TB-Profiler result

Run: SRR6982390
Summary

Run ID: SRR6982390

Sample name:

Date: 04-04-2023 18:36:04

Number of reads: 488426

Percentage reads mapped: 99.62

Strain: lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9534 p.Arg745Cys missense_variant 0.13
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
ccsA 620564 p.Leu225Pro missense_variant 0.12
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 762205 p.Val800Ala missense_variant 0.12
rpoB 762352 c.2557_2562delGACGAG conservative_inframe_deletion 0.14
rpoC 764273 p.Phe302Leu missense_variant 0.13
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777706 p.Ser259Pro missense_variant 0.11
mmpS5 778772 p.Ala45Val missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304183 p.Ala418Glu missense_variant 0.1
Rv1258c 1407095 c.246G>T synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471863 n.18G>T non_coding_transcript_exon_variant 0.12
rrs 1472437 n.592T>C non_coding_transcript_exon_variant 0.17
rrl 1473701 n.46_48delCCG non_coding_transcript_exon_variant 0.18
rrl 1473883 n.226A>T non_coding_transcript_exon_variant 0.25
rrl 1475310 n.1653A>G non_coding_transcript_exon_variant 0.14
rrl 1476232 n.2575G>T non_coding_transcript_exon_variant 0.12
fabG1 1673861 p.Val141Ala missense_variant 0.2
inhA 1674992 p.Ala264Val missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169185 p.Ser476Arg missense_variant 0.11
PPE35 2169496 p.Asp373Tyr missense_variant 0.14
Rv1979c 2222295 c.870A>G synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289429 c.-188G>T upstream_gene_variant 0.14
pncA 2290175 c.-934T>C upstream_gene_variant 0.17
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2715436 c.-104G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3613214 c.-99delG upstream_gene_variant 0.11
fbiB 3642413 c.879G>A synonymous_variant 0.11
clpC1 4040058 p.Gly216Val missense_variant 0.11
embC 4241134 c.1272G>A synonymous_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.14
embB 4246555 c.42G>C synonymous_variant 0.17
embB 4246556 p.Ala15Pro missense_variant 0.17
aftB 4268182 p.Phe219Leu missense_variant 0.11
aftB 4268923 c.-87C>G upstream_gene_variant 0.17
ethA 4327320 p.Gly52* stop_gained 0.14
ethA 4327413 p.Trp21Arg missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0