TB-Profiler result

Run: SRR11972219
Summary

Run ID: SRR11972219

Sample name:

Date: 03-04-2023 05:32:24

Number of reads: 500594

Percentage reads mapped: 99.48

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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9711 p.Met804Val missense_variant 0.11
rpoB 762101 c.2295C>T synonymous_variant 0.2
rpoC 762935 c.-435C>T upstream_gene_variant 0.12
rpoC 763181 c.-189G>A upstream_gene_variant 0.12
rpoC 763662 p.Ala98Val missense_variant 0.15
rpoC 764086 p.Asn239Lys missense_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765820 c.2451G>A synonymous_variant 0.13
rpoC 767033 p.Ser1222Pro missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776278 p.Ile735Phe missense_variant 0.13
mmpL5 777577 p.Met302Val missense_variant 0.12
mmpS5 778600 p.Asn102Lys missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801124 p.Phe106Leu missense_variant 0.1
fbiC 1302954 c.24G>A synonymous_variant 1.0
atpE 1461213 p.Val57Ile missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474787 n.1130A>G non_coding_transcript_exon_variant 0.11
rpsA 1834396 c.855G>A synonymous_variant 0.12
rpsA 1834513 c.972C>T synonymous_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154678 c.1434G>C synonymous_variant 1.0
PPE35 2168980 p.Pro545Ser missense_variant 0.11
PPE35 2169405 p.Asn403Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289697 c.-456G>A upstream_gene_variant 0.12
kasA 2518112 c.-3C>T upstream_gene_variant 0.2
eis 2715567 c.-235G>A upstream_gene_variant 0.15
ahpC 2726409 p.Asp73His missense_variant 1.0
pepQ 2859369 c.1050A>G synonymous_variant 0.17
ribD 2987353 p.Thr172Met missense_variant 0.25
Rv2752c 3064564 p.Glu543Val missense_variant 0.15
Rv2752c 3064594 p.Val533Ala missense_variant 0.18
Rv2752c 3065003 p.His397Tyr missense_variant 0.2
Rv2752c 3067096 c.-905C>T upstream_gene_variant 0.14
thyA 3074616 c.-145T>A upstream_gene_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448351 c.-153G>T upstream_gene_variant 0.12
Rv3083 3449493 c.990G>A synonymous_variant 0.13
fprA 3473963 c.-44G>T upstream_gene_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474030 c.24C>T synonymous_variant 0.17
fprA 3474177 p.His57Gln missense_variant 0.22
fbiB 3641407 c.-128C>T upstream_gene_variant 0.18
clpC1 4038934 p.Ala591Thr missense_variant 0.13
embC 4241132 p.Pro424Ser missense_variant 0.14
embC 4241276 c.1414C>T synonymous_variant 0.17
embC 4241933 p.Ala691Thr missense_variant 0.11
embC 4242471 p.Arg870Gln missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244544 p.Ala438Thr missense_variant 0.11
embB 4246544 p.Thr11Pro missense_variant 0.17
embB 4246548 p.Pro12Gln missense_variant 0.17
embB 4246555 c.42G>C synonymous_variant 0.17
embB 4246556 p.Ala15Pro missense_variant 0.17
embB 4246563 p.Leu17Trp missense_variant 0.17
embB 4246567 c.54G>T synonymous_variant 0.17
embB 4247369 p.Gly286Ser missense_variant 0.12
embB 4248048 p.Ile512Thr missense_variant 0.11
embB 4248087 p.Tyr525Cys missense_variant 0.12
embB 4249408 c.2895G>A synonymous_variant 1.0
embB 4249678 c.3165C>A synonymous_variant 1.0
aftB 4267971 p.Phe289Ser missense_variant 0.11
aftB 4268336 c.501C>T synonymous_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0