TB-Profiler result

Run: SRR6789616
Summary

Run ID: SRR6789616

Sample name:

Date: 04-04-2023 16:03:33

Number of reads: 551259

Percentage reads mapped: 95.09

Strain: lineage4.4.1.1

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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans 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.Ser450Trp missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289009 p.Gly78Val missense_variant 0.11 pyrazinamide
embB 4248003 p.Gln497Arg 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9138 p.Gln613Glu missense_variant 1.0
gyrA 9199 p.Lys633Ile missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575728 c.381C>T synonymous_variant 0.11
mshA 576301 p.Glu318Asp missense_variant 0.14
rpoB 760072 p.Pro89Leu missense_variant 0.17
rpoB 762490 p.Val895Ala missense_variant 0.11
rpoC 763458 p.Lys30Arg missense_variant 0.11
rpoC 764616 p.Asn416Ser missense_variant 1.0
rpoC 765516 p.Leu716His missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775966 p.Ala839Ser missense_variant 0.2
mmpL5 775981 p.Leu834Met missense_variant 0.29
mmpL5 776658 p.Asp608Gly missense_variant 0.12
mmpL5 777416 c.1065G>T synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800902 p.Gly32Trp missense_variant 0.17
fbiC 1303167 p.Ser79Arg missense_variant 0.15
Rv1258c 1406756 c.585T>C synonymous_variant 0.2
embR 1416572 p.Pro259Leu missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471856 n.11A>G non_coding_transcript_exon_variant 0.17
rrl 1473826 n.172delG non_coding_transcript_exon_variant 0.14
rrl 1473875 n.218A>G non_coding_transcript_exon_variant 0.13
rrl 1474686 n.1029A>G non_coding_transcript_exon_variant 0.12
rrl 1475398 n.1741C>A non_coding_transcript_exon_variant 0.11
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.11
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.16
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.11
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.1
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.11
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.11
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.17
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.12
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.27
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.29
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.19
fabG1 1673380 c.-60C>G upstream_gene_variant 0.23
fabG1 1673417 c.-23C>A upstream_gene_variant 0.12
inhA 1674569 p.Ser123Leu missense_variant 0.12
inhA 1674592 p.Ala131Thr missense_variant 0.12
rpsA 1833479 c.-63A>G upstream_gene_variant 0.17
rpsA 1833909 p.Asp123Ala missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101856 c.1186delT frameshift_variant 0.22
ndh 2102990 p.Val18Ala missense_variant 1.0
ndh 2103018 p.Ala9Ser missense_variant 0.13
PPE35 2168088 p.Pro842Leu missense_variant 0.13
PPE35 2168479 p.Thr712Pro missense_variant 1.0
PPE35 2168558 c.2055C>T synonymous_variant 0.14
PPE35 2169044 c.1569G>C synonymous_variant 0.4
PPE35 2169047 p.Ile522Val missense_variant 0.4
PPE35 2169053 c.1560T>C synonymous_variant 1.0
PPE35 2169056 c.1557A>G synonymous_variant 0.4
PPE35 2169059 c.1554G>A synonymous_variant 0.6
PPE35 2169063 p.Met517Thr missense_variant 1.0
PPE35 2169065 p.Ala516Ile missense_variant 0.6
PPE35 2169068 c.1545G>T synonymous_variant 0.6
PPE35 2169071 c.1542A>G synonymous_variant 0.4
PPE35 2169840 p.Gly258Asp missense_variant 1.0
PPE35 2169959 c.654C>A synonymous_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.48
PPE35 2170053 p.Thr187Ser missense_variant 0.48
PPE35 2170369 p.Gln82Lys missense_variant 0.4
Rv1979c 2222441 p.Ala242Pro missense_variant 0.11
Rv1979c 2222702 p.Gly155Ser missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714525 p.His270Asn missense_variant 0.12
ahpC 2725967 c.-226G>T upstream_gene_variant 0.11
folC 2746198 c.1401C>T synonymous_variant 0.2
folC 2746392 p.Val403Leu missense_variant 0.2
pepQ 2859901 p.Ser173Ile missense_variant 0.17
ribD 2987442 p.Phe202Ile missense_variant 0.13
Rv2752c 3064814 c.1369_1377delGTCGGCGAT conservative_inframe_deletion 1.0
thyA 3073868 p.Thr202Ala missense_variant 0.15
thyA 3074235 c.237C>A synonymous_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087730 p.Ser304Trp missense_variant 0.11
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568779 c.-100T>C upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
Rv3236c 3612698 p.Leu140Gln missense_variant 0.33
fbiA 3641403 p.Cys287* stop_gained 0.2
alr 3840580 p.Val281Ile missense_variant 0.11
alr 3841162 p.Ala87Thr missense_variant 0.13
clpC1 4038426 p.Ala760Asp missense_variant 0.14
clpC1 4038989 c.1716T>C synonymous_variant 0.22
embC 4240468 c.606C>T synonymous_variant 0.12
embC 4241663 p.Gly601Arg missense_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243281 p.Ala17Ser missense_variant 0.22
embB 4246544 p.Thr11Pro missense_variant 0.17
embB 4246548 p.Pro12Gln missense_variant 0.48
embB 4246555 c.42G>C synonymous_variant 0.52
embB 4246556 p.Ala15Pro missense_variant 0.52
embB 4246563 p.Leu17Trp missense_variant 0.27
embB 4246567 c.54G>T synonymous_variant 0.27
embB 4247408 p.Asp299Asn missense_variant 0.11
embB 4247863 c.1350C>T synonymous_variant 0.13
embB 4249313 p.Phe934Leu missense_variant 0.12
aftB 4268105 c.732T>C synonymous_variant 0.12
aftB 4268147 c.690C>T synonymous_variant 0.12
aftB 4268209 p.Arg210Cys missense_variant 0.15
ethA 4326601 p.Gln291His missense_variant 0.13
ethR 4327895 p.Ser116Leu missense_variant 0.25
ethA 4328222 c.-749G>A upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407917 p.Arg96Ser missense_variant 0.2
gid 4407986 p.Gly73Arg missense_variant 1.0