TB-Profiler result

Run: SRR29096900
Summary

Run ID: SRR29096900

Sample name:

Date: 2025-02-11T14:15:49.978448

Number of reads: 1764276

Percentage reads mapped: 96.52

Median coverage: 54.0

Strain: lineage4.3.4.2

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.97
lineage4 Euro-American None 1.0
lineage4.3.4 Euro-American (LAM) RD174 0.98
lineage4.3.4.2 Euro-American (LAM) RD174 0.95
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
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 Confidence Comment
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 Drugs Confidence
gyrB 6250 c.1011A>G synonymous_variant 0.24 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6256 c.1017G>A synonymous_variant 0.22 levofloxacin
moxifloxacin
gyrA 6637 c.-665T>G upstream_gene_variant 0.15 levofloxacin
moxifloxacin
gyrA 6640 c.-662A>G upstream_gene_variant 0.15 levofloxacin
moxifloxacin
gyrA 6643 c.-659A>G upstream_gene_variant 0.15 levofloxacin
moxifloxacin
gyrA 6655 c.-647T>C upstream_gene_variant 0.15 levofloxacin
moxifloxacin
gyrA 6670 c.-632G>C upstream_gene_variant 0.19 levofloxacin
moxifloxacin
gyrA 6673 c.-629A>C upstream_gene_variant 0.19 levofloxacin
moxifloxacin
gyrA 6676 c.-626T>G upstream_gene_variant 0.22 levofloxacin
moxifloxacin
gyrA 6709 c.-593A>G upstream_gene_variant 0.22 levofloxacin
moxifloxacin
gyrA 6712 c.-590G>C upstream_gene_variant 0.22 levofloxacin
moxifloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7763 c.462T>C synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7775 c.474C>A synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrA 7781 c.480G>C synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 7784 c.483A>G synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 7790 c.489G>C synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 7793 c.492G>C synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 7796 c.495G>C synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 7799 c.498A>G synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7814 c.513C>G synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9365 c.2064G>A synonymous_variant 0.18 levofloxacin
moxifloxacin
gyrA 9383 c.2082T>G synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
rpoB 761765 c.1959T>C synonymous_variant 0.16 rifampicin
rpoB 761772 p.His656Ala missense_variant 0.16 rifampicin
rpoB 761778 p.Asn658Asp missense_variant 0.18 rifampicin
rpoB 761792 c.1986T>C synonymous_variant 0.16 rifampicin
rpoB 762101 c.2295C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762114 p.Ile770Val missense_variant 0.15 rifampicin Uncertain significance
rpoB 762131 c.2325C>G synonymous_variant 0.15 rifampicin
rpoB 762140 c.2334G>C synonymous_variant 0.16 rifampicin
rpoB 762143 c.2337T>C synonymous_variant 0.16 rifampicin
rpoB 762149 c.2343G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762167 c.2361T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 762233 c.2427G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 762246 c.2440C>T synonymous_variant 0.17 rifampicin
rpoB 762257 c.2451C>G synonymous_variant 0.15 rifampicin
rpoB 762449 c.2643C>A synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 762467 c.-903C>T upstream_gene_variant 0.17 rifampicin
rpoC 763594 c.225C>T synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 763603 c.234C>T synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 763636 c.267T>C synonymous_variant 0.23 rifampicin
rpoC 763657 c.288G>A synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 763660 c.291T>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 763675 c.306C>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 763696 c.327T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 763702 c.333C>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 763717 c.348T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 763723 c.354G>C synonymous_variant 0.17 rifampicin
rpoC 763732 c.363C>G synonymous_variant 0.16 rifampicin
rpoC 763744 c.375G>C synonymous_variant 0.15 rifampicin
rpoC 763765 c.396T>C synonymous_variant 0.17 rifampicin
rpoC 763853 p.Val162Ile missense_variant 0.17 rifampicin
rpoC 763858 c.489A>G synonymous_variant 0.17 rifampicin
rpoC 763872 p.Gly168Ala missense_variant 0.17 rifampicin
rpoC 763876 p.Glu169Asp missense_variant 0.17 rifampicin
rpoC 763879 c.510A>G synonymous_variant 0.17 rifampicin
rpoC 763888 c.519G>C synonymous_variant 0.16 rifampicin
rpoC 763894 c.525A>G synonymous_variant 0.14 rifampicin
rpoC 763900 c.531G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763945 c.576T>C synonymous_variant 0.14 rifampicin
rpoC 764083 c.714A>G synonymous_variant 0.15 rifampicin
rpoC 764098 c.729A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764101 c.732C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764102 p.Val245Ile missense_variant 0.18 rifampicin
rpoC 764112 p.Tyr248Phe missense_variant 0.17 rifampicin
rpoC 764116 c.747C>T synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764188 c.819A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764206 c.837T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764215 c.846A>G synonymous_variant 0.21 rifampicin
rpoC 764236 c.867G>A synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764338 c.969G>A synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764353 c.984G>C synonymous_variant 0.21 rifampicin
rpoC 764365 c.996C>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764405 c.1036A>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764428 c.1059G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764431 c.1062G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764434 c.1065A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764446 c.1077T>C synonymous_variant 0.18 rifampicin
rpoC 764449 c.1080G>C synonymous_variant 0.19 rifampicin
rpoC 764452 c.1083T>C synonymous_variant 0.19 rifampicin
rpoC 764458 c.1089G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764461 c.1092A>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 764560 c.1191T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764566 c.1197C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>C synonymous_variant 0.19 rifampicin
rpoC 764651 c.1282_1284delTCGinsAGC synonymous_variant 0.19 rifampicin
rpoC 764752 c.1383G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 765478 c.2109T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 765499 c.2130C>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 765529 c.2160C>T synonymous_variant 0.17 rifampicin
rpoC 765541 c.2172C>G synonymous_variant 0.2 rifampicin
rpoC 765553 c.2184C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 765556 c.2187G>C synonymous_variant 0.17 rifampicin
rpoC 765559 c.2190G>C synonymous_variant 0.18 rifampicin
rpoC 765580 c.2211G>C synonymous_variant 0.16 rifampicin
rpoC 765625 c.2256C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 765631 p.Asp754Glu missense_variant 0.18 rifampicin
rpoC 765700 c.2331T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 765734 c.2365T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 765739 c.2370G>T synonymous_variant 0.17 rifampicin
rpoC 765883 c.2514C>G synonymous_variant 0.18 rifampicin
rpoC 765886 c.2517C>G synonymous_variant 0.18 rifampicin
rpoC 765892 c.2523T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 766540 p.Asp1057Glu missense_variant 0.24 rifampicin
rpoC 766549 c.3180G>C synonymous_variant 0.19 rifampicin
rpoC 766672 c.3303T>C synonymous_variant 0.19 rifampicin
rpoC 766673 p.Gly1102Asn missense_variant 0.19 rifampicin
rpoC 766726 c.3357T>C synonymous_variant 0.18 rifampicin
rpoC 766738 c.3369G>C synonymous_variant 0.19 rifampicin
rpoC 766900 c.3531T>C synonymous_variant 0.24 rifampicin
rpoC 766933 c.3564A>G synonymous_variant 0.23 rifampicin
rpoC 766945 c.3576A>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 766963 c.3594T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 766972 c.3603G>C synonymous_variant 0.2 rifampicin
rpoC 766996 c.3627C>T synonymous_variant 0.22 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800703 c.-106T>C upstream_gene_variant 0.19 linezolid
rplC 800715 c.-94A>C upstream_gene_variant 0.17 linezolid
rplC 800720 c.-89T>C upstream_gene_variant 0.18 linezolid
rplC 800723 c.-86C>G upstream_gene_variant 0.17 linezolid
rplC 800747 c.-62C>G upstream_gene_variant 0.15 linezolid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474356 n.699T>C non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.6 capreomycin
linezolid
rrl 1474904 n.1247G>A non_coding_transcript_exon_variant 0.6 capreomycin
linezolid
rrl 1475006 n.1349A>T non_coding_transcript_exon_variant 0.44 capreomycin
linezolid
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid
rpsA 1833595 c.54T>C synonymous_variant 0.16 pyrazinamide
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
ndh 2101676 p.Ala456Val missense_variant 0.93 isoniazid
delamanid
ethionamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
thyA 3073868 p.Thr202Ala missense_variant 0.92 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.98 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3877587 c.921A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3877613 p.Ile299Val missense_variant 0.2 rifampicin
rpoA 3877656 c.852T>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3877668 c.840A>G synonymous_variant 0.18 rifampicin
rpoA 3877679 p.Ala277Ser missense_variant 0.22 rifampicin
rpoA 3877686 c.822A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoA 3877692 c.816G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoA 3877704 c.804G>C synonymous_variant 0.19 rifampicin
rpoA 3878217 c.291A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoA 3878226 c.282C>G synonymous_variant 0.21 rifampicin
rpoA 3878232 c.276G>C synonymous_variant 0.19 rifampicin
rpoA 3878247 c.261G>C synonymous_variant 0.18 rifampicin
rpoA 3878962 c.-455G>A upstream_gene_variant 0.17 rifampicin Uncertain significance
rpoA 3878968 c.-461T>C upstream_gene_variant 0.17 rifampicin Uncertain significance
rpoA 3878976 c.-469A>G upstream_gene_variant 0.18 rifampicin Uncertain significance
rpoA 3878986 c.-479G>C upstream_gene_variant 0.18 rifampicin
rpoA 3878998 c.-491C>G upstream_gene_variant 0.16 rifampicin Uncertain significance
rpoA 3879079 c.-572A>G upstream_gene_variant 0.23 rifampicin
rpoA 3879088 c.-581A>C upstream_gene_variant 0.23 rifampicin
rpoA 3879094 c.-587T>C upstream_gene_variant 0.24 rifampicin
rpoA 3879121 c.-614T>G upstream_gene_variant 0.18 rifampicin
rpoA 3879127 c.-620T>C upstream_gene_variant 0.17 rifampicin
rpoA 3879154 c.-647T>C upstream_gene_variant 0.16 rifampicin
rpoA 3879160 c.-653A>G upstream_gene_variant 0.16 rifampicin
clpC1 4038287 c.2418C>T synonymous_variant 0.82 pyrazinamide Not assoc w R
clpC1 4038320 c.2385G>T synonymous_variant 0.18 pyrazinamide
clpC1 4038356 c.2349T>C synonymous_variant 0.19 pyrazinamide
clpC1 4038359 c.2346A>G synonymous_variant 0.19 pyrazinamide
clpC1 4038388 c.2317T>C synonymous_variant 0.21 pyrazinamide
clpC1 4038392 c.2313C>T synonymous_variant 0.21 pyrazinamide
clpC1 4038419 c.2286T>C synonymous_variant 0.17 pyrazinamide
clpC1 4039562 c.1143C>G synonymous_variant 0.15 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R