TB-Profiler result

Run: SRR11033632
Summary

Run ID: SRR11033632

Sample name:

Date: 02-04-2023 20:02:46

Number of reads: 1120456

Percentage reads mapped: 99.06

Strain: lineage4.2.1.1

Drug-resistance: Other

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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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 None 1.0
lineage4.2.1.1 Euro-American (TUR) H3;H4 None 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
gid 4407929 p.Glu92* stop_gained 0.13 streptomycin
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
gyrA 7317 c.16T>C synonymous_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7487 c.186C>T synonymous_variant 0.18
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9111 p.Pro604Thr missense_variant 0.11
gyrA 9192 p.Leu631Met missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575533 c.186C>T synonymous_variant 0.15
mshA 575542 c.195C>T synonymous_variant 0.17
mshA 576108 p.Ala254Gly missense_variant 0.33
rpoB 762576 p.Gln924* stop_gained 0.15
rpoC 765652 p.Gln761His missense_variant 0.5
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776819 c.1662C>A synonymous_variant 0.13
mmpL5 777451 p.Val344Leu missense_variant 1.0
mmpL5 777997 p.Ala162Ser missense_variant 0.11
mmpL5 778947 c.-467C>T upstream_gene_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801114 c.307delG frameshift_variant 0.11
fbiC 1305251 c.2323_2328delATCATG conservative_inframe_deletion 0.29
Rv1258c 1406303 c.1038C>T synonymous_variant 0.25
atpE 1460968 c.-77C>T upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918254 c.315C>T synonymous_variant 0.13
ndh 2102258 p.Ser262Cys missense_variant 0.33
ndh 2102386 c.657G>T synonymous_variant 0.12
PPE35 2168837 c.1776G>A synonymous_variant 0.25
PPE35 2169879 p.Phe245Cys missense_variant 1.0
Rv1979c 2223077 p.Ala30Thr missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517985 c.-130A>G upstream_gene_variant 0.11
kasA 2518388 p.Gly92Arg missense_variant 0.12
eis 2715363 c.-31G>T upstream_gene_variant 0.4
pepQ 2860311 c.108C>T synonymous_variant 0.17
Rv2752c 3065437 p.Ala252Val missense_variant 1.0
Rv2752c 3066071 c.121T>C synonymous_variant 0.14
thyA 3074198 p.Pro92Thr missense_variant 0.2
ald 3086689 c.-131G>T upstream_gene_variant 0.29
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474342 p.Leu112Phe missense_variant 0.15
fprA 3475368 c.1362G>T synonymous_variant 0.15
alr 3840959 c.462G>T synonymous_variant 0.22
rpoA 3877844 p.Ala222Thr missense_variant 0.14
ddn 3986657 c.-187C>T upstream_gene_variant 0.17
ddn 3987092 p.Glu83Asp missense_variant 1.0
clpC1 4039541 c.1164C>A synonymous_variant 0.12
clpC1 4040721 c.-17A>G upstream_gene_variant 0.18
clpC1 4040853 c.-149T>C upstream_gene_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244370 p.Arg380Cys missense_variant 0.2
embA 4246260 p.Asp1010Tyr missense_variant 0.15
embA 4246338 p.Leu1036Met missense_variant 0.12
aftB 4267859 p.Trp326* stop_gained 0.2
ethR 4328032 p.Ala162Thr missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408213 c.-11C>T upstream_gene_variant 1.0