TB-Profiler result

Run: SRR12830387
Summary

Run ID: SRR12830387

Sample name:

Date: 03-04-2023 06:58:57

Number of reads: 439389

Percentage reads mapped: 99.78

Strain: lineage4.3.3

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
lineage4.3.3 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
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 5474 p.Asp79Asn missense_variant 0.13
gyrB 5527 c.288C>T synonymous_variant 0.12
gyrB 5562 p.Lys108Arg missense_variant 0.12
gyrB 6608 p.Val457Phe missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9651 p.Ile784Val missense_variant 0.12
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766711 c.3342C>A synonymous_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776372 c.2109C>A synonymous_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304519 p.Ala530Glu missense_variant 0.13
Rv1258c 1406597 c.744G>T synonymous_variant 0.13
Rv1258c 1406863 p.Ile160Phe missense_variant 0.25
embR 1416980 p.Val123Gly missense_variant 0.2
embR 1417511 c.-164C>G upstream_gene_variant 0.11
embR 1417521 c.-175delC upstream_gene_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474059 n.402C>A non_coding_transcript_exon_variant 0.17
rrl 1474921 n.1264C>T non_coding_transcript_exon_variant 1.0
rpsA 1833942 p.Val134Ala missense_variant 0.11
rpsA 1834568 p.Asp343Tyr missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102308 c.735G>A synonymous_variant 1.0
katG 2154239 p.Thr625Ser missense_variant 0.17
katG 2154661 p.Arg484His missense_variant 0.12
PPE35 2170263 p.Leu117Pro missense_variant 1.0
Rv1979c 2223056 c.108delA frameshift_variant 0.14
Rv1979c 2223167 c.-3G>T upstream_gene_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518736 p.Ala208Thr missense_variant 0.14
kasA 2518919 p.Gly269Ser missense_variant 1.0
eis 2714313 p.Cys340* stop_gained 0.2
eis 2714475 c.858C>T synonymous_variant 0.14
eis 2714958 c.375C>A synonymous_variant 0.12
folC 2747520 p.Leu27Met missense_variant 0.17
thyX 3067436 c.510C>T synonymous_variant 0.15
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074297 p.Leu59Met missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087311 c.492C>T synonymous_variant 0.12
ald 3087706 p.Tyr296Phe missense_variant 0.14
ald 3087767 c.948G>C synonymous_variant 0.13
Rv3083 3449563 p.Gly354Ser missense_variant 0.27
Rv3083 3449854 p.Met451Val missense_variant 1.0
Rv3083 3449865 c.1362G>A synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612255 p.Val288Ile missense_variant 0.12
Rv3236c 3612479 p.Pro213Leu missense_variant 0.12
fbiA 3640636 p.Ser32Thr missense_variant 0.2
fbiB 3642496 p.Leu321Pro missense_variant 0.1
alr 3841553 c.-133G>T upstream_gene_variant 0.17
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039252 p.Ala485Ser missense_variant 0.15
clpC1 4039306 p.Gln467Lys missense_variant 0.13
clpC1 4039793 c.912C>G synonymous_variant 0.15
embC 4241882 c.2020C>T synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246787 p.Pro92Thr missense_variant 0.14
embB 4248849 p.Pro779Gln missense_variant 0.14
aftB 4268083 p.Gln252* stop_gained 0.17
aftB 4268697 p.Pro47Leu missense_variant 0.13
aftB 4268763 p.Arg25His missense_variant 0.12
aftB 4269282 c.-446G>A upstream_gene_variant 0.18
ubiA 4269713 p.Gly41Cys missense_variant 0.12
ethA 4326401 p.Gly358Val missense_variant 0.14
ethA 4327578 c.-105C>A upstream_gene_variant 0.18
whiB6 4338194 c.328C>A synonymous_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407955 p.Arg83Gln missense_variant 0.13
gid 4408156 p.Leu16Arg missense_variant 1.0