TB-Profiler result

Run: SRR12830389
Summary

Run ID: SRR12830389

Sample name:

Date: 03-04-2023 06:59:01

Number of reads: 460474

Percentage reads mapped: 99.79

Strain: lineage4.3.3

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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 5050 c.-190G>A upstream_gene_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490822 p.Gln14Lys missense_variant 0.12
fgd1 491250 c.468G>T synonymous_variant 0.13
rpoC 763977 p.Arg203Leu missense_variant 0.12
rpoC 764068 p.Gln233His missense_variant 0.11
rpoC 764459 p.Glu364* stop_gained 0.14
rpoC 764476 c.1107C>T synonymous_variant 0.17
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766292 p.Cys975Ser missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778516 c.-36C>T upstream_gene_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472221 n.376G>T non_coding_transcript_exon_variant 0.2
rrl 1474921 n.1264C>T non_coding_transcript_exon_variant 1.0
rrl 1475011 n.1354G>A non_coding_transcript_exon_variant 0.12
rpsA 1833403 c.-139G>C upstream_gene_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102308 c.735G>A synonymous_variant 1.0
katG 2155147 p.Thr322Lys missense_variant 0.14
katG 2156563 c.-452G>T upstream_gene_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518799 p.Pro229Thr missense_variant 0.12
kasA 2518919 p.Gly269Ser missense_variant 1.0
folC 2747134 c.465C>T synonymous_variant 0.14
folC 2747245 c.354G>T synonymous_variant 0.18
Rv2752c 3065645 c.545_546delCC frameshift_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449854 p.Met451Val missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474445 p.Gly147Arg missense_variant 0.13
fprA 3474971 p.Val322Gly missense_variant 0.17
whiB7 3568732 c.-53C>G upstream_gene_variant 0.13
Rv3236c 3611985 p.Pro378Thr missense_variant 0.12
fbiA 3640387 c.-156G>T upstream_gene_variant 0.2
alr 3840462 p.Arg320Leu missense_variant 0.14
alr 3840592 p.Val277Met missense_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4241363 p.Leu501Ile missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249243 c.2730G>A synonymous_variant 0.17
aftB 4267655 c.1182C>G synonymous_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338619 c.-98T>A upstream_gene_variant 0.12
gid 4408156 p.Leu16Arg missense_variant 1.0