TB-Profiler result

Run: ERR11465152
Summary

Run ID: ERR11465152

Sample name:

Date: 2024-10-05T03:59:03.525576

Number of reads: 2022043

Percentage reads mapped: 99.14

Median coverage: 42.0

Strain: lineage4.3.4.1

Spoligotype:

Drug-resistance: Sensitive

Download CSV Download TXT Download JSON
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
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 6242 p.Arg335Lys missense_variant 0.15 levofloxacin
moxifloxacin
gyrB 6250 c.1011A>G synonymous_variant 0.14 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6253 c.1014G>C synonymous_variant 0.13 levofloxacin
moxifloxacin
gyrB 6292 c.1053G>C synonymous_variant 0.13 levofloxacin
moxifloxacin
gyrA 6634 c.-668T>C upstream_gene_variant 0.15 levofloxacin
moxifloxacin
gyrA 6640 c.-662A>C upstream_gene_variant 0.15 levofloxacin
moxifloxacin
gyrA 6643 c.-659A>G upstream_gene_variant 0.16 levofloxacin
moxifloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7394 c.93T>C synonymous_variant 0.13 levofloxacin Not assoc w R - Interim
moxifloxacin
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8250 p.Glu317Gln missense_variant 0.99 levofloxacin
moxifloxacin
gyrA 8829 c.1528T>C 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
Rv0010c 13483 p.Ala26Thr missense_variant 1.0 isoniazid Uncertain significance
mshA 575824 c.477T>A synonymous_variant 0.16 isoniazid
ethionamide
hadA 731789 c.-141A>G upstream_gene_variant 0.15 isoniazid
hadA 731843 c.-87T>C upstream_gene_variant 0.12 isoniazid
nusG 734499 c.246G>C synonymous_variant 0.16 rifampicin
nusG 734910 c.657C>G synonymous_variant 0.13 rifampicin
mmaA3 737358 c.792A>C synonymous_variant 0.19 isoniazid
rpoB 760101 c.295T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760430 c.624T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760611 c.805_807delTTGinsCTC synonymous_variant 0.16 rifampicin
rpoB 760670 c.864G>C synonymous_variant 0.14 rifampicin
rpoB 760674 c.868T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 760679 c.873A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761948 c.2142G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761954 c.2148C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761999 c.2193G>C synonymous_variant 0.18 rifampicin
rpoB 762008 c.2202C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762038 c.2232C>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 762101 c.2295C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762114 p.Ile770Val missense_variant 0.13 rifampicin Uncertain significance
rpoB 763127 c.3321G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763139 c.-231C>T upstream_gene_variant 0.14 rifampicin
rpoC 763142 c.-228C>G upstream_gene_variant 0.15 rifampicin
rpoC 763546 c.177A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763570 c.201G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763573 c.204G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763765 c.396T>C synonymous_variant 0.15 rifampicin
rpoC 763774 c.405G>C synonymous_variant 0.14 rifampicin
rpoC 763781 p.Ser138Ala missense_variant 0.15 rifampicin
rpoC 763807 c.438T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763813 c.444C>G synonymous_variant 0.16 rifampicin
rpoC 764153 p.Gln262Lys missense_variant 0.21 rifampicin
rpoC 764431 c.1062G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764434 c.1065A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764449 c.1080G>C synonymous_variant 0.17 rifampicin
rpoC 764452 c.1083T>C synonymous_variant 0.17 rifampicin
rpoC 764458 c.1089G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764461 c.1092A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764485 c.1116G>C synonymous_variant 0.19 rifampicin
rpoC 764491 c.1122G>T synonymous_variant 0.2 rifampicin
rpoC 764497 c.1128A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764500 c.1131C>G synonymous_variant 0.13 rifampicin
rpoC 764521 c.1152T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 764527 c.1158C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764530 c.1161C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764536 c.1167G>T synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 764539 c.1170C>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 765425 p.Lys686Glu missense_variant 0.12 rifampicin
rpoC 765478 c.2109T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765499 c.2130C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766738 c.3369G>T synonymous_variant 0.16 rifampicin
rpoC 766765 c.3396A>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766771 c.3402G>C synonymous_variant 0.12 rifampicin
rpoC 766774 c.3405T>C synonymous_variant 0.13 rifampicin
rpoC 766777 c.3408C>G synonymous_variant 0.13 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776695 p.Val596Ile missense_variant 0.13 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781793 c.234G>C synonymous_variant 0.14 streptomycin
rplC 800516 c.-293G>C upstream_gene_variant 0.25 linezolid
rplC 800531 c.-278T>C upstream_gene_variant 0.12 linezolid
rplC 800654 c.-155T>C upstream_gene_variant 0.15 linezolid
fbiC 1304715 c.1785G>T synonymous_variant 0.16 pretomanid
delamanid
clofazimine
fbiC 1304724 c.1794A>G synonymous_variant 0.24 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
fbiC 1304727 c.1797A>G synonymous_variant 0.25 pretomanid
delamanid
clofazimine
sigE 1364434 p.Arg8Trp missense_variant 1.0 pyrazinamide Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471986 n.141C>T non_coding_transcript_exon_variant 0.32 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.15 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472489 n.644A>G non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.16 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.44 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrl 1474202 n.545T>C non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1474753 n.1096A>G non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475031 n.1374G>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid
rrl 1475088 n.1431A>G non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475480 n.1823A>G non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475532 n.1875A>G non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475544 n.1887A>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475707 n.2050T>G non_coding_transcript_exon_variant 0.3 capreomycin
linezolid
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476256 n.2599A>C non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1476583 n.2926G>C non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
inhA 1674690 c.489C>G synonymous_variant 0.15 isoniazid
ethionamide
inhA 1674858 c.657G>A synonymous_variant 0.17 isoniazid
ethionamide
rpsA 1833694 c.153G>C synonymous_variant 0.16 pyrazinamide
rpsA 1833697 c.156C>G synonymous_variant 0.14 pyrazinamide
rpsA 1833847 c.306C>G synonymous_variant 0.2 pyrazinamide
rpsA 1834456 c.915T>G synonymous_variant 0.17 pyrazinamide
rpsA 1834639 c.1098T>C synonymous_variant 0.17 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
Rv1979c 2222854 p.Ile104Thr missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2517941 c.-174C>G upstream_gene_variant 0.14 isoniazid
Rv2477c 2783185 c.858G>C synonymous_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
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 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3877740 c.768G>C synonymous_variant 0.13 rifampicin
rpoA 3877776 c.732T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3877848 c.660C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3878947 c.-440G>C upstream_gene_variant 0.12 rifampicin Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
clpC1 4038755 c.1950G>T synonymous_variant 0.17 pyrazinamide
clpC1 4038767 c.1938G>C synonymous_variant 0.13 pyrazinamide
clpC1 4038773 c.1932T>C synonymous_variant 0.12 pyrazinamide
clpC1 4038790 c.1915C>T synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
clpC1 4038812 c.1893T>C synonymous_variant 0.2 pyrazinamide
clpC1 4038839 c.1866G>C synonymous_variant 0.13 pyrazinamide
clpC1 4038842 c.1863G>C synonymous_variant 0.14 pyrazinamide
clpC1 4038878 c.1827A>G synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
clpC1 4038905 c.1800A>C synonymous_variant 0.16 pyrazinamide
clpC1 4038908 c.1797C>G synonymous_variant 0.18 pyrazinamide
clpC1 4038911 c.1794G>T synonymous_variant 0.18 pyrazinamide
clpC1 4038914 c.1791G>C synonymous_variant 0.18 pyrazinamide
clpC1 4038917 c.1788C>T synonymous_variant 0.16 pyrazinamide
clpC1 4038923 c.1782A>G synonymous_variant 0.18 pyrazinamide
clpC1 4038932 c.1773G>C synonymous_variant 0.18 pyrazinamide
clpC1 4038953 c.1752A>G synonymous_variant 0.17 pyrazinamide
clpC1 4038965 c.1740T>C synonymous_variant 0.24 pyrazinamide
clpC1 4038971 c.1734T>C synonymous_variant 0.17 pyrazinamide
clpC1 4039121 c.1584T>C synonymous_variant 0.17 pyrazinamide
clpC1 4039124 c.1581C>G synonymous_variant 0.16 pyrazinamide
clpC1 4039220 c.1485G>C synonymous_variant 0.15 pyrazinamide
clpC1 4039517 c.1188C>G synonymous_variant 0.13 pyrazinamide
clpC1 4039991 c.714G>A synonymous_variant 1.0 pyrazinamide Not assoc w R
clpC1 4040393 c.312G>C synonymous_variant 0.12 pyrazinamide Not assoc w R - Interim
clpC1 4040423 c.282A>G synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
clpC1 4040444 c.261C>G synonymous_variant 0.13 pyrazinamide
clpC1 4040450 c.255A>G synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
clpC1 4040537 c.168G>C synonymous_variant 0.13 pyrazinamide
clpC1 4040644 c.61A>C synonymous_variant 0.13 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