TB-Profiler result

Run: ERR2515281
Summary

Run ID: ERR2515281

Sample name:

Date: 31-03-2023 20:51:02

Number of reads: 390507

Percentage reads mapped: 99.85

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
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 8508 p.Glu403Lys missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575909 p.Leu188Val missense_variant 1.0
mshA 576619 c.1272C>T synonymous_variant 0.12
ccsA 620658 c.768C>T synonymous_variant 0.1
rpoC 762533 c.-837T>C upstream_gene_variant 0.12
rpoB 763234 p.Glu1143Val missense_variant 0.12
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766159 c.2790C>T synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778346 c.-644G>A upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474988 n.1331C>A non_coding_transcript_exon_variant 0.2
rrl 1475107 n.1450G>A non_coding_transcript_exon_variant 0.15
rrl 1475371 n.1714T>A non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918540 p.Pro201Thr missense_variant 0.18
tlyA 1918601 p.His221Arg missense_variant 0.22
PPE35 2168294 p.Glu773Asp missense_variant 0.15
PPE35 2169254 c.1359C>T synonymous_variant 0.11
Rv1979c 2222749 p.Leu139Pro missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289184 p.Ala20Ser missense_variant 0.13
kasA 2518919 p.Gly269Ser missense_variant 1.0
folC 2746664 p.Phe312Tyr missense_variant 0.11
folC 2747225 p.Arg125Gln missense_variant 1.0
ribD 2987313 p.Leu159Phe missense_variant 0.15
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449308 p.Leu269Met missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475074 c.1068C>T synonymous_variant 0.14
whiB7 3568557 c.123A>T synonymous_variant 0.14
Rv3236c 3612704 p.Glu138Ala missense_variant 0.12
Rv3236c 3612719 p.Ile133Thr missense_variant 0.13
alr 3840410 c.1010delG frameshift_variant 0.12
alr 3841442 c.-22G>A upstream_gene_variant 0.12
rpoA 3878264 p.Ser82Gly missense_variant 0.13
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4240767 p.Arg302Leu missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243337 c.105G>C synonymous_variant 0.12
embA 4245065 c.1833G>A synonymous_variant 0.17
embA 4245875 p.Lys881Asn missense_variant 0.2
embA 4246192 p.Phe987Ser missense_variant 0.11
embB 4247111 c.599delT frameshift_variant 0.11
aftB 4267929 p.Arg303Leu missense_variant 1.0
ubiA 4269406 p.Lys143Arg missense_variant 0.11
ethA 4327064 p.Cys137Tyr missense_variant 0.11
ethR 4328024 c.477delA frameshift_variant 0.12
whiB6 4338367 p.Leu52Gln missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0