TB-Profiler result

Run: SRR6785262
Summary

Run ID: SRR6785262

Sample name:

Date: 2024-10-05T02:29:26.908267

Number of reads: 1269697

Percentage reads mapped: 81.71

Median coverage: 31.0

Strain: lineage4.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2 Euro-American None 0.94
lineage4 Euro-American None 0.98
lineage4.2.1 Euro-American (TUR) None 0.94
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 6238 c.999G>A synonymous_variant 0.24 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 6700 c.-602T>C upstream_gene_variant 0.29 levofloxacin
moxifloxacin
gyrA 6703 c.-599G>C upstream_gene_variant 0.28 levofloxacin
moxifloxacin
gyrA 6709 c.-593A>G upstream_gene_variant 0.3 levofloxacin
moxifloxacin
gyrA 6712 c.-590G>C upstream_gene_variant 0.33 levofloxacin
moxifloxacin
gyrA 6728 c.-574_-572delCTAinsTTG upstream_gene_variant 0.26 levofloxacin
moxifloxacin
gyrA 6742 c.-560A>G upstream_gene_variant 0.24 levofloxacin
moxifloxacin
gyrB 6745 c.1506T>G synonymous_variant 0.21 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491247 c.465C>T synonymous_variant 0.88 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
rpoB 760101 c.295T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760112 c.306T>C synonymous_variant 0.2 rifampicin
rpoB 760118 c.312T>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 760121 c.315T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 760130 p.Asp108Glu missense_variant 0.19 rifampicin Uncertain significance
rpoB 760139 c.333A>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 760142 c.336C>G synonymous_variant 0.2 rifampicin
rpoB 760181 c.375T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 760184 c.378A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760196 c.390C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760298 c.492G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 760376 p.Asp190Glu missense_variant 0.15 rifampicin Uncertain significance
rpoB 760380 p.Thr192Leu missense_variant 0.15 rifampicin
rpoB 760406 c.600G>C synonymous_variant 0.18 rifampicin
rpoB 760412 c.606C>G synonymous_variant 0.2 rifampicin
rpoB 760424 c.618C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 760430 c.624T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 760475 c.669A>G synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoB 760481 c.675G>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 760484 c.678A>G synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 760522 p.Ser239Asn missense_variant 0.27 rifampicin Uncertain significance
rpoB 760532 c.726T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 760533 p.Val243Thr missense_variant 0.23 rifampicin
rpoB 760541 c.735G>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoB 760547 c.741G>C synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoB 760563 p.Arg253Met missense_variant 0.22 rifampicin Uncertain significance
rpoB 760591 p.Val262Ala missense_variant 0.27 rifampicin
rpoB 760611 c.805T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 760946 c.1140A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760982 c.1176G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 760985 c.1179G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 760991 c.1185G>C synonymous_variant 0.2 rifampicin
rpoB 761006 c.1200C>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 761015 c.1209G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 761021 c.1215G>C synonymous_variant 0.2 rifampicin
rpoC 762989 c.-381G>C upstream_gene_variant 0.14 rifampicin
rpoB 762995 c.3189G>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763456 c.87A>G synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoC 763486 c.117T>G synonymous_variant 0.28 rifampicin
rpoC 763528 c.159G>A synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoC 763546 c.177A>G synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 763570 c.201G>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 763573 c.204G>C synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoC 763594 c.225C>T synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 763603 c.234C>T synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 763636 c.267T>C synonymous_variant 0.23 rifampicin
rpoC 763660 c.291T>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 763675 c.306C>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 763717 c.348T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 763723 c.354G>C synonymous_variant 0.18 rifampicin
rpoC 763732 c.363C>G synonymous_variant 0.18 rifampicin
rpoC 763741 c.372C>T synonymous_variant 0.15 rifampicin
rpoC 763744 c.375G>C synonymous_variant 0.15 rifampicin
rpoC 763765 c.396T>C synonymous_variant 0.17 rifampicin
rpoC 763774 c.405G>C synonymous_variant 0.18 rifampicin
rpoC 764044 c.675T>C synonymous_variant 0.17 rifampicin
rpoC 764059 c.690G>T synonymous_variant 0.18 rifampicin
rpoC 764083 c.714A>G synonymous_variant 0.16 rifampicin
rpoC 764752 c.1383G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764764 c.1395T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764809 c.1440C>T synonymous_variant 0.21 rifampicin Not assoc w R
rpoC 764815 c.1446A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764827 c.1458G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764858 c.1489T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764872 c.1503A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765478 c.2109T>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 765499 c.2130C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 765529 c.2160C>T synonymous_variant 0.18 rifampicin
rpoC 765541 c.2172C>G synonymous_variant 0.19 rifampicin
rpoC 766447 c.3078T>C synonymous_variant 0.21 rifampicin
rpoC 766462 c.3093G>C synonymous_variant 0.19 rifampicin
rpoC 766540 p.Asp1057Glu missense_variant 0.23 rifampicin
rpoC 766801 c.3432C>G synonymous_variant 0.32 rifampicin
rpoC 766804 c.3435A>G synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 766861 c.3492G>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 766864 c.3495G>C synonymous_variant 0.27 rifampicin
rpoC 767158 c.3789T>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 767180 p.Ala1271Gln missense_variant 0.21 rifampicin
rpoC 767191 c.3822C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 0.97 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
rpsL 781628 c.69T>C synonymous_variant 0.23 streptomycin Not assoc w R - Interim
rpsL 781700 c.141G>C synonymous_variant 0.29 streptomycin
rpsL 781703 c.144G>T synonymous_variant 0.29 streptomycin
rpsL 781715 c.156T>C synonymous_variant 0.31 streptomycin
rpsL 781728 c.169T>C synonymous_variant 0.33 streptomycin
rpsL 781736 c.177T>C synonymous_variant 0.33 streptomycin
rpsL 781742 c.183C>T synonymous_variant 0.35 streptomycin
rpsL 781748 c.189C>G synonymous_variant 0.34 streptomycin
rpsL 781754 c.195G>C synonymous_variant 0.32 streptomycin
rpsL 781760 c.201T>C synonymous_variant 0.27 streptomycin
rpsL 781772 c.213C>A synonymous_variant 0.23 streptomycin
rpsL 781808 c.249C>T synonymous_variant 0.25 streptomycin
rpsL 781811 c.252C>T synonymous_variant 0.26 streptomycin
rpsL 781832 c.273T>C synonymous_variant 0.18 streptomycin
rplC 800204 c.-605T>C upstream_gene_variant 0.97 linezolid
rplC 800720 c.-89T>C upstream_gene_variant 0.14 linezolid
rplC 800723 c.-86C>G upstream_gene_variant 0.15 linezolid
rplC 800747 c.-62C>G upstream_gene_variant 0.16 linezolid
fbiC 1304559 p.Glu543Asp missense_variant 0.16 pretomanid
delamanid
clofazimine
fbiC 1304565 c.1635C>G synonymous_variant 0.15 pretomanid
delamanid
clofazimine
fbiC 1304568 c.1638T>C synonymous_variant 0.15 pretomanid
delamanid
clofazimine
fbiC 1304613 c.1683T>C synonymous_variant 0.18 pretomanid
delamanid
clofazimine
fbiC 1304634 c.1704C>G synonymous_variant 0.19 pretomanid
delamanid
clofazimine
fbiC 1304640 c.1710A>C synonymous_variant 0.18 pretomanid
delamanid
clofazimine
fbiC 1304646 c.1716T>C synonymous_variant 0.16 pretomanid
delamanid
clofazimine
sigE 1364706 c.294G>A synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473899 n.242A>C non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473943 n.286G>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid
rpsA 1833589 c.48A>T synonymous_variant 0.26 pyrazinamide
rpsA 1833595 c.54T>C synonymous_variant 0.25 pyrazinamide
rpsA 1833661 c.120A>G synonymous_variant 0.18 pyrazinamide
rpsA 1833667 c.126C>G synonymous_variant 0.18 pyrazinamide
rpsA 1833802 c.261A>G synonymous_variant 0.19 pyrazinamide
rpsA 1833811 c.270G>T synonymous_variant 0.17 pyrazinamide
rpsA 1833847 c.306C>G synonymous_variant 0.18 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.19 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.18 pyrazinamide
rpsA 1833886 c.345C>G synonymous_variant 0.18 pyrazinamide
rpsA 1834451 c.910T>C synonymous_variant 0.26 pyrazinamide
rpsA 1834465 c.924T>C synonymous_variant 0.24 pyrazinamide
rpsA 1834468 c.927A>G synonymous_variant 0.24 pyrazinamide
rpsA 1834489 c.948T>C synonymous_variant 0.24 pyrazinamide
rpsA 1834513 c.972C>G synonymous_variant 0.24 pyrazinamide
rpsA 1834528 c.987T>C synonymous_variant 0.26 pyrazinamide
rpsA 1834540 c.999G>C synonymous_variant 0.24 pyrazinamide
rpsA 1834633 c.1092A>G synonymous_variant 0.23 pyrazinamide
rpsA 1834639 c.1098T>C synonymous_variant 0.28 pyrazinamide
rpsA 1834654 p.Glu371Asp missense_variant 0.21 pyrazinamide
rpsA 1834690 c.1149T>C synonymous_variant 0.22 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
bacA 2063685 c.1044G>A synonymous_variant 0.95 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 1.0 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
PPE35 2167033 c.343_*615del stop_lost&conservative_inframe_deletion&splice_region_variant 0.97 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ribD 2986910 c.72C>A synonymous_variant 1.0 para-aminosalicylic_acid
thyX 3067545 p.Glu134Ala missense_variant 0.32 para-aminosalicylic_acid
thyX 3067549 p.Thr133Ala missense_variant 0.32 para-aminosalicylic_acid
thyX 3067556 p.His130Gln missense_variant 0.33 para-aminosalicylic_acid
thyX 3067559 c.387C>G synonymous_variant 0.35 para-aminosalicylic_acid
thyX 3067565 p.Asp127Glu missense_variant 0.36 para-aminosalicylic_acid
thyX 3067814 c.132T>C synonymous_variant 0.22 para-aminosalicylic_acid
ald 3086742 c.-78A>C upstream_gene_variant 0.96 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625636 c.978C>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
bedaquiline
rpoA 3879121 c.-614T>G upstream_gene_variant 0.16 rifampicin
rpoA 3879127 c.-620T>C upstream_gene_variant 0.16 rifampicin
rpoA 3879154 c.-647T>C upstream_gene_variant 0.18 rifampicin
rpoA 3879160 c.-653A>G upstream_gene_variant 0.18 rifampicin
rpoA 3879178 c.-671T>C upstream_gene_variant 0.16 rifampicin
rpoA 3879190 c.-683C>G upstream_gene_variant 0.13 rifampicin
rpoA 3879222 c.-715T>C upstream_gene_variant 0.16 rifampicin
rpoA 3879226 c.-719G>C upstream_gene_variant 0.16 rifampicin
rpoA 3879229 c.-722A>G upstream_gene_variant 0.16 rifampicin
rpoA 3879232 c.-725A>G upstream_gene_variant 0.16 rifampicin
clpC1 4038388 c.2317T>C synonymous_variant 0.23 pyrazinamide
clpC1 4038640 p.Asp689Asn missense_variant 0.19 pyrazinamide
clpC1 4038653 c.2052C>T synonymous_variant 0.19 pyrazinamide
clpC1 4038671 c.2034T>C synonymous_variant 0.15 pyrazinamide
clpC1 4038683 c.2022T>C synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
clpC1 4038695 c.2010C>G synonymous_variant 0.14 pyrazinamide
clpC1 4038953 c.1752A>G synonymous_variant 0.17 pyrazinamide
clpC1 4038956 c.1749T>C synonymous_variant 0.15 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245248 c.2016G>C synonymous_variant 0.18 ethambutol
embA 4245257 c.2025A>G synonymous_variant 0.2 ethambutol
embB 4249594 c.3081G>A synonymous_variant 0.95 ethambutol Not assoc w R - Interim
ethA 4328376 c.-903G>C upstream_gene_variant 0.91 ethionamide
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