TB-Profiler result

Run: ERR11465151

Summary

Run ID: ERR11465151

Sample name:

Date: 2024-10-04T02:54:24.686866

Number of reads: 1435501

Percentage reads mapped: 99.11

Median coverage: 30.0

Strain: lineage4.3.4.1

Spoligotype:

Drug-resistance: Sensitive


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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 1.0
lineage4.3.4.1 Euro-American (LAM) RD174 1.0
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
dnaA 546 c.546C>G synonymous_variant 0.12 isoniazid
gyrA 6634 c.-668T>C upstream_gene_variant 0.14 levofloxacin
moxifloxacin
gyrA 6640 c.-662A>C upstream_gene_variant 0.14 levofloxacin
moxifloxacin
gyrA 6643 c.-659A>G upstream_gene_variant 0.14 levofloxacin
moxifloxacin
gyrA 6655 c.-647T>C upstream_gene_variant 0.14 levofloxacin
moxifloxacin
gyrB 6745 c.1506T>C synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6775 c.1536G>C synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 6781 c.-521C>T upstream_gene_variant 0.16 levofloxacin
moxifloxacin
gyrB 6793 c.1554T>C synonymous_variant 0.12 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6798 p.Gly520Ala missense_variant 0.16 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
gyrB 6824 c.1585C>T synonymous_variant 0.17 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 8250 p.Glu317Gln missense_variant 1.0 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
hadA 731789 c.-141A>G upstream_gene_variant 0.19 isoniazid
nusG 734499 c.246G>C synonymous_variant 0.21 rifampicin
nusG 734910 c.657C>G synonymous_variant 0.17 rifampicin
rpoB 760118 c.312T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 760121 c.315T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 760184 c.378A>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 760196 c.390C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761954 c.2148C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761999 c.2193G>C synonymous_variant 0.12 rifampicin
rpoB 762008 c.2202C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762038 c.2232C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 763127 c.3321G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 763142 c.-228C>G upstream_gene_variant 0.13 rifampicin
rpoC 763259 c.-111G>C upstream_gene_variant 0.12 rifampicin
rpoB 763268 c.3462C>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 763660 c.291T>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763675 c.306C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763732 c.363C>G synonymous_variant 0.13 rifampicin
rpoC 763741 c.372C>T synonymous_variant 0.14 rifampicin
rpoC 763744 c.375G>C synonymous_variant 0.13 rifampicin
rpoC 764239 c.870T>C synonymous_variant 0.32 rifampicin
rpoC 764245 c.876C>T synonymous_variant 0.3 rifampicin
rpoC 764431 c.1062G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764434 c.1065A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764746 c.1377G>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764791 c.1422C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764797 c.1428G>C synonymous_variant 0.14 rifampicin
rpoC 764995 c.1626C>G synonymous_variant 0.93 rifampicin Not assoc w R
rpoC 765826 c.2457T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 766504 c.3135G>C synonymous_variant 0.23 rifampicin
rpoC 766517 p.Thr1050Ala missense_variant 0.25 rifampicin
rpoC 766522 c.3153C>A synonymous_variant 0.25 rifampicin
rpoC 766525 c.3156G>C synonymous_variant 0.23 rifampicin
rpoC 766528 c.3159T>G synonymous_variant 0.23 rifampicin
rpoC 766530 p.Arg1054Gln missense_variant 0.22 rifampicin
rpoC 766537 c.3168G>A synonymous_variant 0.22 rifampicin
rpoC 766540 p.Asp1057Glu missense_variant 0.22 rifampicin
rpoC 766546 p.Glu1059Asp missense_variant 0.22 rifampicin
rpoC 766549 c.3180G>C synonymous_variant 0.21 rifampicin
rpoC 766843 c.3474T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 766846 c.3477C>G synonymous_variant 0.18 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 800633 c.-176T>C upstream_gene_variant 0.15 linezolid
rplC 800654 c.-155T>C upstream_gene_variant 0.18 linezolid
rplC 800759 c.-50C>T upstream_gene_variant 0.15 linezolid
rplC 800762 c.-47T>G upstream_gene_variant 0.14 linezolid
fbiC 1304817 c.1887T>C synonymous_variant 0.18 pretomanid
delamanid
clofazimine
fbiC 1304826 c.1896G>C synonymous_variant 0.18 pretomanid
delamanid
clofazimine
fbiC 1304829 c.1899T>C synonymous_variant 0.19 pretomanid
delamanid
clofazimine
fbiC 1304832 c.1902C>G synonymous_variant 0.19 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
fbiC 1304853 c.1923C>T synonymous_variant 0.18 pretomanid
delamanid
clofazimine
fbiC 1304856 c.1926C>G synonymous_variant 0.17 pretomanid
delamanid
clofazimine
fbiC 1304869 c.1939C>T synonymous_variant 0.17 pretomanid
delamanid
clofazimine
fbiC 1304874 c.1944C>T synonymous_variant 0.17 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 0.29 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472489 n.644A>G non_coding_transcript_exon_variant 0.22 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.23 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.55 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.28 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1473717 n.60G>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.4 capreomycin
linezolid
rrl 1474753 n.1096A>G non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid
rrl 1475088 n.1431A>G non_coding_transcript_exon_variant 0.38 capreomycin
linezolid
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.22 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 0.22 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475532 n.1875A>G non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475544 n.1887A>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475707 n.2050T>G non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476256 n.2599A>C non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1476583 n.2926G>C non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rpsA 1833829 c.288A>G synonymous_variant 0.31 pyrazinamide
rpsA 1833832 c.291G>A synonymous_variant 0.34 pyrazinamide
rpsA 1833838 c.297G>C synonymous_variant 0.24 pyrazinamide
rpsA 1833841 c.300C>G synonymous_variant 0.24 pyrazinamide
rpsA 1833847 c.306C>G synonymous_variant 0.28 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.24 pyrazinamide
rpsA 1833862 c.321G>T synonymous_variant 0.19 pyrazinamide
rpsA 1833892 c.351G>A synonymous_variant 0.19 pyrazinamide
rpsA 1833894 p.Ala118Glu missense_variant 0.19 pyrazinamide
rpsA 1833949 c.408T>C synonymous_variant 0.19 pyrazinamide
rpsA 1834303 c.762T>G synonymous_variant 0.23 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.23 pyrazinamide
rpsA 1834690 c.1149T>C synonymous_variant 0.26 pyrazinamide
rpsA 1834732 c.1191T>C synonymous_variant 0.35 pyrazinamide
rpsA 1834733 p.Ala398Pro missense_variant 0.31 pyrazinamide
rpsA 1834738 c.1197A>G synonymous_variant 0.33 pyrazinamide
rpsA 1834747 c.1206A>G synonymous_variant 0.3 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
Rv2477c 2782528 c.1515G>T synonymous_variant 0.17 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2782537 c.1506T>C synonymous_variant 0.13 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2782540 c.1503T>C synonymous_variant 0.13 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
thyA 3073868 p.Thr202Ala missense_variant 0.97 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 3877593 c.915C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877602 c.906C>T synonymous_variant 0.16 rifampicin
rpoA 3877608 c.900G>A synonymous_variant 0.16 rifampicin
rpoA 3877656 c.852T>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3877848 c.660C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877857 c.651G>A synonymous_variant 0.17 rifampicin
rpoA 3877926 c.582G>C synonymous_variant 0.2 rifampicin
clpC1 4038287 c.2418C>T synonymous_variant 0.97 pyrazinamide Not assoc w R
clpC1 4039226 c.1479T>C synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
clpC1 4039241 c.1464G>C synonymous_variant 0.21 pyrazinamide
clpC1 4039517 c.1188C>G synonymous_variant 0.2 pyrazinamide
clpC1 4039576 p.Ala377Ser missense_variant 0.19 pyrazinamide
clpC1 4039991 c.714G>A synonymous_variant 1.0 pyrazinamide Not assoc w R
clpC1 4040411 c.294T>C synonymous_variant 0.18 pyrazinamide Not assoc w R - Interim
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