TB-Profiler result

Run: SRR6982160
Summary

Run ID: SRR6982160

Sample name:

Date: 04-04-2023 18:29:08

Number of reads: 485946

Percentage reads mapped: 99.26

Strain: lineage4.1.1.2

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
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.2 Euro-American (X-type) X1 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
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 8118 p.Glu273* stop_gained 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 619794 c.-97C>A upstream_gene_variant 0.17
rpoB 759785 c.-22T>C upstream_gene_variant 0.14
rpoB 761617 p.Asn604Ser missense_variant 0.1
rpoC 764068 p.Gln233His missense_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406115 p.Ala409Val missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476087 n.2431delA non_coding_transcript_exon_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155296 c.816C>T synonymous_variant 1.0
PPE35 2168157 p.Ile819Thr missense_variant 0.12
PPE35 2168473 c.2139dupC frameshift_variant 0.11
Rv1979c 2222864 p.Thr101Pro missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288895 c.338_346delGCACGCCAC disruptive_inframe_deletion 0.42
kasA 2518348 c.234A>T synonymous_variant 0.11
kasA 2518731 p.Pro206Leu missense_variant 0.11
kasA 2519258 p.Leu382Ile missense_variant 0.12
eis 2715229 p.Ala35Asp missense_variant 0.11
pepQ 2860078 p.Leu114Pro missense_variant 0.11
ribD 2987396 c.558T>C synonymous_variant 0.11
Rv2752c 3067149 c.-958A>G upstream_gene_variant 0.11
thyA 3073935 c.537C>T synonymous_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449787 c.1284C>T synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475180 p.Gly392Arg missense_variant 0.14
fprA 3475298 p.Arg431Gln missense_variant 0.12
whiB7 3568780 c.-101A>G upstream_gene_variant 0.11
whiB7 3568782 c.-106_-104delACA upstream_gene_variant 0.12
whiB7 3568788 c.-109G>T upstream_gene_variant 0.12
whiB7 3568789 c.-110A>C upstream_gene_variant 0.12
fbiB 3642170 c.636G>A synonymous_variant 0.15
rpoA 3878369 p.Pro47Ser missense_variant 0.13
clpC1 4039676 c.1029G>A synonymous_variant 1.0
embC 4241717 c.1855C>A synonymous_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243833 p.Ala201Thr missense_variant 1.0
embB 4246930 p.Gln139His missense_variant 1.0
embB 4247601 p.Leu363Pro missense_variant 0.1
embB 4249408 c.2895G>A synonymous_variant 1.0
ethA 4327546 c.-73T>C upstream_gene_variant 0.67
whiB6 4338595 c.-75delG upstream_gene_variant 1.0