 (MQ=255)
ccgccACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGaacaac < 2:336864/90‑1 (MQ=255)
ccgccACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGaacaac < 1:232626/90‑1 (MQ=255)
gccACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAg > 2:360671/1‑90 (MQ=255)
gccACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAg > 1:656882/1‑90 (MQ=255)
aCGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTAc > 2:268096/1‑90 (MQ=255)
tgtctttctGCCACCGCCAGGGCAACATAGTACGGCCACCCGGCGGCCTCCCCTTCCCCTGGAACCAACCGCAGAGGAACAACAGTACaa < 2:99069/88‑1 (MQ=255)
gTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACaa > 2:323358/1‑90 (MQ=255)
ttctGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATc < 2:668548/90‑1 (MQ=255)
|
AACAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATC > NZ_CP009273/2345327‑2345488
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 29 ≤ 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
ATCCCCAGCAGGAACAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCACCGCAATGCTCGACGTCGCC > NZ_CP009273/2345315‑2345509
|
ATCCCCAGCAGGAACAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGG > SRR3722079.191547/1‑100 (MQ=60)
ctctctggtctcgtgggctcggagatgtgtataagagacagGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCATAGTAC < SRR3722079.734251/59‑1 (MQ=60)
AGCAGCGGCGGAATACCACCCCCGCCGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGAC < SRR3722079.588438/100‑1 (MQ=60)
AGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGAC < SRR3722079.257323/100‑1 (MQ=60)
AGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGAC < SRR3722079.526604/100‑1 (MQ=60)
tggtctcgtgggctcggagatgtgtataagagacagGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCA < SRR3722079.229052/64‑1 (MQ=60)
agagacagGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACC < SRR3722079.23590/92‑1 (MQ=60)
GTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCtgtctcttatacacatctccgagcccacgagaccaga > SRR3722079.556992/1‑63 (MQ=60)
GTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACctgtctcttatacacatctccgagcccacgaga > SRR3722079.617896/1‑67 (MQ=60)
TGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAAC < SRR3722079.756235/100‑1 (MQ=60)
ACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAG > SRR3722079.663692/1‑100 (MQ=60)
CCGCCACGTTCTTTCTGCGACCACCAGTGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACA < SRR3722079.138484/100‑1 (MQ=60)
CCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACA < SRR3722079.234596/100‑1 (MQ=60)
gagacaGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCACCGCAATGC < SRR3722079.833734/94‑1 (MQ=60)
CCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACctgtctcttatacacatctccgagcccacgaga > SRR3722079.344502/1‑67 (MQ=60)
|
ATCCCCAGCAGGAACAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCACCGCAATGCTCGACGTCGCC > NZ_CP009273/2345315‑2345509
|
| 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: ‑ |
