TB-Profiler result

Run: SRR6982143
Summary

Run ID: SRR6982143

Sample name:

Date: 04-04-2023 18:28:42

Number of reads: 684979

Percentage reads mapped: 98.69

Strain: lineage4.3.3;lineage4.1.1.3;lineage2.2.1

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
lineage2 East-Asian Beijing RD105 0.07
lineage4 Euro-American LAM;T;S;X;H None 0.97
lineage4.3 Euro-American (LAM) mainly-LAM None 0.62
lineage4.1 Euro-American T;X;H None 0.15
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.06
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.26
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.64
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 0.24
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 8040 p.Gly247Ser missense_variant 0.62
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.19
rpoB 760876 p.Val357Gly missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 0.21
rpoC 764995 c.1626C>G synonymous_variant 0.59
rpoC 765150 p.Gly594Glu missense_variant 0.3
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778227 p.Gly85Ala missense_variant 0.43
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781435 c.-125G>C upstream_gene_variant 0.22
rpsL 781584 p.Arg9Cys missense_variant 0.11
Rv1258c 1406295 p.Val349Ala missense_variant 0.13
Rv1258c 1406325 p.Arg339Leu missense_variant 0.17
Rv1258c 1406760 c.580_581insC frameshift_variant 0.17
embR 1416989 c.358delA frameshift_variant 0.12
embR 1417189 c.159C>T synonymous_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.71
fabG1 1673353 c.-87G>T upstream_gene_variant 0.11
fabG1 1674035 p.Gln199Arg missense_variant 0.1
rpsA 1834177 c.636A>C synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2153958 c.2154G>A synonymous_variant 0.15
PPE35 2167760 c.2853G>T synonymous_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 0.11
Rv1979c 2223051 p.Glu38Asp missense_variant 0.44
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>G upstream_gene_variant 0.15
kasA 2518919 p.Gly269Ser missense_variant 0.84
Rv2752c 3064565 p.Glu543Lys missense_variant 0.11
Rv2752c 3065431 p.Ala254Val missense_variant 0.48
Rv2752c 3065824 p.Pro123Leu missense_variant 0.63
thyA 3073868 p.Thr202Ala missense_variant 0.75
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087246 p.Gln143Lys missense_variant 0.2
fprA 3473958 c.-49C>A upstream_gene_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612453 c.662_663delGG frameshift_variant 0.17
Rv3236c 3612813 p.Thr102Ala missense_variant 0.22
fbiA 3641059 c.520delG frameshift_variant 0.11
fbiB 3642817 p.Tyr428Phe missense_variant 0.12
rpoA 3878417 p.Gly31Ser missense_variant 0.11
rpoA 3878647 c.-140G>A upstream_gene_variant 0.67
clpC1 4038287 c.2418C>T synonymous_variant 0.43
embC 4241661 c.1804dupG frameshift_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.41
embA 4245130 p.Pro633Gln missense_variant 0.11
embB 4245956 c.-558G>T upstream_gene_variant 0.1
embA 4246066 p.Asp945Gly missense_variant 0.11
embB 4249408 c.2895G>A synonymous_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407798 c.405G>T synonymous_variant 0.2
gid 4408074 p.Arg43Ser missense_variant 0.11
gid 4408156 p.Leu16Arg missense_variant 0.55