TB-Profiler result

Run: ERR11081388
Summary

Run ID: ERR11081388

Sample name:

Date: 08-04-2023 19:18:44

Number of reads: 503336

Percentage reads mapped: 99.64

Strain: lineage4.3

Drug-resistance: MDR-TB

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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
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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491378 p.Gly199Asp missense_variant 0.14
ccsA 620162 p.Leu91Pro missense_variant 0.2
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304524 p.Ala532Thr missense_variant 0.12
Rv1258c 1406175 p.Cys389Tyr missense_variant 0.17
Rv1258c 1407212 c.128delA frameshift_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rpsA 1834923 p.Gly461Asp missense_variant 0.15
tlyA 1917810 c.-130C>A upstream_gene_variant 0.12
tlyA 1917816 c.-124G>A upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519098 c.984C>T synonymous_variant 0.18
folC 2746844 p.Ala252Val missense_variant 0.12
thyX 3067588 p.Pro120Ser missense_variant 0.15
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074495 c.-24C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339234 c.117G>A synonymous_variant 0.22
fbiD 3339631 p.Arg172Cys missense_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474058 p.Ala18Thr missense_variant 0.21
fprA 3474988 p.Pro328Ser missense_variant 0.12
Rv3236c 3611983 c.1134G>A synonymous_variant 0.2
Rv3236c 3612017 p.Pro367Leu missense_variant 0.22
Rv3236c 3612796 c.321G>A synonymous_variant 0.12
fbiB 3641301 c.-234C>T upstream_gene_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038890 c.1815G>A synonymous_variant 0.18
clpC1 4039163 c.1542G>A synonymous_variant 0.22
clpC1 4039533 p.Asn391Ser missense_variant 0.11
embC 4240014 p.Pro51Leu missense_variant 0.12
embC 4240060 c.198G>A synonymous_variant 0.13
embC 4240602 p.Ala247Val missense_variant 0.12
embC 4240792 p.Met310Ile missense_variant 0.22
embC 4240850 c.988C>T synonymous_variant 0.2
embC 4240949 p.Val363Ile missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243091 c.-142C>T upstream_gene_variant 0.14
embA 4243501 p.Leu90Gln missense_variant 0.2
embA 4243723 p.Pro164Leu missense_variant 0.2
embA 4244657 c.1425G>A synonymous_variant 0.22
embA 4244660 c.1428G>A synonymous_variant 0.22
embA 4245413 c.2181C>T synonymous_variant 0.15
embA 4245473 c.2241C>T synonymous_variant 0.17
embB 4246286 c.-228G>A upstream_gene_variant 0.22
embB 4247134 c.621C>T synonymous_variant 0.2
embB 4247551 c.1038C>T synonymous_variant 0.15
embB 4247612 p.Arg367Cys missense_variant 0.15
aftB 4267747 p.Ser364Pro missense_variant 0.1
ubiA 4269218 p.Ile206Val missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4408234 c.-33delT upstream_gene_variant 1.0
PPE35 2163533 c.2428_*4115del stop_lost&conservative_inframe_deletion&splice_region_variant 1.0