TB-Profiler result

Run: SRR4034391
Summary

Run ID: SRR4034391

Sample name:

Date: 2024-03-26T14:51:18.760571

Number of reads: 13923902

Percentage reads mapped: 57.05

Median coverage: 221.0

Strain: lineage4.1.2.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 1.0
lineage4.1.2 Euro-American None 1.0
lineage4.1.2.1 Euro-American (Haarlem) RD182 1.0
lineage4 Euro-American None 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Tyr Assoc w R
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-16C>G Uncertain significance Mutation from literature
embB p.Glu405Asp Uncertain significance Mutation from literature
pyrazinamide pncA p.His71Tyr Assoc w R
streptomycin gid p.Ala134Glu Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine ald c.133delA Mutation from literature
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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
rpoB 761139 p.His445Tyr missense_variant 0.99 rifampicin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 1.0 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289031 p.His71Tyr missense_variant 0.99 pyrazinamide Assoc w R
ald 3086951 c.133delA frameshift_variant 1.0 cycloserine Mutation from literature
embA 4243217 c.-16C>G upstream_gene_variant 1.0 ethambutol Uncertain significance Mutation from literature
embB 4247728 p.Glu405Asp missense_variant 0.99 ethambutol Uncertain significance Mutation from literature
gid 4407802 p.Ala134Glu missense_variant 1.0 streptomycin Assoc w R
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 645 c.645A>C synonymous_variant 1.0 isoniazid 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 491591 p.Lys270Met missense_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 1.0 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 1.0 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 762863 c.-507T>G upstream_gene_variant 0.11 rifampicin
rpoB 762872 p.Met1022Ile missense_variant 0.2 rifampicin Uncertain significance
rpoB 762878 p.Ile1024Met missense_variant 0.22 rifampicin
rpoB 762879 p.Met1025Leu missense_variant 0.23 rifampicin Uncertain significance
rpoB 762899 c.3093G>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoB 762925 p.Thr1040Ile missense_variant 0.38 rifampicin
rpoB 762929 c.3123G>C synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoB 762939 c.3133_3135delATGinsCC frameshift_variant&missense_variant 0.33 rifampicin
rpoB 762942 p.Ile1046Val missense_variant 0.31 rifampicin Uncertain significance
rpoC 762980 c.-390T>C upstream_gene_variant 0.18 rifampicin
rpoC 762983 c.-387C>T upstream_gene_variant 0.17 rifampicin
rpoC 762989 c.-381G>C upstream_gene_variant 0.16 rifampicin
rpoC 762998 c.-372G>A upstream_gene_variant 0.14 rifampicin
rpoC 764419 c.1050C>G synonymous_variant 0.12 rifampicin
rpoC 764428 c.1059G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764434 c.1065A>G synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 764435 c.1066_1068delAGGinsCC frameshift_variant&missense_variant 0.12 rifampicin
rpoC 764443 p.Ile358Met missense_variant 0.11 rifampicin
rpoC 764446 p.Asp359Glu missense_variant 0.11 rifampicin
rpoC 764450 c.1081_1083delGGTinsCG frameshift_variant&missense_variant 0.11 rifampicin
rpoC 764461 p.Glu364Asp missense_variant 0.12 rifampicin
rpoC 764471 p.Asn368Arg missense_variant 0.11 rifampicin
rpoC 764479 c.1110G>A synonymous_variant 0.12 rifampicin
rpoC 765150 p.Gly594Glu missense_variant 1.0 rifampicin Not assoc w R
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
Rv1258c 1406813 c.528T>C synonymous_variant 1.0 streptomycin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
pyrazinamide Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471876 n.31G>A non_coding_transcript_exon_variant 0.21 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471877 n.32A>G non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin
amikacin Uncertain significance
rrs 1471892 n.47G>A non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1471893 n.48T>G non_coding_transcript_exon_variant 0.22 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471896 n.51T>C non_coding_transcript_exon_variant 0.22 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1471917 n.72G>A non_coding_transcript_exon_variant 0.26 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471918 n.74_78delAAGGT non_coding_transcript_exon_variant 0.27 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471934 n.89A>T non_coding_transcript_exon_variant 0.26 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471935 n.92_96delCTCGA non_coding_transcript_exon_variant 0.28 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471948 n.103A>G non_coding_transcript_exon_variant 0.27 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.19 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472181 n.336G>A non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.2 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.22 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.19 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Uncertain significance
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.12 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.11 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472338 n.493A>C non_coding_transcript_exon_variant 0.14 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472349 n.504A>T non_coding_transcript_exon_variant 0.16 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472374 n.529T>A non_coding_transcript_exon_variant 0.16 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472382 n.537G>T non_coding_transcript_exon_variant 0.16 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.13 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.51 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472715 n.870C>A non_coding_transcript_exon_variant 0.5 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.66 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.66 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.66 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.66 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.64 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.56 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.47 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.12 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473201 n.1356_1357delACinsT non_coding_transcript_exon_variant 0.13 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474838 n.1181C>T non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.25 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474875 n.1218G>A non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1474876 n.1219T>A non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1474883 n.1226T>C non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1474893 n.1236G>A non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1474899 n.1242T>C non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1474903 n.1246T>C non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474910 n.1253C>G non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474920 n.1263G>A non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475499 n.1842C>G non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475539 n.1882A>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475540 n.1883C>T non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475550 n.1893A>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475553 n.1896G>C non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475555 n.1898T>G non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475571 n.1914A>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475575 n.1918C>A non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475577 n.1920C>G non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475791 n.2134A>G non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.27 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476266 n.2609G>A non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1476279 n.2622G>C non_coding_transcript_exon_variant 0.3 capreomycin
linezolid
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476281 n.2624T>A non_coding_transcript_exon_variant 0.3 capreomycin
linezolid
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.51 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.52 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.72 capreomycin
linezolid
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.72 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476339 n.2682G>A non_coding_transcript_exon_variant 0.74 capreomycin
linezolid
rrl 1476356 n.2699C>T non_coding_transcript_exon_variant 0.78 capreomycin
linezolid
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.77 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>A non_coding_transcript_exon_variant 0.75 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.78 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.79 capreomycin
linezolid
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.7 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.69 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.62 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.61 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.6 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.59 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.6 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.43 capreomycin
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.38 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
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 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518076 c.-39C>T upstream_gene_variant 1.0 isoniazid
Rv2680 2996034 c.-71G>A upstream_gene_variant 0.24 capreomycin Uncertain significance
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.44 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.34 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840259 p.Tyr388Asp missense_variant 1.0 cycloserine
embC 4239298 c.-565C>T upstream_gene_variant 0.99 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 1.0 ethambutol Not assoc w R
embB 4247738 p.Ala409Pro missense_variant 0.99 ethambutol Uncertain significance
ethA 4326842 p.Tyr211Ser missense_variant 0.99 ethionamide Uncertain significance
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