TB-Profiler result

Run: ERR4972550
Summary

Run ID: ERR4972550

Sample name:

Date: 01-04-2023 21:46:23

Number of reads: 331921

Percentage reads mapped: 89.87

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 2154799 p.Trp438* stop_gained 0.33 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288930 p.Ser104Arg missense_variant 1.0 pyrazinamide
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 5947 c.708C>T synonymous_variant 0.13
gyrA 6406 c.-896C>T upstream_gene_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9417 p.Asn706Tyr missense_variant 0.14
fgd1 490757 c.-26T>A upstream_gene_variant 1.0
fgd1 491351 p.Asp190Val missense_variant 0.4
rpoB 760133 c.327C>A synonymous_variant 0.15
rpoB 761075 c.1271delT frameshift_variant 0.22
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765889 c.2521_2522dupCG frameshift_variant 0.22
rpoC 766649 p.Gly1094Ser missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775855 p.Gly876Arg missense_variant 0.5
mmpL5 777682 p.Val267Met missense_variant 0.33
mmpL5 778345 p.Leu46Phe missense_variant 0.17
mmpL5 778951 c.-471G>T upstream_gene_variant 0.15
mmpR5 779137 p.Arg50Trp missense_variant 0.2
mmpR5 779303 c.315delT frameshift_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303752 c.822A>G synonymous_variant 0.17
fbiC 1303787 p.His286Leu missense_variant 0.22
fbiC 1304826 c.1900delT frameshift_variant 0.18
Rv1258c 1406570 c.771G>A synonymous_variant 0.18
embR 1417517 c.-170T>A upstream_gene_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrs 1472471 n.626G>A non_coding_transcript_exon_variant 0.29
rrl 1476669 n.3012C>A non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918034 p.Val32Gly missense_variant 0.22
ndh 2102403 p.Leu214Phe missense_variant 0.11
katG 2154962 c.1150C>T synonymous_variant 0.25
katG 2155454 p.Leu220Val missense_variant 0.25
PPE35 2168260 c.2352delT frameshift_variant 0.25
PPE35 2169691 p.Gly308Cys missense_variant 0.13
PPE35 2170545 p.Pro23Leu missense_variant 0.25
PPE35 2170698 c.-86G>A upstream_gene_variant 0.11
Rv1979c 2221794 c.1371C>A synonymous_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288969 p.Glu91Asp missense_variant 0.22
eis 2714438 p.Met299Leu missense_variant 0.18
eis 2715056 p.Arg93Trp missense_variant 0.2
ahpC 2726306 c.114C>T synonymous_variant 0.22
folC 2746687 c.912C>A synonymous_variant 0.15
folC 2747639 c.-41C>A upstream_gene_variant 0.18
ribD 2986903 c.67_69delCTC conservative_inframe_deletion 0.17
Rv2752c 3065953 p.Thr80Ile missense_variant 1.0
thyX 3067606 p.Ser114Thr missense_variant 0.5
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087686 c.867C>A synonymous_variant 0.4
Rv3083 3449484 c.981G>A synonymous_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474224 c.223delC frameshift_variant 0.14
fprA 3474517 p.Asp171Asn missense_variant 0.2
Rv3236c 3612332 c.784dupG frameshift_variant 0.18
rpoA 3877527 c.981C>T synonymous_variant 0.22
clpC1 4038287 c.2418C>T synonymous_variant 1.0
panD 4044387 c.-106G>A upstream_gene_variant 0.22
embC 4241861 p.Glu667Lys missense_variant 0.2
embC 4242402 p.Arg847His missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244637 p.Val469Met missense_variant 0.13
embB 4249620 c.3108delG frameshift_variant 0.12
aftB 4267596 p.Tyr414Cys missense_variant 0.33
aftB 4268083 p.Gln252* stop_gained 0.33
aftB 4268741 c.96G>A synonymous_variant 0.25
aftB 4268779 p.Gly20Arg missense_variant 0.22
ubiA 4269319 p.Leu172Pro missense_variant 1.0
ethR 4326568 c.-981G>A upstream_gene_variant 0.33
ethA 4327491 c.-18C>G upstream_gene_variant 0.18
ethR 4327680 p.Asp44Glu missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0