TB-Profiler result

Run: ERR4816878
Summary

Run ID: ERR4816878

Sample name:

Date: 01-04-2023 14:40:53

Number of reads: 312311

Percentage reads mapped: 99.7

Strain: lineage4.9

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
lineage4.9 Euro-American (H37Rv-like) T1 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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289081 p.Pro54Leu missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
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 7776 p.Arg159Trp missense_variant 0.29
fgd1 491027 p.Asn82Ser missense_variant 0.13
fgd1 491223 c.441C>A synonymous_variant 0.14
mshA 576400 c.1053C>T synonymous_variant 1.0
ccsA 620653 c.767delG frameshift_variant 0.25
rpoB 759615 c.-192A>C upstream_gene_variant 0.4
rpoB 761461 p.Arg552Leu missense_variant 1.0
rpoB 762661 p.Arg952Lys missense_variant 0.29
rpoC 766427 p.Val1020Ile missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801023 p.Ala72Asp missense_variant 0.17
fbiC 1303366 p.Thr146Pro missense_variant 0.15
fbiC 1303827 c.897A>G synonymous_variant 0.22
fbiC 1304438 p.Glu503Gly missense_variant 0.33
fbiC 1305223 p.Asp765Tyr missense_variant 0.18
fbiC 1305293 p.Trp788* stop_gained 0.14
embR 1416628 c.720C>A synonymous_variant 0.15
embR 1417169 p.Trp60Leu missense_variant 0.11
embR 1417405 c.-58A>G upstream_gene_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473535 n.-123C>T upstream_gene_variant 0.67
inhA 1674672 c.471C>A synonymous_variant 0.14
rpsA 1833857 p.Arg106Ser missense_variant 0.29
rpsA 1834090 c.549G>T synonymous_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168047 p.Leu856Val missense_variant 0.22
PPE35 2168051 p.Val854Ile missense_variant 0.22
PPE35 2168488 p.Ile709Val missense_variant 0.25
Rv1979c 2222716 p.Ala150Asp missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519095 c.981C>A synonymous_variant 0.33
eis 2714569 p.Ala255Gly missense_variant 0.25
ahpC 2726083 c.-110G>A upstream_gene_variant 0.14
ald 3086765 c.-55G>T upstream_gene_variant 0.1
ald 3087367 p.Ala183Val missense_variant 1.0
Rv3236c 3612450 p.Leu223Met missense_variant 0.17
fbiA 3640422 c.-121G>T upstream_gene_variant 0.15
fbiA 3640798 p.Trp86Arg missense_variant 0.15
alr 3841365 p.Gly19Ala missense_variant 0.12
rpoA 3877536 c.972C>T synonymous_variant 1.0
ddn 3987123 p.Ala94Thr missense_variant 0.15
clpC1 4040878 c.-174T>C upstream_gene_variant 0.22
panD 4044058 p.Ala75Asp missense_variant 0.18
embB 4246935 p.Thr141Lys missense_variant 0.29
embB 4247461 p.Met316Ile missense_variant 0.12
aftB 4268456 c.381G>T synonymous_variant 0.14
ubiA 4269124 p.Ala237Val missense_variant 1.0
whiB6 4338307 p.Ala72Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0