TB-Profiler result

Run: SRR4035713
Summary

Run ID: SRR4035713

Sample name:

Date: 04-04-2023 07:15:12

Number of reads: 977936

Percentage reads mapped: 99.47

Strain: lineage4.1.2

Drug-resistance: Other

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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
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
tlyA 1918269 c.330_331insA frameshift_variant 0.14 capreomycin
folC 2747141 p.Glu153Gly missense_variant 0.14 para-aminosalicylic_acid
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 5213 c.-27G>A upstream_gene_variant 0.12
gyrB 5355 p.Glu39Gly missense_variant 0.18
gyrB 5812 c.573C>T synonymous_variant 0.13
gyrB 6965 p.Ser576Gly missense_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7840 p.Gly180Asp missense_variant 0.15
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 763188 p.Asn1128Asp missense_variant 0.11
rpoC 763202 c.-168A>G upstream_gene_variant 0.11
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775995 p.Ile829Thr missense_variant 0.14
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpL5 777366 p.Arg372Leu missense_variant 0.14
mmpR5 779299 p.Glu104Lys missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303515 c.585G>A synonymous_variant 0.12
fbiC 1304898 c.1968G>A synonymous_variant 0.14
Rv1258c 1406465 c.876G>A synonymous_variant 0.2
Rv1258c 1406490 p.Arg284His missense_variant 0.13
embR 1417213 c.135C>T synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 0.91
rrs 1472682 n.837T>C non_coding_transcript_exon_variant 0.11
rrl 1476531 n.2874T>C non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918277 p.Val113Ala missense_variant 0.14
ndh 2102350 c.693G>C synonymous_variant 0.1
katG 2156213 c.-102A>G upstream_gene_variant 0.12
PPE35 2169320 p.Leu431Phe missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
folC 2746846 c.753C>T synonymous_variant 0.14
folC 2747296 c.302delT frameshift_variant 0.18
pepQ 2859456 c.963G>A synonymous_variant 0.18
Rv2752c 3065666 c.526T>C synonymous_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448681 p.Phe60Leu missense_variant 0.12
Rv3083 3449597 c.1096delC frameshift_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.94
fprA 3475358 p.Leu451Ser missense_variant 0.11
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
Rv3236c 3613231 c.-116delT upstream_gene_variant 0.14
fbiB 3642378 p.Glu282Lys missense_variant 0.17
rpoA 3877760 p.Pro250Ser missense_variant 0.13
rpoA 3877977 p.Lys177Asn missense_variant 0.11
rpoA 3877993 p.Leu172Pro missense_variant 0.13
clpC1 4038761 c.1942_1943dupAC frameshift_variant 0.17
clpC1 4039118 c.1587C>T synonymous_variant 0.14
embC 4239924 p.Asp21Val missense_variant 0.17
embC 4240388 p.Asn176Asp missense_variant 0.13
embC 4242228 p.Gly789Ala missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243458 p.Cys76Arg missense_variant 0.11
embA 4243714 p.Thr161Ile missense_variant 0.12
embA 4244226 p.Gly332* stop_gained 0.14
embB 4246802 p.Val97Leu missense_variant 0.11
embB 4248024 p.Glu504Gly missense_variant 0.12
embB 4249639 c.3126G>A synonymous_variant 0.2
aftB 4267929 p.Arg303Gln missense_variant 0.25
aftB 4267945 p.Tyr298His missense_variant 0.2
aftB 4267954 p.Ala295Thr missense_variant 0.2
aftB 4268458 p.Ala127Pro missense_variant 0.14
aftB 4268783 c.54C>T synonymous_variant 0.18
ethR 4327642 p.Thr32Ala missense_variant 0.13
ethR 4328122 p.Pro192Ala missense_variant 0.12
ethR 4328166 p.Ile206Met missense_variant 0.12
ethR 4328174 p.Thr209Ile missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408423 c.-221G>A upstream_gene_variant 0.18