TB-Profiler result

Run: SRR6896307

Summary

Run ID: SRR6896307

Sample name:

Date: 04-04-2023 18:01:56

Number of reads: 629299

Percentage reads mapped: 99.45

Strain: lineage4.3.3

Drug-resistance: Sensitive


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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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
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 6908 p.Glu557* stop_gained 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490912 p.Trp44Arg missense_variant 0.12
mshA 576650 p.Asp435Tyr missense_variant 0.12
ccsA 620210 p.Trp107Leu missense_variant 0.12
ccsA 620475 c.585G>T synonymous_variant 0.17
rpoB 760035 p.Val77Met missense_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766751 p.Arg1128Ser missense_variant 0.12
rpoC 766993 p.Met1208Ile missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777374 p.Glu369Asp missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1461085 p.Gly14Val missense_variant 0.12
rrs 1471653 n.-193C>G upstream_gene_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 1.0
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917975 c.36C>T synonymous_variant 0.12
PPE35 2170533 p.Ala27Glu missense_variant 0.18
Rv1979c 2223051 p.Glu38Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289785 c.-544A>G upstream_gene_variant 0.11
kasA 2518919 p.Gly269Ser missense_variant 1.0
kasA 2519245 c.1131T>C synonymous_variant 0.11
folC 2746414 p.Glu395Asp missense_variant 0.11
folC 2747633 c.-35A>T upstream_gene_variant 0.15
pepQ 2859592 p.Ala276Gly missense_variant 0.11
pepQ 2859605 p.Gly272Trp missense_variant 0.13
pepQ 2859716 p.Arg235Cys missense_variant 0.18
Rv2752c 3065824 p.Pro123Leu missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087188 c.369C>T synonymous_variant 0.12
Rv3083 3448638 p.Trp45* stop_gained 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612389 p.Gly243Ala missense_variant 0.12
fbiA 3641149 p.Leu203Met missense_variant 0.13
rpoA 3877751 p.Asp253Tyr missense_variant 0.13
rpoA 3877839 c.669G>T synonymous_variant 0.14
clpC1 4038259 p.Ala816Pro missense_variant 0.11
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039101 c.1603delA frameshift_variant 0.17
clpC1 4040085 p.Arg207Leu missense_variant 0.12
embC 4241981 p.Pro707Ser missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244708 c.1476C>A synonymous_variant 0.12
embA 4244751 p.Val507Leu missense_variant 0.11
embA 4245793 p.Ser854Trp missense_variant 0.12
embB 4246544 p.Thr11Pro missense_variant 0.14
embB 4246548 p.Pro12Gln missense_variant 0.13
embB 4246555 c.42G>C synonymous_variant 0.12
embB 4246556 p.Ala15Pro missense_variant 0.12
embB 4246559 c.50delT frameshift_variant 0.13
embB 4246587 p.Gly25Val missense_variant 0.13
embB 4246767 p.Cys85Phe missense_variant 0.13
embB 4248719 p.Gly736Cys missense_variant 0.14
embB 4249443 p.Tyr977Phe missense_variant 0.14
aftB 4267906 p.Val311Met missense_variant 0.11
ubiA 4268965 p.Ala290Glu missense_variant 0.15
ubiA 4269195 p.Tyr213* stop_gained 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0