TB-Profiler result

Run: ERR3077961

Summary

Run ID: ERR3077961

Sample name:

Date: 01-04-2023 00:12:47

Number of reads: 407091

Percentage reads mapped: 99.6

Strain: lineage4.3.3

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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 761139 p.His445Ser missense_variant 1.0 rifampicin
rpoB 761142 p.Lys446Gln missense_variant 1.0 rifampicin
fabG1 1673432 c.-8T>C upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embA 4243217 c.-16C>T upstream_gene_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 6361 p.Lys374Asn missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7604 p.Gln101His missense_variant 0.12
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9092 c.1793delA frameshift_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9723 p.Glu808* stop_gained 0.14
fgd1 491027 p.Asn82Thr missense_variant 0.22
mshA 575909 p.Leu188Val missense_variant 1.0
mshA 576654 p.Ala436Glu missense_variant 0.15
ccsA 619796 c.-95G>A upstream_gene_variant 0.18
ccsA 620007 c.117T>C synonymous_variant 0.33
rpoB 759672 c.-135G>T upstream_gene_variant 0.12
rpoB 760785 p.Leu327Met missense_variant 0.2
rpoB 761291 c.1485G>T synonymous_variant 0.22
rpoB 761559 p.Thr585Ser missense_variant 0.15
rpoB 761600 c.1794T>C synonymous_variant 0.2
rpoC 763375 c.6C>A synonymous_variant 0.13
rpoC 763612 p.Glu81Asp missense_variant 0.13
rpoC 764559 p.Arg397Leu missense_variant 0.12
rpoC 764626 c.1257C>A synonymous_variant 0.14
rpoC 764847 p.Glu493Gly missense_variant 0.13
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766278 p.Thr970Asn missense_variant 0.17
rpoC 767137 p.Lys1256Asn missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303158 p.His76Gln missense_variant 0.12
fbiC 1303170 c.240C>A synonymous_variant 0.13
fbiC 1303258 p.Val110Leu missense_variant 0.14
fbiC 1303828 p.His300Asn missense_variant 0.14
Rv1258c 1407358 c.-18G>T upstream_gene_variant 0.17
embR 1416682 c.666C>A synonymous_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471970 n.125G>T non_coding_transcript_exon_variant 0.12
rrs 1471976 n.131C>A non_coding_transcript_exon_variant 0.12
rrs 1472393 n.548G>A non_coding_transcript_exon_variant 0.25
rrl 1474720 n.1063C>A non_coding_transcript_exon_variant 0.14
rrl 1474892 n.1235G>T non_coding_transcript_exon_variant 0.17
rrl 1475565 n.1908G>T non_coding_transcript_exon_variant 0.15
rrl 1476184 n.2527G>A non_coding_transcript_exon_variant 0.29
rpsA 1833925 c.384C>A synonymous_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918222 p.Gly95Trp missense_variant 0.15
ndh 2101738 p.Gln435His missense_variant 0.14
ndh 2103201 c.-159C>A upstream_gene_variant 0.22
katG 2156016 c.96C>T synonymous_variant 0.2
PPE35 2167916 c.2696delT frameshift_variant 0.2
Rv1979c 2222440 p.Ala242Asp missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
kasA 2519122 c.1008G>T synonymous_variant 0.18
eis 2714340 c.993C>A synonymous_variant 0.29
ahpC 2726265 p.Lys25Gln missense_variant 0.2
ahpC 2726486 c.294A>T synonymous_variant 0.13
folC 2747395 c.204T>C synonymous_variant 0.17
folC 2747601 c.-3G>T upstream_gene_variant 0.13
folC 2747628 c.-30G>T upstream_gene_variant 0.12
folC 2747785 c.-187C>G upstream_gene_variant 0.2
ribD 2987606 c.768C>A synonymous_variant 0.13
Rv2752c 3064671 c.1521C>A synonymous_variant 0.14
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087022 p.Ala68Asp missense_variant 0.15
ald 3087544 p.Pro242Gln missense_variant 0.12
fbiD 3339540 c.423C>A synonymous_variant 0.17
Rv3083 3448578 c.75C>T synonymous_variant 0.18
Rv3083 3448624 p.Leu41Met missense_variant 0.22
Rv3083 3449347 p.Asp282Tyr missense_variant 0.18
Rv3083 3449578 p.Ile359Val missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474720 c.714G>C synonymous_variant 0.25
fprA 3474790 p.Pro262Thr missense_variant 0.13
Rv3236c 3612623 p.Tyr165Phe missense_variant 0.25
fbiA 3640568 p.Gly9Val missense_variant 0.15
fbiA 3641285 p.Gly248Val missense_variant 0.17
fbiB 3642384 p.Leu284Ile missense_variant 0.15
alr 3840659 c.762C>A synonymous_variant 0.12
alr 3841099 p.Pro108Thr missense_variant 0.17
rpoA 3877677 c.831G>T synonymous_variant 0.22
ddn 3986714 c.-130C>T upstream_gene_variant 1.0
ddn 3987144 p.Gln101Lys missense_variant 0.12
ddn 3987161 c.318G>A synonymous_variant 0.14
ddn 3987200 c.357C>A synonymous_variant 0.14
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038327 p.Glu793Gly missense_variant 0.2
clpC1 4038406 p.Val767Leu missense_variant 0.11
clpC1 4038827 p.Glu626Asp missense_variant 0.12
clpC1 4039622 c.1083C>A synonymous_variant 0.14
clpC1 4039682 c.1023C>A synonymous_variant 0.14
embC 4239886 c.24C>A synonymous_variant 0.13
embC 4240406 p.Ala182Thr missense_variant 0.14
embC 4240864 p.Trp334Cys missense_variant 0.18
embC 4241298 p.Ala479Glu missense_variant 0.17
embC 4242043 p.Met727Ile missense_variant 0.18
embC 4242220 c.2358A>C synonymous_variant 0.43
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244751 p.Val507Leu missense_variant 0.22
embA 4244834 c.1602G>T synonymous_variant 0.15
embA 4244900 c.1668G>T synonymous_variant 0.2
embA 4245155 c.1923C>A synonymous_variant 0.18
embB 4245992 c.-522C>A upstream_gene_variant 0.13
embB 4246804 c.291G>T synonymous_variant 0.15
embB 4246878 p.Arg122Leu missense_variant 0.2
embB 4247176 c.663G>T synonymous_variant 0.18
embB 4247885 p.Gly458Ser missense_variant 0.18
embB 4247966 p.Ala485Thr missense_variant 0.12
embB 4249045 c.2532G>A synonymous_variant 0.14
aftB 4268126 c.711G>T synonymous_variant 0.17
ethA 4326106 c.1368C>A synonymous_variant 0.2
ethA 4326309 p.Ala389Ser missense_variant 0.13
ethR 4327099 c.-450C>A upstream_gene_variant 0.12
ethR 4328053 p.His169Tyr missense_variant 0.12
whiB6 4338367 p.Leu52Gln missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407656 p.Ala183Ser missense_variant 0.25
gid 4408125 p.Leu26Phe missense_variant 0.13
gid 4408156 p.Leu16Arg missense_variant 1.0