TB-Profiler result

Run: SRR6856003

Summary

Run ID: SRR6856003

Sample name:

Date: 04-04-2023 17:52:49

Number of reads: 314067

Percentage reads mapped: 99.61

Strain: lineage4.3.2.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.2 Euro-American (LAM) LAM3 None 1.0
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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 5520 p.Pro94Leu missense_variant 1.0
gyrB 5764 c.525C>T synonymous_variant 0.13
gyrB 6462 p.Asn408Ile missense_variant 0.13
gyrB 6548 p.Gly437* stop_gained 0.12
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8295 p.Tyr332His missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490736 c.-47G>T upstream_gene_variant 0.22
fgd1 491681 p.Tyr300Phe missense_variant 0.17
mshA 576414 c.1069delC frameshift_variant 0.14
rpoB 759697 c.-110A>T upstream_gene_variant 0.12
rpoB 762085 c.2281delG frameshift_variant 0.18
rpoC 762957 c.-413C>T upstream_gene_variant 0.18
rpoC 763563 p.Tyr65Phe missense_variant 0.12
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765393 p.Glu675Gly missense_variant 0.15
rpoC 766121 p.Thr918Ala missense_variant 0.12
rpoC 766510 c.3141C>T synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775677 p.Lys935Arg missense_variant 0.22
mmpL5 777900 p.Ala194Val missense_variant 0.12
mmpL5 778048 p.Lys145Glu missense_variant 0.12
mmpL5 778618 c.-138G>A upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781542 c.-18A>G upstream_gene_variant 0.12
rplC 800696 c.-113C>T upstream_gene_variant 0.11
fbiC 1304432 p.Ser501* stop_gained 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471734 n.-112G>A upstream_gene_variant 0.12
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1473629 n.-29T>A upstream_gene_variant 0.12
rrl 1474120 n.463A>G non_coding_transcript_exon_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102653 c.390T>C synonymous_variant 0.14
katG 2153957 p.Lys719Gln missense_variant 0.25
katG 2155393 p.Asp240Gly missense_variant 0.1
PPE35 2170347 p.Gln89Arg missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746566 p.Ala345Thr missense_variant 0.22
Rv2752c 3066143 c.49C>A synonymous_variant 0.11
Rv2752c 3066200 c.-9G>A upstream_gene_variant 0.12
thyX 3067287 p.Ala220Asp missense_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568572 c.108C>G synonymous_variant 0.18
whiB7 3568730 c.-52delC upstream_gene_variant 0.18
Rv3236c 3611988 p.Leu377Met missense_variant 0.17
Rv3236c 3612007 c.1110C>A synonymous_variant 0.18
fbiA 3640543 p.Val1Met missense_variant 0.15
fbiB 3640872 c.-663C>A upstream_gene_variant 0.12
fbiB 3641842 p.Gln103Arg missense_variant 0.11
ddn 3986785 c.-59G>A upstream_gene_variant 0.13
ddn 3986913 p.Ile24Val missense_variant 0.11
ddn 3986949 p.Gly36Cys missense_variant 0.11
ddn 3987186 p.Thr115Ser missense_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038595 p.His704Asp missense_variant 0.12
clpC1 4038842 c.1862delT frameshift_variant 0.17
clpC1 4038883 p.Gly608Ser missense_variant 0.17
panD 4044107 p.Ala59Thr missense_variant 0.13
embC 4240317 p.Cys152Phe missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245012 p.Arg594Ser missense_variant 0.22
embA 4245826 p.Asp865Gly missense_variant 0.12
embB 4249540 c.3027C>A synonymous_variant 0.17
aftB 4268506 p.Arg111Trp missense_variant 0.33
ethA 4327224 p.Tyr84His missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407723 c.480C>A synonymous_variant 0.12
gid 4408156 p.Leu16Arg missense_variant 1.0