TB-Profiler result

Run: ERR2229608
Summary

Run ID: ERR2229608

Sample name:

Date: 31-03-2023 17:21:20

Number of reads: 786288

Percentage reads mapped: 99.16

Strain: lineage4.8

Drug-resistance: HR-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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
katG 2155959 c.152delA frameshift_variant 0.13 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 8474 c.1173G>T synonymous_variant 0.12
mshA 575355 p.Gly3Asp missense_variant 0.13
mshA 575961 p.Gln205Leu missense_variant 0.11
mshA 576444 p.Gly366Asp missense_variant 0.2
rpoB 761152 p.Leu449Gln missense_variant 0.23
rpoC 766399 c.3030G>T synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776055 p.Val809Glu missense_variant 0.18
mmpL5 776537 p.Met648Ile missense_variant 0.25
mmpL5 778212 p.Ala90Glu missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303144 p.Ser72Pro missense_variant 0.23
fbiC 1303155 c.225G>A synonymous_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303897 p.Leu323Met missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476522 n.2865G>A non_coding_transcript_exon_variant 0.14
fabG1 1673346 c.-94C>G upstream_gene_variant 0.14
fabG1 1673349 c.-91G>C upstream_gene_variant 0.15
fabG1 1673573 p.Thr45Asn missense_variant 0.17
fabG1 1673932 p.Arg165Ser missense_variant 0.12
inhA 1674311 p.Val37Glu missense_variant 0.22
inhA 1674624 c.423A>T synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2153980 p.Tyr711Phe missense_variant 0.18
katG 2154840 c.1272G>A synonymous_variant 0.12
PPE35 2167784 c.2829C>T synonymous_variant 0.14
PPE35 2167814 c.2799C>T synonymous_variant 0.22
PPE35 2167988 c.2625C>G synonymous_variant 0.15
PPE35 2168113 p.Phe834Leu missense_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.14
PPE35 2169281 c.1332T>G synonymous_variant 0.17
PPE35 2169287 c.1326T>C synonymous_variant 0.14
PPE35 2169457 p.His386Asp missense_variant 0.2
PPE35 2169902 p.Leu237Phe missense_variant 0.23
PPE35 2169910 p.Asn235Tyr missense_variant 0.23
PPE35 2170048 p.Leu189Val missense_variant 0.23
PPE35 2170053 p.Thr187Ser missense_variant 0.25
Rv1979c 2222080 p.Ala362Glu missense_variant 0.17
Rv1979c 2223120 c.45T>A synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2859997 p.Ala141Glu missense_variant 0.12
Rv2752c 3065709 c.483C>T synonymous_variant 0.2
Rv2752c 3065824 p.Pro123Leu missense_variant 0.17
thyX 3067543 p.Ala135Ser missense_variant 0.12
thyX 3067782 p.Ala55Asp missense_variant 0.12
fbiD 3339340 p.Leu75Met missense_variant 0.15
fprA 3474928 p.Gly308Ser missense_variant 0.12
whiB7 3568533 c.147G>A synonymous_variant 0.14
Rv3236c 3612010 c.1107G>A synonymous_variant 0.18
Rv3236c 3612958 c.159C>T synonymous_variant 0.2
alr 3841078 p.Pro115Thr missense_variant 0.13
alr 3841546 c.-126C>A upstream_gene_variant 0.25
ddn 3986904 p.Met21Val missense_variant 0.12
clpC1 4038271 p.Pro812Ser missense_variant 1.0
clpC1 4038707 c.1998C>A synonymous_variant 0.14
clpC1 4039161 p.His515Gly missense_variant 0.17
clpC1 4039645 p.His354Asp missense_variant 0.21
clpC1 4040057 c.648C>T synonymous_variant 0.14
clpC1 4040144 c.561G>C synonymous_variant 0.2
embC 4240586 p.Gly242Cys missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247028 p.Leu172Arg missense_variant 0.18
embB 4249349 p.Val946Phe missense_variant 0.11
aftB 4267328 c.1509G>T synonymous_variant 0.14
aftB 4267448 c.1389G>A synonymous_variant 0.12
aftB 4268619 p.Val73Gly missense_variant 0.33
ethA 4326339 p.Asn379Asp missense_variant 0.2
whiB6 4338280 p.Ile81Thr missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0