TB-Profiler result

Run: ERR7910877
Summary

Run ID: ERR7910877

Sample name:

Date: 02-04-2023 06:33:18

Number of reads: 626222

Percentage reads mapped: 96.21

Strain: lineage4.1.1

Drug-resistance: MDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289213 p.Gln10Pro missense_variant 1.0 pyrazinamide
embB 4247574 p.Asp354Ala missense_variant 1.0 ethambutol
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
gyrB 6052 p.Ile271Met missense_variant 1.0
gyrB 7113 p.Thr625Asn missense_variant 0.12
gyrA 7186 c.-116C>G upstream_gene_variant 0.12
gyrA 7216 c.-86G>C upstream_gene_variant 0.11
gyrB 7221 p.Ser661Thr missense_variant 0.9
gyrA 7234 c.-68C>T upstream_gene_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7631 c.330G>C synonymous_variant 0.12
gyrA 7637 c.336C>G synonymous_variant 0.12
gyrA 7658 c.357A>C synonymous_variant 0.13
gyrA 7664 c.363T>C synonymous_variant 0.14
gyrA 7670 c.369A>G synonymous_variant 0.15
gyrA 7679 c.378G>C synonymous_variant 0.14
gyrA 7685 c.384G>A synonymous_variant 0.13
gyrA 7688 c.387C>T synonymous_variant 0.13
gyrA 7694 c.393A>G synonymous_variant 0.13
gyrA 7697 c.396C>G synonymous_variant 0.14
gyrA 7710 c.409_411delTTGinsCTC synonymous_variant 0.12
gyrA 7715 c.414G>C synonymous_variant 0.12
gyrA 7721 c.420G>A synonymous_variant 0.12
gyrA 7725 c.424C>T synonymous_variant 0.14
gyrA 7728 c.427_429delAGGinsCGT synonymous_variant 0.14
gyrA 8619 c.1318T>C synonymous_variant 0.11
gyrA 8624 c.1323G>C synonymous_variant 0.12
gyrA 8636 c.1335A>C synonymous_variant 0.13
gyrA 8642 c.1341A>G synonymous_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491403 c.621G>A synonymous_variant 0.13
mshA 575390 p.Gln15Lys missense_variant 0.12
ccsA 620406 c.519delC frameshift_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765513 p.Lys715Thr missense_variant 1.0
rpoC 766181 p.Val938Ile missense_variant 0.11
rpoC 766861 c.3492G>C synonymous_variant 0.13
rpoC 766864 c.3495G>C synonymous_variant 0.12
rpoC 766876 c.3507C>T synonymous_variant 0.12
rpoC 766882 c.3513C>T synonymous_variant 0.13
rpoC 766894 c.3525T>C synonymous_variant 0.15
rpoC 766895 c.3526T>C synonymous_variant 0.15
rpoC 766900 c.3531T>C synonymous_variant 0.15
rpoC 767058 p.Thr1230Ile missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776998 p.Thr495Ser missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416699 p.Leu217Val missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.11
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.12
rrl 1473899 n.242A>C non_coding_transcript_exon_variant 0.12
inhA 1673865 c.-337C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167742 c.2871C>A synonymous_variant 0.2
Rv1979c 2222047 p.His373Leu missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290233 c.-992C>A upstream_gene_variant 0.17
kasA 2518504 c.390T>C synonymous_variant 0.11
kasA 2518506 p.Ala131Glu missense_variant 0.12
kasA 2518519 c.405G>C synonymous_variant 0.11
kasA 2518528 c.414C>G synonymous_variant 0.13
ahpC 2726732 p.Lys180Asn missense_variant 0.11
folC 2746295 p.Asn435Ile missense_variant 0.12
folC 2747116 c.483G>A synonymous_variant 0.12
folC 2747760 c.-162G>C upstream_gene_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612740 p.Tyr126Phe missense_variant 0.14
alr 3840977 c.444C>G synonymous_variant 0.11
rpoA 3877656 c.852T>G synonymous_variant 0.13
rpoA 3877668 c.840A>G synonymous_variant 0.12
rpoA 3877679 p.Ala277Ser missense_variant 0.13
rpoA 3877878 c.630G>A synonymous_variant 0.11
clpC1 4038530 p.Glu725Asp missense_variant 0.18
clpC1 4038908 c.1797C>G synonymous_variant 0.27
clpC1 4038914 c.1791G>C synonymous_variant 0.21
clpC1 4038923 c.1780_1782delCTAinsTTG synonymous_variant 0.2
clpC1 4038953 c.1752A>G synonymous_variant 0.13
clpC1 4038956 c.1749T>C synonymous_variant 0.14
clpC1 4038965 c.1740T>C synonymous_variant 0.13
clpC1 4038971 c.1734T>C synonymous_variant 0.12
clpC1 4038974 c.1731T>C synonymous_variant 0.12
clpC1 4038989 c.1716T>C synonymous_variant 0.14
clpC1 4038997 c.1708T>C synonymous_variant 0.15
clpC1 4039004 c.1701C>G synonymous_variant 0.15
clpC1 4039022 c.1683A>G synonymous_variant 0.11
clpC1 4039097 c.1608G>C synonymous_variant 0.12
clpC1 4039103 c.1602T>C synonymous_variant 0.11
clpC1 4039106 c.1599G>C synonymous_variant 0.11
clpC1 4039112 c.1593C>G synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4245444 p.Asp738Tyr missense_variant 0.13
embA 4245703 p.Ser824* stop_gained 0.11
embB 4249408 c.2895G>A synonymous_variant 0.94
ethA 4326900 p.Pro192Ser missense_variant 1.0
ethA 4327128 p.Trp116Arg missense_variant 0.11
ethA 4327130 p.Arg115Leu missense_variant 0.11
whiB6 4338594 c.-73T>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407980 p.Pro75Ser missense_variant 1.0