TB-Profiler result

Run: SRR21277780

Summary

Run ID: SRR21277780

Sample name:

Date: 04-04-2023 01:41:44

Number of reads: 13067698

Percentage reads mapped: 96.97

Strain: lineage4.4.2

Drug-resistance: HR-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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.2 Euro-American T1;T2 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
gyrA 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
katG 2155733 p.Gln127* stop_gained 0.12 isoniazid
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490682 c.-101C>A upstream_gene_variant 0.14
fgd1 491295 c.513C>A synonymous_variant 0.11
mshA 575258 c.-90G>A upstream_gene_variant 0.12
mshA 576601 c.1254C>T synonymous_variant 0.25
rpoC 764545 c.1176C>A synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303686 c.756C>T synonymous_variant 1.0
Rv1258c 1406577 p.Gln255Arg missense_variant 0.99
Rv1258c 1406940 p.Arg134Leu missense_variant 0.12
Rv1258c 1406968 p.Asp125Tyr missense_variant 0.2
Rv1258c 1407210 p.Ala44Asp missense_variant 0.13
Rv1258c 1407503 c.-163C>T upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834228 c.687C>T synonymous_variant 1.0
tlyA 1917953 p.Ala5Asp missense_variant 0.2
tlyA 1917955 p.Arg6Ser missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918246 p.Arg103Cys missense_variant 0.17
tlyA 1918541 p.Pro201Gln missense_variant 0.11
katG 2154107 p.Glu669Lys missense_variant 1.0
PPE35 2170103 c.510C>A synonymous_variant 0.43
PPE35 2170116 p.Pro166Gln missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518644 p.Ala177Val missense_variant 0.13
kasA 2518649 p.Ala179Thr missense_variant 0.12
kasA 2519018 p.Pro302Thr missense_variant 0.17
kasA 2519161 c.1047G>T synonymous_variant 0.12
eis 2714986 p.Ala116Glu missense_variant 0.14
folC 2746299 p.Glu434* stop_gained 0.11
folC 2746314 p.Arg429Trp missense_variant 0.13
folC 2746384 p.His405Gln missense_variant 0.15
folC 2746387 c.1212C>A synonymous_variant 0.12
folC 2746637 p.Leu321His missense_variant 0.1
folC 2746864 c.735G>A synonymous_variant 0.11
folC 2747338 c.261C>A synonymous_variant 0.1
folC 2747461 c.138C>T synonymous_variant 0.99
folC 2747783 c.-185G>T upstream_gene_variant 0.12
pepQ 2859982 p.Ala146Asp missense_variant 0.11
pepQ 2860232 p.Gln63Lys missense_variant 0.12
pepQ 2860583 c.-165G>T upstream_gene_variant 0.11
pepQ 2860589 c.-171G>T upstream_gene_variant 0.71
ribD 2986659 c.-180G>T upstream_gene_variant 0.14
ribD 2987300 c.462G>A synonymous_variant 0.14
Rv2752c 3066099 p.Met31Ile missense_variant 1.0
Rv2752c 3067174 c.-983A>T upstream_gene_variant 0.16
thyX 3067275 p.Pro224His missense_variant 0.25
thyX 3067277 c.669C>G synonymous_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474922 p.Asp306Asn missense_variant 0.17
fprA 3474927 c.921C>A synonymous_variant 0.22
fprA 3474997 p.Gly331Trp missense_variant 0.17
Rv3236c 3612177 c.940C>A synonymous_variant 0.19
fbiB 3641376 c.-159G>T upstream_gene_variant 0.11
fbiB 3641638 p.Ala35Val missense_variant 0.12
fbiB 3642394 p.Pro287Leu missense_variant 0.15
fbiB 3642691 p.Val386Asp missense_variant 0.11
fbiB 3642706 p.Arg391Leu missense_variant 0.12
rpoA 3878574 c.-67G>T upstream_gene_variant 0.11
clpC1 4039618 c.1087C>A synonymous_variant 0.11
clpC1 4040227 p.Gly160* stop_gained 0.11
embC 4241265 p.Gly468Val missense_variant 0.1
embC 4242366 p.Ser835Tyr missense_variant 0.16
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242772 c.-461G>T upstream_gene_variant 0.14
embA 4243514 c.282G>A synonymous_variant 0.11
embA 4243648 p.Leu139Pro missense_variant 0.11
embA 4243680 p.Ala150Ser missense_variant 0.11
embA 4243967 c.735G>T synonymous_variant 0.17
embA 4244206 p.Arg325His missense_variant 0.13
embA 4245440 c.2208C>A synonymous_variant 0.13
embB 4246508 c.-6G>A upstream_gene_variant 1.0
embB 4246591 c.78G>A synonymous_variant 1.0
embB 4247221 c.708G>A synonymous_variant 0.11
embB 4247299 c.786G>T synonymous_variant 0.13
embB 4247305 c.792C>T synonymous_variant 0.16
embB 4247921 p.His470Tyr missense_variant 0.14
embB 4248590 p.Ala693Thr missense_variant 0.11
aftB 4268306 p.Phe177Leu missense_variant 0.11
aftB 4268478 p.Ala120Val missense_variant 0.12
aftB 4268482 p.Pro119Thr missense_variant 0.12
aftB 4268492 c.345G>T synonymous_variant 0.11
aftB 4268928 c.-92C>T upstream_gene_variant 1.0
aftB 4269375 c.-539G>A upstream_gene_variant 1.0
ethA 4328023 c.-550G>T upstream_gene_variant 0.11
ethA 4328433 c.-960G>T upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0