TB-Profiler result

Run: SRR3675277
Summary

Run ID: SRR3675277

Sample name:

Date: 04-04-2023 05:25:24

Number of reads: 460594

Percentage reads mapped: 99.43

Strain: lineage4.1.1.3

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 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 6558 p.Gly440Asp missense_variant 0.4
gyrA 7362 p.Glu21Gln missense_variant 0.89
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9759 p.Glu820* stop_gained 0.14
fgd1 491027 p.Asn82Thr missense_variant 0.18
ccsA 620748 c.858T>G synonymous_variant 0.33
rpoB 759615 c.-192A>C upstream_gene_variant 0.33
rpoB 759620 c.-187A>C upstream_gene_variant 0.38
rpoB 760701 p.Arg299Ser missense_variant 0.17
rpoC 764251 p.Lys294Asn missense_variant 0.2
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
fbiC 1304516 p.Ala529Asp missense_variant 0.22
atpE 1460855 c.-190T>C upstream_gene_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473142 n.1297G>T non_coding_transcript_exon_variant 0.2
rrl 1474053 n.396G>A non_coding_transcript_exon_variant 0.2
rrl 1474602 n.945C>A non_coding_transcript_exon_variant 0.67
rrl 1474754 n.1097C>A non_coding_transcript_exon_variant 0.29
fabG1 1673357 c.-83G>A upstream_gene_variant 0.11
fabG1 1673359 c.-81T>C upstream_gene_variant 0.11
fabG1 1673361 c.-79C>G upstream_gene_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918436 p.Ala166Gly missense_variant 1.0
ndh 2102655 p.His130Asn missense_variant 0.13
katG 2155913 p.Glu67Lys missense_variant 0.17
PPE35 2169964 p.Leu217Val missense_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.35
PPE35 2170053 p.Thr187Ser missense_variant 0.38
Rv1979c 2223053 p.Glu38Lys missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>A synonymous_variant 0.17
Rv2752c 3064609 p.Arg528Leu missense_variant 0.25
Rv2752c 3067182 c.-991C>A upstream_gene_variant 0.15
thyX 3067884 p.Pro21His missense_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449564 p.Gly354Val missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038298 p.Asp803Tyr missense_variant 0.12
embC 4242193 c.2331G>T synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243179 c.-54T>C upstream_gene_variant 0.12
embB 4246490 c.-24G>C upstream_gene_variant 1.0
embB 4246601 p.Ala30Thr missense_variant 0.14
embB 4249335 p.Ala941Asp missense_variant 0.11
embB 4249408 c.2895G>A synonymous_variant 1.0
aftB 4268426 c.411C>A synonymous_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407666 c.537C>A synonymous_variant 0.12