TB-Profiler result

Run: ERR7801222
Summary

Run ID: ERR7801222

Sample name:

Date: 02-04-2023 05:59:35

Number of reads: 832705

Percentage reads mapped: 99.47

Strain: lineage4.3.4.2.1

Drug-resistance: Other

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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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.99
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 0.99
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
tlyA 1917979 c.44delG frameshift_variant 0.11 capreomycin
ethA 4326423 c.1051delG frameshift_variant 0.11 ethionamide
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 6140 p.Val301Leu missense_variant 1.0
gyrB 6806 p.Arg523Cys missense_variant 0.29
gyrB 7158 c.1931_1933delCCG disruptive_inframe_deletion 0.21
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 619705 c.-186G>T upstream_gene_variant 0.14
ccsA 620124 c.234G>T synonymous_variant 0.33
ccsA 620201 p.Arg104Leu missense_variant 0.15
rpoB 761259 p.Gly485Arg missense_variant 0.12
rpoB 762507 p.Leu901Ile missense_variant 0.18
rpoC 764971 c.1602C>G synonymous_variant 0.1
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765574 p.Asp735Glu missense_variant 0.12
rpoC 765600 p.Glu744Gly missense_variant 0.14
rpoC 766636 p.Phe1089Leu missense_variant 0.15
mmpL5 775621 c.2859delC frameshift_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776988 p.Pro498Gln missense_variant 0.29
mmpL5 777351 p.Arg377Leu missense_variant 0.18
mmpL5 777592 p.Ser297Pro missense_variant 0.12
mmpL5 778249 p.Ile78Val missense_variant 0.12
mmpS5 778598 c.307delA frameshift_variant 0.14
mmpS5 778655 p.Ala84Glu missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800983 p.Pro59Thr missense_variant 0.12
fbiC 1303866 p.Glu312Asp missense_variant 0.17
fbiC 1304016 c.1086C>A synonymous_variant 0.17
fbiC 1304220 c.1290G>A synonymous_variant 0.22
fbiC 1304429 p.Arg500Leu missense_variant 0.14
fbiC 1304498 p.Pro523His missense_variant 0.13
fbiC 1305120 p.Gln730His missense_variant 0.16
fbiC 1305496 p.Ala856Ser missense_variant 0.14
Rv1258c 1407250 p.Pro31Thr missense_variant 0.14
Rv1258c 1407407 c.-67G>T upstream_gene_variant 0.12
embR 1417525 c.-178G>T upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472403 n.558G>T non_coding_transcript_exon_variant 0.17
rrs 1472411 n.567dupA non_coding_transcript_exon_variant 0.18
rrl 1473404 n.-254C>A upstream_gene_variant 0.12
rrl 1473828 n.171G>T non_coding_transcript_exon_variant 0.22
rrl 1474377 n.720G>T non_coding_transcript_exon_variant 0.33
rrl 1474999 n.1342C>A non_coding_transcript_exon_variant 0.33
rrl 1475105 n.1448G>T non_coding_transcript_exon_variant 0.14
rrl 1475602 n.1945G>T non_coding_transcript_exon_variant 0.15
inhA 1674701 p.Ala167Val missense_variant 0.15
inhA 1674880 p.Pro227Thr missense_variant 0.2
tlyA 1917881 c.-59C>A upstream_gene_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102146 c.897G>T synonymous_variant 0.17
ndh 2102239 c.804C>A synonymous_variant 0.18
ndh 2102712 c.328_330delACC conservative_inframe_deletion 0.17
ndh 2103035 p.Pro3Arg missense_variant 0.1
katG 2154021 c.2091C>A synonymous_variant 0.17
katG 2154963 c.1149G>A synonymous_variant 0.15
PPE35 2168179 p.Pro812Ser missense_variant 0.15
PPE35 2170034 c.579G>T synonymous_variant 0.25
Rv1979c 2222163 c.1002G>T synonymous_variant 0.14
Rv1979c 2222211 c.954G>T synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518527 p.Ser138Tyr missense_variant 0.14
kasA 2518717 c.603C>A synonymous_variant 0.13
kasA 2519276 p.Glu388* stop_gained 0.15
eis 2714865 c.468C>T synonymous_variant 0.17
ahpC 2726703 p.Asp171Tyr missense_variant 0.14
ahpC 2726714 p.Cys174* stop_gained 0.13
folC 2746694 p.Ala302Val missense_variant 0.15
folC 2746967 p.Gly211Val missense_variant 0.15
folC 2747038 c.561C>A synonymous_variant 0.15
pepQ 2859741 c.678C>A synonymous_variant 0.14
Rv2752c 3065151 c.1041G>T synonymous_variant 0.15
Rv2752c 3065159 p.Glu345* stop_gained 0.14
Rv2752c 3065254 p.Ser313* stop_gained 0.38
Rv2752c 3065460 c.732G>T synonymous_variant 0.12
Rv2752c 3065647 p.Pro182Tyr missense_variant 0.18
Rv2752c 3067065 c.-874G>T upstream_gene_variant 0.14
thyX 3067250 c.696G>T synonymous_variant 0.17
thyX 3067637 p.Gln103His missense_variant 0.13
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087086 p.Gln89His missense_variant 0.12
fbiD 3338965 c.-153C>G upstream_gene_variant 0.1
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474258 c.252C>A synonymous_variant 0.15
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612183 p.Ala312Ser missense_variant 0.12
Rv3236c 3613079 p.Val13Ala missense_variant 0.12
fbiA 3640720 p.Pro60Thr missense_variant 0.15
fbiB 3640749 c.-786G>T upstream_gene_variant 0.2
fbiA 3640783 p.Gln81Lys missense_variant 0.17
fbiA 3641389 p.Gly283Trp missense_variant 0.18
fbiB 3641783 c.249G>T synonymous_variant 0.12
fbiB 3641970 p.Val146Leu missense_variant 0.2
fbiB 3642604 p.Ala357Glu missense_variant 0.13
alr 3840719 c.702A>G synonymous_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039296 p.Ser470* stop_gained 0.14
panD 4044036 c.246G>T synonymous_variant 0.14
panD 4044110 p.Tyr58His missense_variant 0.29
panD 4044233 p.Cys17Arg missense_variant 0.12
embC 4241215 c.1353C>A synonymous_variant 0.18
embC 4242145 c.2283C>A synonymous_variant 0.17
embC 4242607 p.Met915Ile missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244279 c.1047G>T synonymous_variant 0.17
embA 4244337 p.Leu369Val missense_variant 0.15
embA 4244769 p.Gly513Trp missense_variant 0.33
embA 4245423 p.Ser731Thr missense_variant 0.17
embA 4245960 p.Gln910Lys missense_variant 0.13
embA 4246142 p.Leu970Phe missense_variant 0.22
embB 4246214 c.-300C>A upstream_gene_variant 0.2
embA 4246236 p.Leu1002Ile missense_variant 0.11
embB 4247400 p.Asn296Ile missense_variant 0.12
embB 4248421 c.1908G>T synonymous_variant 0.13
embB 4248921 p.Val803Ala missense_variant 0.11
embB 4249696 p.Trp1061Cys missense_variant 0.2
aftB 4267088 c.1749C>A synonymous_variant 0.2
aftB 4267283 c.1554C>A synonymous_variant 0.14
aftB 4267746 c.1090delT frameshift_variant 0.13
aftB 4267949 c.888C>A synonymous_variant 0.17
aftB 4268009 c.828G>T synonymous_variant 0.14
aftB 4268450 c.387A>T synonymous_variant 0.12
ethA 4326974 p.Trp167Leu missense_variant 0.22
ethA 4327119 p.His119Asn missense_variant 0.15
ethR 4327570 p.Gln8Lys missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0