TB-Profiler result

Run: ERR2515496
Summary

Run ID: ERR2515496

Sample name:

Date: 31-03-2023 20:58:13

Number of reads: 382719

Percentage reads mapped: 99.78

Strain: lineage4.3.4.2.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 0.99
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.99
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 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 5768 p.Pro177Thr missense_variant 0.11
gyrB 6140 p.Val301Leu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576538 c.1192delT frameshift_variant 0.15
mshA 576588 p.Gly414Val missense_variant 0.11
rpoB 762546 p.His914Asn missense_variant 0.11
rpoB 762804 p.Gly1000Ser missense_variant 0.33
rpoC 763555 c.186C>T synonymous_variant 0.13
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766620 p.Gln1084Pro missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777531 p.Ile317Thr missense_variant 0.2
mmpL5 778470 p.Gln4Arg missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305494 c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT frameshift_variant&stop_lost&splice_region_variant 0.25
Rv1258c 1406665 p.Arg226Cys missense_variant 0.12
embR 1416696 p.Ser218Pro missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474232 n.575C>A non_coding_transcript_exon_variant 0.12
rrl 1474573 n.916C>A non_coding_transcript_exon_variant 0.11
rrl 1476098 n.2441G>T non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918707 p.Leu256Phe missense_variant 0.12
PPE35 2168185 p.Thr810Ala missense_variant 0.1
Rv1979c 2222295 c.870A>G synonymous_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289421 c.-180C>T upstream_gene_variant 0.11
folC 2746180 c.1419C>A synonymous_variant 0.14
folC 2746285 p.Asp438Glu missense_variant 0.12
folC 2746596 p.Ser335Gly missense_variant 0.13
ribD 2987490 p.Tyr218Asn missense_variant 0.11
Rv2752c 3065364 c.828G>T synonymous_variant 0.12
thyX 3067319 c.627G>A synonymous_variant 0.18
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568436 p.Pro82Ser missense_variant 0.15
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
fbiA 3641173 p.Leu211Met missense_variant 0.17
fbiB 3641241 c.-294G>A upstream_gene_variant 0.12
fbiB 3641732 p.Asp66Glu missense_variant 1.0
alr 3840719 c.702A>G synonymous_variant 1.0
rpoA 3878412 p.Tyr32* stop_gained 0.25
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4242281 p.Ser807Gly missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4245932 c.-582C>T upstream_gene_variant 0.14
embB 4248381 p.Arg623Pro missense_variant 0.11
embB 4248963 p.Ala817Glu missense_variant 0.12
embB 4249210 c.2697G>T synonymous_variant 0.11
ethA 4326461 p.Ile338Thr missense_variant 0.11
ethR 4327742 p.Phe65Ser missense_variant 0.14
ethA 4327797 c.-324G>T upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
fbiC 1305494 c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN frameshift_variant&stop_lost&splice_region_variant 1.0