TB-Profiler result

Run: SRR3732575
Summary

Run ID: SRR3732575

Sample name:

Date: 04-04-2023 05:35:58

Number of reads: 1606275

Percentage reads mapped: 99.53

Strain: lineage4.1.1

Drug-resistance: Sensitive

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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
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 5597 p.Leu120Val missense_variant 0.12
gyrB 5628 p.Ala130Glu missense_variant 0.12
gyrB 6052 p.Ile271Met missense_variant 1.0
gyrB 6253 c.1014G>T synonymous_variant 0.13
gyrB 6819 p.Ile527Thr missense_variant 0.12
gyrB 7221 p.Ser661Thr missense_variant 1.0
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 491337 c.555C>A synonymous_variant 0.13
rpoB 762408 p.Ala868Pro missense_variant 0.14
rpoC 763525 c.156C>T synonymous_variant 0.2
rpoC 764175 p.Asp269Val missense_variant 0.13
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766933 c.3564A>G synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776470 p.Glu671* stop_gained 0.2
mmpL5 776600 c.1881G>T synonymous_variant 0.22
mmpL5 776745 p.Arg579Leu missense_variant 0.12
mmpL5 779061 c.-581G>A upstream_gene_variant 0.17
mmpR5 779186 p.Gly66Val missense_variant 0.18
mmpR5 779297 p.Gly103Val missense_variant 0.33
mmpS5 779620 c.-715G>T upstream_gene_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781931 c.372C>A synonymous_variant 0.4
rplC 800928 c.120C>A synonymous_variant 0.33
fbiC 1302844 c.-87C>A upstream_gene_variant 0.12
Rv1258c 1406527 p.Leu272Met missense_variant 0.2
Rv1258c 1406561 c.780G>T synonymous_variant 0.18
embR 1416699 p.Leu217Val missense_variant 1.0
embR 1417094 p.Gly85Asp missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472252 n.407G>T non_coding_transcript_exon_variant 0.29
rrs 1472343 n.498C>T non_coding_transcript_exon_variant 0.33
rrl 1474232 n.575C>A non_coding_transcript_exon_variant 0.5
fabG1 1673521 p.Gly28Trp missense_variant 0.15
inhA 1673865 c.-337C>T upstream_gene_variant 1.0
inhA 1674369 c.168A>G synonymous_variant 0.22
rpsA 1833349 c.-193C>A upstream_gene_variant 0.12
rpsA 1834521 p.Ala327Asp missense_variant 0.18
rpsA 1834600 c.1059G>T synonymous_variant 0.14
rpsA 1834706 p.Asn389Asp missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102950 p.Lys31Asn missense_variant 0.12
katG 2154035 p.Arg693Cys missense_variant 0.15
PPE35 2167958 c.2655G>T synonymous_variant 0.18
PPE35 2168225 c.2388C>A synonymous_variant 0.18
PPE35 2168254 p.Pro787Thr missense_variant 0.18
PPE35 2169041 c.1572G>A synonymous_variant 0.12
PPE35 2169063 p.Met517Thr missense_variant 0.12
PPE35 2169066 p.Ala516Val missense_variant 0.12
PPE35 2169071 c.1542A>G synonymous_variant 0.12
Rv1979c 2221873 p.Ser431Tyr missense_variant 0.2
Rv1979c 2222443 p.Ala241Asp missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518013 c.-102G>T upstream_gene_variant 0.15
kasA 2518037 c.-78G>A upstream_gene_variant 0.12
eis 2714422 p.Ala304Glu missense_variant 0.12
ahpC 2726338 p.Val49Gly missense_variant 0.2
ahpC 2726577 p.Gly129Ser missense_variant 0.18
Rv2752c 3066108 c.84C>A synonymous_variant 0.12
Rv2752c 3066128 p.Gly22Cys missense_variant 0.12
thyA 3073713 c.759G>T synonymous_variant 0.18
thyA 3073874 p.Ile200Val missense_variant 0.12
thyA 3074222 p.Ala84Ser missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087393 p.Ala192Thr missense_variant 0.17
Rv3083 3449721 c.1218G>A synonymous_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474363 c.357G>T synonymous_variant 0.14
fprA 3475224 c.1218G>T synonymous_variant 0.13
whiB7 3568777 c.-98C>A upstream_gene_variant 0.13
Rv3236c 3612304 c.813C>A synonymous_variant 0.29
Rv3236c 3612324 p.Pro265Thr missense_variant 0.29
fbiB 3640647 c.-888G>T upstream_gene_variant 0.13
clpC1 4038773 p.Asp644Glu missense_variant 0.11
clpC1 4038776 p.Glu643Asp missense_variant 0.11
clpC1 4038782 c.1923G>C synonymous_variant 0.11
clpC1 4039868 c.837C>A synonymous_variant 0.12
clpC1 4040433 p.Ser91Ile missense_variant 0.12
clpC1 4040507 c.198C>A synonymous_variant 0.2
clpC1 4040600 c.105A>G synonymous_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4243071 p.Ala1070Val missense_variant 0.12
embA 4244245 p.Ile338Thr missense_variant 0.11
embA 4245864 p.Trp878Arg missense_variant 0.14
embB 4245944 c.-570C>G upstream_gene_variant 0.15
embA 4246195 p.Pro988His missense_variant 0.15
embB 4248768 p.Asp752Val missense_variant 0.2
embB 4249408 c.2895G>A synonymous_variant 1.0
embB 4249507 p.Gln998His missense_variant 0.2
embB 4249626 p.Gly1038Val missense_variant 0.22
aftB 4266996 p.Gly614Val missense_variant 0.22
aftB 4267141 p.Leu566Met missense_variant 0.2
aftB 4267290 p.Ala516Glu missense_variant 0.14
aftB 4268291 c.546C>T synonymous_variant 0.14
aftB 4268898 c.-62G>A upstream_gene_variant 0.22
aftB 4269159 c.-323G>T upstream_gene_variant 0.29
ubiA 4269251 p.Glu195Lys missense_variant 0.18
ethA 4326208 c.1266G>T synonymous_variant 0.15
ethA 4327044 p.Asp144Tyr missense_variant 0.12
ethR 4327260 c.-289G>T upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338680 c.-159G>T upstream_gene_variant 0.12
whiB6 4338689 c.-168C>A upstream_gene_variant 0.12