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 I229 R1
|
214 |
17.4 |
943020 |
97.5% |
919444 |
87.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,249,013 |
T→C |
R430R (CGT→CGC) |
dinF → |
MATE family efflux transporter DinF |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,249,013 | 0 | T | C | 100.0%
| 59.1
/ NA
| 20 | R430R (CGT→CGC) | dinF | MATE family efflux transporter DinF |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (15/5); total (15/5) |
CCGTGGCTGGGTAATCATGCTTTGTGGCTGGCATTAACCGTCTTTCTGGCGTTGCGCGGGCTTTCTCTGGCGGCTATCTGGCGGCGTCACTGGCGCAATGGTACCTGGTTTGCCGCAACGTGACGGTTAAAAATTCTGAATAAATAATCCTAAGCCAAATTGC > NZ_CP009273/4248927‑4249089
|
ccGTGGCTGGGTAATCATGCTTTGTGGCTGGCATTAACCGTCTTTCTGGCGTTGCGCGGGCTTTCTCTGGCGGCTATCTGGCGGCGCCAc > 2:229961/1‑90 (MQ=255)
ccGTGGCTGGGTAATCATGCTTTGTGGCTGGCATTAACCGTCTTTCTGGCGTTGCGCGGGCTTTCTCTGGCGGCTATCTGGCGGCGCCAc > 2:140437/1‑90 (MQ=255)
cTGGGTAATCATGCTTTGTGGCTGGCATTAACCGTCTTTCTGGCGTTGCGCGGGCTTTCTCTGGCGGCTATCTGGCGGCGCCACTGgcgc < 1:93832/90‑1 (MQ=255)
aTCATGCTTTGTGGCTGGCATTAACCGTCTTTCTGGCGTTGCGCGGGCTTTCTCTGGCGGCTATCTGGCGGCGCCACTGGCGCAATGGTa > 2:470030/1‑90 (MQ=255)
gCTTTGTGGCTGGCATTAACCGTCTTTCTGGCGTTGCGCGGGCTTTCTCTGGCGGCTATCTGGCGGCGCCACTGGCGCAATGGTACCTgg > 1:197028/1‑90 (MQ=255)
gCTTTGTGGCTGGCATTAACCGTCTTTCTGGCGTTGCGCGGGCTTTCTCTGGCGGCTATCTGGCGGCGCCACTGGCGCAATGGTACCTgg > 1:393350/1‑90 (MQ=255)
gCTTTGTGGCTGGCATTAACCGTCTTTCTGGCGTTGCGCGGGCTTTCTCTGGCGGCTATCTGGCGGCGCCACTGGCGCAATGGTACCTgg > 2:431002/1‑90 (MQ=255)
gtgGCTGGCATTAACCGTCTTTCTGGCGTTGCGCGGGCTTTCTCTGGCGGCTATCTGGCGGCGCCACTGGCGCAATGGTACCTGGTTTGc > 2:168230/1‑90 (MQ=255)
tAACCGTCTTTCTGGCGTTGCGCGGGCTTTCTCTGGCGGCTATCTGGCGGCGCCACTGGCGCAATGGTACCTGGTTTGCCGCAACGTGAc < 1:470030/90‑1 (MQ=255)
aaCCGTCTTTCTGGCGTTGCGCGGGCTTTCTCTGGCGGCTATCTGGCGGCGCCACTGGCGCAATGGTACCTGGTTTGCCGCAACGTGACg > 2:196043/1‑90 (MQ=255)
gTCTTTCTGGCGTTGCGCGGGCTTTCTCTGGCGGCTATCTGGCGGCGCCACTGGCGCAATGGTACCTGGTTTGCCGCAACGTGACGGTTa > 1:155520/1‑90 (MQ=255)
gTCTTTCTGGCGTTGCGCGGGCTTTCTCTGGCGGCTATCTGGCGGCGCCACTGGCGCAATGGTACCTGGTTTGCCGCAACGTGACGGTTa > 2:199804/1‑90 (MQ=255)
tCTTTCTGGCGTTGCGCGGGCTTTCTCTGGCGGCTATCTGGCGGCGCCACTGgcgc < 1:434346/56‑1 (MQ=255)
tCTTTCTGGCGTTGCGCGGGCTTTCTCTGGCGGCTATCTGGCGGCGCCACTGgcgc > 2:434346/1‑56 (MQ=255)
tGGCGTTGCGCGGGCTTTCTCTGGCGGCTATCTGGCGGCGCCACTGGCGCAATGGTACCTGGTTTGCCGCAACGTGACGGTTAAAAATTc > 1:263463/1‑90 (MQ=255)
gTTGCGCGGGCTTTCTCTGGCGGCTATCTGGCGGCGCCACTGGCGCAATGGTACCTGGTTTGCCGCAACGTGACGGTTAAAAATTCTGaa < 1:426715/90‑1 (MQ=255)
tGCGCGGGCTTTCTCTGGCGGCTATCTGGCGGCGCCACTGGCGCAATGGTACCTGGTTTGCCGCAACGTGACGGTTAAAAATTCTGaata > 2:2991/1‑90 (MQ=255)
ggcggcTATCTGGCGGCGCCACTGGCGCAATGGTACCTGGTTTGCCGCAACGTGACGGTTAAAAATTCTGAATAAATAATCCTAAGCCaa > 2:448327/1‑90 (MQ=255)
ggcggcTATCTGGCGGCGCCACTGGCGCAATGGTACCTGGTTTGCCGCAACGTGACGGTTAAAAATTCTGAATAAATAATCCTAAGCCaa > 2:61298/1‑90 (MQ=255)
cTATCTGGCGGCGCCACTGGCGCAATGGTACCTGGTTTGCCGCAACGTGACGGTTAAAAATTCTGAATAAATAATCCTAAGCCAAATTGc < 2:263463/90‑1 (MQ=255)
|
CCGTGGCTGGGTAATCATGCTTTGTGGCTGGCATTAACCGTCTTTCTGGCGTTGCGCGGGCTTTCTCTGGCGGCTATCTGGCGGCGTCACTGGCGCAATGGTACCTGGTTTGCCGCAACGTGACGGTTAAAAATTCTGAATAAATAATCCTAAGCCAAATTGC > NZ_CP009273/4248927‑4249089
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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
GCTGCCGTGGCTGGGTAATCATGCTTTGTGGCTGGCATTAACCGTCTTTCTGGCGTTGCGCGGGCTTTCTCTGGCGGCTATCTGGCGGCGTCACTGGCGCAATGGTACCTGGTTTGCCGCAACGTGACGGTTAAAAATTCTGAATAAATAATCCTAAGCCAAATTGCTGACTACACTTAATCTCACGT > NZ_CP009273/4248923‑4249110
|
GCTGCCGTGGCTGGGTAATCATGCTTTGTGGCTGGCATTAACCGTCTTTCTGGCGTTGCGCGGGCTTTCTCTGGCGGCTATCTGGCGGCGCCACTGGCGC < SRR3722113.435568/100‑1 (MQ=60)
ctcggagatgtgtataagagacaGGCATTAACCGTCTTTCTGGCGTTGCGCGGGCTTTCTCTGGCGGCTATCTGGCGGCGCCACTGGCGCAATGGTACCT < SRR3722113.438948/77‑1 (MQ=60)
CTGGGTAATCATGCTTTGTGGCTGGCATTAACCGTCTTTCTGGCGTTGCGCGGGCTTTCTCTGGCGGCTATCTGGCGGCGCCACTGGCGCAATGGTACCT < SRR3722113.94676/100‑1 (MQ=60)
GGGTAATCATGCTTTGTGGCTGGCATTAACCGTCTTTCTGGCGTTGCGCGGGCTTTCTCTGGCGGCTATCTGGCGGCGCCACTGGCGCAATGGTACCTGG > SRR3722113.198558/1‑100 (MQ=60)
GGGTAATCATGCTTTGTGGCTGGCATTAACCGTCTTTCTGGCGTTGCGCGGGCTTTCTCTGGCGGCTATCTGGCGGCGCCACTGGCGCAATGGTACCTGG > SRR3722113.397475/1‑100 (MQ=60)
GGCATTAACCGTCTTTCTGGCGTTGCGCGGGCTTTCTCTGGCGGCTATCTGGCGGCGCCACTGGCGCAATGGTACCTGGTTTGCCGCAACGTGACGGTTA > SRR3722113.156812/1‑100 (MQ=60)
TAACCGTCTTTCTGGCGTTGCGCGGGCTTTCTCTGGCGGCTATCTGGCGGCGCCACTGGCGCAATGGTACCTGGTTTGCCGCAACGTGACGGTTAAAAAT < SRR3722113.475017/100‑1 (MQ=60)
ACCGTCTTTCTGGCGTTGCGCGGGCTTTCTCTGGCGGCTATCTGGCGGCGCCACTGGCGCAATGGTACCTGGTTTGCCGCAACGTGACGGTTAAAAATTC > SRR3722113.265780/1‑100 (MQ=60)
GTTGCGCGGGCTTTCTCTGGCGGCTATCTGGCGGCGCCACTGGCGCAATGGTACCTGGTTTGCCGCAACGTGACGGTTAAAAATTCTGAATAAATAATCC < SRR3722113.431219/100‑1 (MQ=60)
CGCCACTGGCGCAATGGTACCTGGTTTGCCGCAACGTGACGGTTAAAAATTCTGAATAAATAATCCTAAGCCAAATTGCTGACTACACTTAATCTCACGT > SRR3722113.33121/1‑100 (MQ=60)
|
GCTGCCGTGGCTGGGTAATCATGCTTTGTGGCTGGCATTAACCGTCTTTCTGGCGTTGCGCGGGCTTTCTCTGGCGGCTATCTGGCGGCGTCACTGGCGCAATGGTACCTGGTTTGCCGCAACGTGACGGTTAAAAATTCTGAATAAATAATCCTAAGCCAAATTGCTGACTACACTTAATCTCACGT > NZ_CP009273/4248923‑4249110
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
