TB-Profiler result

Run: SRR6982316
Summary

Run ID: SRR6982316

Sample name:

Date: 04-04-2023 18:33:53

Number of reads: 374529

Percentage reads mapped: 99.58

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 0.99
lineage4.1.2 Euro-American T;H None 0.98
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.98
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 5144 c.-96A>G upstream_gene_variant 0.11
gyrB 6122 p.Ala295Thr missense_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
ccsA 620237 p.Leu116Pro missense_variant 0.13
ccsA 620548 p.Pro220Ser missense_variant 0.22
ccsA 620655 p.Trp255Cys missense_variant 0.14
rpoB 759878 c.72C>T synonymous_variant 0.14
rpoB 759899 p.Asn31Lys missense_variant 0.12
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 0.95
rpoC 765842 p.Thr825Ser missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.12
mmpL5 776459 c.2022G>C synonymous_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417083 p.Asp89Tyr missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474117 n.460A>G non_coding_transcript_exon_variant 0.1
rrl 1474359 n.702C>A non_coding_transcript_exon_variant 0.13
inhA 1674942 c.741T>C synonymous_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102182 p.Arg287Ser missense_variant 0.13
ndh 2102831 p.Pro71Leu missense_variant 0.18
katG 2155540 p.Trp191Leu missense_variant 0.13
PPE35 2168208 p.Asp802Gly missense_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.95
ahpC 2726702 c.510C>A synonymous_variant 0.13
pepQ 2860200 c.219G>A synonymous_variant 0.15
Rv2752c 3065116 p.Gly359Val missense_variant 0.12
Rv2752c 3066103 p.Asn30Ser missense_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474011 p.Arg2His missense_variant 0.12
fprA 3475056 c.1050C>G synonymous_variant 0.14
fprA 3475095 c.1089G>T synonymous_variant 0.13
Rv3236c 3612443 p.Ile225Asn missense_variant 0.1
Rv3236c 3613171 c.-55G>A upstream_gene_variant 0.15
fbiA 3640397 c.-146G>T upstream_gene_variant 0.11
alr 3841546 c.-126C>A upstream_gene_variant 0.18
rpoA 3877872 c.635delG frameshift_variant 0.12
ddn 3986788 c.-56T>C upstream_gene_variant 0.1
clpC1 4039524 p.Phe394Ser missense_variant 0.12
clpC1 4039989 p.Pro239His missense_variant 0.12
embC 4240719 p.Phe286Ser missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244617 p.Ala462Glu missense_variant 0.13
embA 4245810 p.Pro860Ser missense_variant 0.18
embB 4247733 p.Ile407Asn missense_variant 0.11
embB 4249476 p.Trp988Leu missense_variant 0.11
ubiA 4269504 c.329delG frameshift_variant 0.11
ethA 4326176 p.Glu433Val missense_variant 0.2
whiB6 4338505 p.Ala6Val missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448949 c.447_*1566del frameshift_variant&stop_lost&splice_region_variant 1.0