TB-Profiler result

Run: SRR11972189
Summary

Run ID: SRR11972189

Sample name:

Date: 03-04-2023 05:31:20

Number of reads: 128741

Percentage reads mapped: 98.42

Strain: lineage1

Drug-resistance: RR-TB

Download CSV Download TXT Download PDF Download JSON
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage1 Indo-Oceanic EAI RD239 1.0
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9047 c.1746C>T synonymous_variant 0.83
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9443 c.2142G>A synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575428 c.81G>A synonymous_variant 0.33
mshA 576000 p.Asp218Ala missense_variant 1.0
ccsA 619958 p.Val23Ala missense_variant 0.5
ccsA 620331 c.441C>T synonymous_variant 0.4
rpoB 760490 c.684C>T synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765360 p.Ala664Val missense_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776395 p.Phe696Leu missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302743 c.-188C>T upstream_gene_variant 0.18
fbiC 1303508 p.Pro193Leu missense_variant 0.29
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1674032 p.Ile198Thr missense_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101991 p.Leu351Gln missense_variant 0.29
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2168657 c.1956T>C synonymous_variant 0.15
PPE35 2170280 c.333C>G synonymous_variant 0.22
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518870 c.757delC frameshift_variant 0.22
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726250 p.Gly20Ser missense_variant 0.4
Rv2752c 3064612 p.Ile527Asn missense_variant 0.29
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3064964 p.Ala410Ser missense_variant 0.25
Rv2752c 3065305 p.Ala296Val missense_variant 1.0
Rv2752c 3065898 c.294C>A synonymous_variant 0.29
thyA 3073946 p.Phe176Leu missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449890 p.Leu463Ile missense_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 0.83
fbiA 3641411 p.Val290Ala missense_variant 0.29
fbiA 3641514 p.Cys324* stop_gained 0.18
fbiB 3641633 c.99C>T synonymous_variant 0.15
clpC1 4038385 p.Arg774Trp missense_variant 0.17
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240722 p.Val287Ala missense_variant 0.22
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242909 p.Phe1016Tyr missense_variant 0.4
embA 4243641 c.414_415delGC frameshift_variant 0.4
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embA 4246429 p.Ala1066Val missense_variant 0.22
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4268345 c.492C>A synonymous_variant 0.29
ubiA 4269106 p.Tyr243Phe missense_variant 0.33
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326193 c.1281A>G synonymous_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0