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 I210 R1
|
226 |
19.6 |
1130256 |
95.4% |
1078264 |
84.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
661,892 |
A→C |
G594G (GGT→GGG) |
mrdA ← |
peptidoglycan DD‑transpeptidase MrdA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 661,892 | 0 | A | C | 94.3%
| 108.2
/ ‑2.0
| 35 | G594G (GGT→GGG) | mrdA | peptidoglycan DD‑transpeptidase MrdA |
| Reads supporting (aligned to +/- strand): ref base A (1/1); new base C (15/18); total (16/19) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.58e-01 |
CCGCAGGCAGATCGGTGTTGTTATCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCACCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGTCACGTAAACG > NZ_CP009273/661807‑661975
|
ccGCAGGCAGATCGGTGTTGTTATCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGt < 2:174168/90‑1 (MQ=255)
gttATCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGAc > 2:93204/1‑90 (MQ=255)
tATCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAg > 2:262163/1‑90 (MQ=255)
cACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCa > 1:6646/1‑90 (MQ=255)
cAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTg < 2:466620/90‑1 (MQ=255)
cAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTg < 1:362523/90‑1 (MQ=255)
aGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGc > 1:379102/1‑90 (MQ=255)
cATAATGTGGTCGAGGATCTGGCGCATCAGTGTCCCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCgg < 1:311100/90‑1 (MQ=255)
tAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGAt < 1:360672/90‑1 (MQ=255)
tAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGAt < 2:6646/90‑1 (MQ=255)
tAAGGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCCCCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGAt < 2:381765/90‑1 (MQ=255)
aaTGTGGTCGAGGATCTGGCGCATCAGTGTCCCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGAtt < 1:61960/90‑1 (MQ=255)
aTGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGAttg > 1:24935/1‑90 (MQ=255)
aTGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGAttg > 1:292535/1‑90 (MQ=255)
ggTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGAt < 1:45988/84‑1 (MQ=255)
ggTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGAt > 2:45988/1‑84 (MQ=255)
tCGAGGATCTGGCGCATCAGTGTACCACCCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTAt < 1:541521/90‑1 (MQ=255)
tCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTAt < 2:201083/90‑1 (MQ=255)
cGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATg > 2:383231/1‑90 (MQ=255)
ggATCTGGCGCATCAGTGTACCACCCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCgg < 1:318401/76‑1 (MQ=255)
ggATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCgg > 2:318401/1‑76 (MQ=255)
ggATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGgcg > 1:191888/1‑90 (MQ=255)
cTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCg > 1:98868/1‑71 (MQ=255)
cTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCg < 2:98868/71‑1 (MQ=255)
gcgcATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGc < 2:156631/90‑1 (MQ=255)
cATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGt < 2:120213/90‑1 (MQ=255)
aGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGtcatc < 2:395427/90‑1 (MQ=255)
gtACCAACCGCCGGACCCGCACCACCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGtcatc > 2:120836/1‑87 (MQ=255)
gtACCAACCGCCGGACCCGCACCACCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGtcatc < 1:120836/87‑1 (MQ=255)
aaCCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGAt > 2:426925/1‑56 (MQ=255)
aaCCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGAt < 1:426925/56‑1 (MQ=255)
aaCCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTtgtg > 1:368063/1‑90 (MQ=255)
cgccgGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGTc > 1:149446/1‑90 (MQ=255)
ccGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGTCACGTAAAc < 2:413127/90‑1 (MQ=255)
cGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGTCACGTAAACg > 1:347748/1‑90 (MQ=255)
|
CCGCAGGCAGATCGGTGTTGTTATCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCACCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGTCACGTAAACG > NZ_CP009273/661807‑661975
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 27 ≤ 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
CCGCAGGCAGATCGGTGTTGTTATCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCACCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGTCACGTAAACG > NZ_CP009273/661807‑661975
|
ggcgcccaccgagatctacactaagatggtcgtcggcagcgtcagatgtgtataagagacagGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAAT < SRR3722092.490919/38‑1 (MQ=60)
GTGTTGTTATCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCA > SRR3722092.6763/1‑100 (MQ=60)
GTTATCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGC > SRR3722092.386281/1‑100 (MQ=60)
ACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTG > SRR3722092.25363/1‑100 (MQ=60)
ACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTG > SRR3722092.297618/1‑100 (MQ=60)
CAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTG < SRR3722092.369250/100‑1 (MQ=60)
acagATGTGGTCGAGGATCTGGCGCATCAGTGTCCCACCCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTAT < SRR3722092.324030/96‑1 (MQ=60)
CATAATGTGGTCGAGGATCTGGCGCATCAGTGTCCCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTAT < SRR3722092.316593/100‑1 (MQ=60)
gcgtcagatgtgtataagagacagTCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGG < SRR3722092.435204/76‑1 (MQ=60)
TAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGG < SRR3722092.367344/100‑1 (MQ=60)
TAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGG < SRR3722092.46776/100‑1 (MQ=60)
AATGTGGTCGAGGATCTGGCGCATCAGTGTCCCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGC < SRR3722092.62967/100‑1 (MQ=60)
ATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCG > SRR3722092.195083/1‑100 (MQ=60)
GGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTActgtctctt > SRR3722092.100562/1‑91 (MQ=60)
TCGAGGATCTGGCGCATCAGTGTACCACCCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGG < SRR3722092.552396/100‑1 (MQ=60)
TCAGTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTG > SRR3722092.374957/1‑100 (MQ=60)
AGAGTACCAACCGCCGGACCCGCACCACCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGT < SRR3722092.122891/100‑1 (MQ=60)
GTGTACCAACCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGTC > SRR3722092.151958/1‑100 (MQ=60)
CCGCCGGACCCGCACCCCCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGTCACGTAAACG > SRR3722092.354026/1‑100 (MQ=60)
|
CCGCAGGCAGATCGGTGTTGTTATCACCCAGCATAATGTGGTCGAGGATCTGGCGCATCAGTGTACCAACCGCCGGACCCGCACCACCGTTCTCCAGAATCATGGCGACAGCCACTTGCGGATTGTTGTATGGCGCAAAGGCGGTCATCAGTTTGTGGTCACGTAAACG > NZ_CP009273/661807‑661975
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
