TB-Profiler result

Run: ERR4818256
Summary

Run ID: ERR4818256

Sample name:

Date: 01-04-2023 15:27:23

Number of reads: 647680

Percentage reads mapped: 99.47

Strain: lineage4.1.1

Drug-resistance: HR-TB

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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
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
katG 2154080 c.2031delC frameshift_variant 0.5 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
folC 2747151 p.Ser150Gly missense_variant 1.0 para-aminosalicylic_acid
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 5555 p.Gly106Ser missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9126 c.1828delC frameshift_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491170 p.Ala130Ser missense_variant 0.15
rpoC 762524 c.-846G>T upstream_gene_variant 0.14
rpoC 763809 p.Glu147Gly missense_variant 0.15
rpoC 764663 p.Val432Leu missense_variant 0.14
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765249 p.Leu627Ser missense_variant 0.12
rpoC 765262 c.1893C>G synonymous_variant 0.13
rpoC 767293 c.3924C>T synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776066 c.2415C>A synonymous_variant 0.15
mmpL5 776430 p.Arg684Leu missense_variant 0.18
mmpL5 778552 c.-72C>T upstream_gene_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406506 p.Ala279Thr missense_variant 0.12
embR 1417492 c.-145G>T upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474285 n.628C>A non_coding_transcript_exon_variant 0.4
inhA 1673368 c.-834A>G upstream_gene_variant 1.0
inhA 1674347 p.Arg49His missense_variant 0.13
inhA 1674449 p.Gly83Val missense_variant 0.29
inhA 1674997 p.Thr266Ser missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155671 c.441G>T synonymous_variant 0.22
PPE35 2168084 c.2529G>A synonymous_variant 1.0
PPE35 2168662 p.Ile651Leu missense_variant 0.13
PPE35 2168792 c.1821A>T synonymous_variant 0.17
PPE35 2169719 c.894C>T synonymous_variant 0.25
PPE35 2170633 c.-21C>T upstream_gene_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726210 c.18T>C synonymous_variant 1.0
ribD 2986919 p.Glu27Asp missense_variant 1.0
thyA 3074251 p.Glu74Val missense_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087434 c.615G>A synonymous_variant 0.15
ald 3087444 p.Ala209Thr missense_variant 0.15
ald 3087733 p.Val305Ala missense_variant 0.18
ald 3087756 p.Leu313Met missense_variant 0.18
fbiD 3339240 c.123C>A synonymous_variant 0.22
fbiD 3339333 c.216G>A synonymous_variant 1.0
Rv3083 3449017 p.Asp172Asn missense_variant 0.18
fprA 3473827 c.-180C>T upstream_gene_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640892 p.Gln117Arg missense_variant 0.2
fbiA 3641062 p.Val174Leu missense_variant 0.15
fbiA 3641447 p.Thr302Met missense_variant 1.0
alr 3840914 c.507G>T synonymous_variant 0.17
alr 3841516 c.-96G>A upstream_gene_variant 0.12
rpoA 3877553 p.Glu319Lys missense_variant 1.0
clpC1 4039148 c.1557C>T synonymous_variant 0.12
clpC1 4040182 p.Gly175Ser missense_variant 0.13
embC 4240897 c.1035C>G synonymous_variant 1.0
embC 4242516 p.Val885Ala missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242692 c.-541C>A upstream_gene_variant 0.13
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244496 p.Ala422Ser missense_variant 0.12
embA 4244554 p.Gln441Pro missense_variant 0.14
embA 4244736 p.Tyr502His missense_variant 0.14
embA 4245708 p.Ala826Thr missense_variant 0.11
embB 4245794 c.-720G>A upstream_gene_variant 0.12
embB 4249268 p.Asp919Tyr missense_variant 0.15
embB 4249408 c.2895G>A synonymous_variant 1.0
aftB 4267443 p.Met465Thr missense_variant 0.14
aftB 4268747 c.90C>T synonymous_variant 0.13
ethA 4326426 p.Gly350Arg missense_variant 1.0
ethA 4326656 p.Pro273Leu missense_variant 0.12
ethA 4327605 c.-132C>T upstream_gene_variant 0.18
ethA 4328255 c.-782A>G upstream_gene_variant 0.11
whiB6 4338593 c.-73delT upstream_gene_variant 1.0
whiB6 4338596 c.-75G>C upstream_gene_variant 1.0
whiB6 4338625 c.-104C>T upstream_gene_variant 0.17
gid 4408168 p.Phe12Ser missense_variant 1.0