TB-Profiler result

Run: ERR11465801
Summary

Run ID: ERR11465801

Sample name:

Date: 2024-04-15T18:05:41.001423

Number of reads: 836677

Percentage reads mapped: 98.11

Median coverage: 20.0

Strain: lineage4.3.4.1

Spoligotype:

Drug-resistance: Other

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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 0.99
lineage4.3.4.1 Euro-American (LAM) RD174 0.99
lineage4 Euro-American None 1.0
lineage4.3.4 Euro-American (LAM) RD174 1.0
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 rrs n.462C>T Uncertain significance Mutation from literature
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
rrs 1472307 n.462C>T non_coding_transcript_exon_variant 0.23 streptomycin Uncertain significance Mutation from literature
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
dnaA 582 c.582A>C synonymous_variant 0.25 isoniazid Not assoc w R - Interim
gyrA 6673 c.-629A>T upstream_gene_variant 0.26 levofloxacin
moxifloxacin
gyrB 6680 c.1441C>T synonymous_variant 0.25 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7178 c.-124T>C upstream_gene_variant 0.2 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 7847 c.546G>C synonymous_variant 0.27 levofloxacin
moxifloxacin
gyrA 7853 c.552C>T synonymous_variant 0.28 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7859 c.558A>C synonymous_variant 0.23 levofloxacin
moxifloxacin
gyrA 7886 c.585T>C synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrA 7892 c.591G>C synonymous_variant 0.21 levofloxacin
moxifloxacin
gyrA 7898 p.Asp199Glu missense_variant 0.21 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13483 p.Ala26Thr missense_variant 1.0 isoniazid Uncertain significance
fgd1 491610 c.828A>G synonymous_variant 0.17 clofazimine
pretomanid
delamanid
fgd1 491616 c.834A>G synonymous_variant 0.17 clofazimine
pretomanid
delamanid
rpoB 760181 c.375T>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoB 760184 c.378A>G synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoB 761537 c.1731C>G synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoB 761573 c.1767C>G synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoB 761579 c.1773G>C synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoB 761582 c.1776G>A synonymous_variant 0.37 rifampicin
rpoB 761606 c.1800C>G synonymous_variant 0.4 rifampicin
rpoB 761612 c.1806G>T synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoB 761615 c.1809A>C synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoB 761636 c.1830G>T synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoB 761645 c.1839C>G synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoB 761648 c.1842T>C synonymous_variant 0.36 rifampicin
rpoC 763594 c.225C>T synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 763615 c.246G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 763618 c.249C>T synonymous_variant 0.2 rifampicin
rpoC 763624 c.255C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763696 c.327T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 763699 c.330G>C synonymous_variant 0.22 rifampicin
rpoC 763702 c.333C>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 763709 c.340C>T synonymous_variant 0.22 rifampicin
rpoC 763714 c.345G>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 763717 c.348T>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 763732 c.363C>G synonymous_variant 0.2 rifampicin
rpoC 763735 c.366G>C synonymous_variant 0.2 rifampicin
rpoC 764764 c.1395T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764803 c.1434C>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764809 c.1440C>T synonymous_variant 0.18 rifampicin Not assoc w R
rpoC 764812 c.1443C>G synonymous_variant 0.18 rifampicin
rpoC 764815 c.1446A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764824 c.1455T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764833 c.1464A>G synonymous_variant 0.2 rifampicin
rpoC 764836 c.1467G>A synonymous_variant 0.23 rifampicin
rpoC 764842 c.1473C>T synonymous_variant 0.26 rifampicin
rpoC 764858 c.1489T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764869 c.1500C>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764875 c.1506C>G synonymous_variant 0.18 rifampicin
rpoC 764893 c.1524T>C synonymous_variant 0.15 rifampicin
rpoC 764896 c.1527C>T synonymous_variant 0.14 rifampicin
rpoC 764995 c.1626C>G synonymous_variant 0.86 rifampicin Not assoc w R
rpoC 765499 c.2130C>G synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 765508 c.2139C>G synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 766003 c.2634G>C synonymous_variant 0.3 rifampicin
rpoC 766585 c.3216T>C synonymous_variant 0.21 rifampicin
rpoC 766607 c.3238_3240delATCinsCG frameshift_variant&missense_variant 0.23 rifampicin
rpoC 766618 c.3249G>T synonymous_variant 0.24 rifampicin
rpoC 766624 c.3255G>C synonymous_variant 0.27 rifampicin
rpoC 766645 c.3276A>G synonymous_variant 0.33 rifampicin
rpoC 766657 c.3288A>G synonymous_variant 0.33 rifampicin
rpoC 766667 p.Ser1100Ala missense_variant 0.33 rifampicin Uncertain significance
rpoC 767059 c.3690T>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 767062 c.3693C>A synonymous_variant 0.24 rifampicin
rpoC 767098 c.3729T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 767119 c.3750A>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 767134 c.3765C>A synonymous_variant 0.16 rifampicin
rpoC 767152 c.3783T>G synonymous_variant 0.19 rifampicin
rpoC 767155 c.3786C>G synonymous_variant 0.19 rifampicin
rpoC 767180 p.Ala1271Gln missense_variant 0.16 rifampicin
rpoC 767191 c.3822C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 767206 c.3837C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 767302 c.3933C>G synonymous_variant 0.26 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781808 c.249C>T synonymous_variant 0.21 streptomycin
rpsL 781832 c.273T>C synonymous_variant 0.25 streptomycin
rpsL 781865 c.306G>C synonymous_variant 0.23 streptomycin
rpsL 781868 c.309T>C synonymous_variant 0.23 streptomycin
rpsL 781871 c.312G>C synonymous_variant 0.23 streptomycin
rpsL 781892 c.333A>G synonymous_variant 0.25 streptomycin
rpsL 781898 c.339A>T synonymous_variant 0.25 streptomycin
rpsL 781904 c.345C>T synonymous_variant 0.21 streptomycin Not assoc w R - Interim
rpsL 781907 c.348T>C synonymous_variant 0.21 streptomycin
rplC 800747 c.-62C>G upstream_gene_variant 0.17 linezolid
fbiC 1303536 c.606G>C synonymous_variant 0.23 clofazimine
pretomanid
delamanid
fbiC 1304869 c.1939C>T synonymous_variant 0.23 clofazimine
pretomanid
delamanid
sigE 1364434 p.Arg8Trp missense_variant 1.0 pyrazinamide Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.22 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Uncertain significance
rrs 1473290 n.1445delCinsTT non_coding_transcript_exon_variant 0.18 streptomycin
kanamycin
capreomycin
amikacin
rrl 1473839 n.182G>T non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1474266 n.609T>C non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474291 n.634_649delTTTCCTCTCCGGAGGAinsC non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474308 n.651G>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1474716 n.1059A>C non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475479 n.1822C>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475480 n.1823A>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475573 n.1916G>A non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.29 capreomycin
linezolid Uncertain significance
rrl 1475604 n.1947A>C non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid
rrl 1475606 n.1949T>C non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1833661 c.120A>G synonymous_variant 0.18 pyrazinamide
rpsA 1833664 c.123C>A synonymous_variant 0.18 pyrazinamide
rpsA 1833724 c.183C>G synonymous_variant 0.31 pyrazinamide
rpsA 1833727 c.186G>C synonymous_variant 0.32 pyrazinamide
rpsA 1833742 c.201A>G synonymous_variant 0.27 pyrazinamide
rpsA 1833745 c.204G>C synonymous_variant 0.26 pyrazinamide
rpsA 1833802 c.261A>G synonymous_variant 0.29 pyrazinamide
rpsA 1833811 c.270G>T synonymous_variant 0.23 pyrazinamide
rpsA 1833820 c.279G>A synonymous_variant 0.26 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.43 pyrazinamide
rpsA 1833859 c.318C>T synonymous_variant 0.43 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.35 pyrazinamide
rpsA 1833894 p.Ala118Glu missense_variant 0.31 pyrazinamide
rpsA 1834030 c.489C>G synonymous_variant 0.35 pyrazinamide
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
Rv1979c 2222854 p.Ile104Thr missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
thyA 3073868 p.Thr202Ala missense_variant 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0 pyrazinamide Not assoc w R
mtrB 3625744 c.870G>A synonymous_variant 0.29 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625747 c.867G>C synonymous_variant 0.27 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625753 c.859_861delGCCinsAT frameshift_variant&missense_variant 0.3 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3625765 c.849C>G synonymous_variant 0.38 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625774 c.840G>A synonymous_variant 0.41 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625806 c.808A>C synonymous_variant 0.37 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625807 c.807C>G synonymous_variant 0.35 bedaquiline
rifampicin Not assoc w R - Interim
lpqB 3625828 c.-918G>C upstream_gene_variant 0.45 bedaquiline
rifampicin
mtrB 3625852 c.762A>G synonymous_variant 0.47 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625867 c.747A>G synonymous_variant 0.44 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625912 c.702G>C synonymous_variant 0.5 bedaquiline
rifampicin
mtrB 3625915 c.699G>T synonymous_variant 0.5 bedaquiline
rifampicin
mtrB 3627011 c.-398T>G upstream_gene_variant 0.23 bedaquiline
rifampicin
rpoA 3877613 p.Ile299Val missense_variant 0.48 rifampicin
rpoA 3877656 c.852T>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoA 3877665 c.843C>A synonymous_variant 0.31 rifampicin
rpoA 3877668 c.840A>G synonymous_variant 0.29 rifampicin
rpoA 3877677 c.829_831delGCGinsTC frameshift_variant&missense_variant 0.36 rifampicin
rpoA 3877680 c.828G>C synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoA 3877686 c.822A>G synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoA 3877692 c.816G>C synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoA 3877704 c.804G>C synonymous_variant 0.44 rifampicin
rpoA 3878364 c.144A>C synonymous_variant 0.21 rifampicin
rpoA 3878370 c.138T>C synonymous_variant 0.19 rifampicin
rpoA 3878385 c.123C>G synonymous_variant 0.19 rifampicin
clpC1 4038287 c.2418C>T synonymous_variant 0.89 pyrazinamide Not assoc w R
clpC1 4038725 c.1980C>G synonymous_variant 0.15 pyrazinamide
clpC1 4039991 c.714G>A synonymous_variant 1.0 pyrazinamide Not assoc w R
panD 4044090 c.192C>A synonymous_variant 0.35 pyrazinamide
glpK 4138574 c.1182G>C synonymous_variant 0.25 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4240795 c.933C>G synonymous_variant 0.15 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245077 c.1845G>C synonymous_variant 0.21 ethambutol
embA 4245083 c.1851A>G synonymous_variant 0.18 ethambutol Not assoc w R - Interim
embA 4245113 c.1881C>A synonymous_variant 0.15 ethambutol
embA 4245137 c.1905T>C synonymous_variant 0.16 ethambutol
embB 4247512 c.999T>C synonymous_variant 0.23 ethambutol
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R