TB-Profiler result

Run: SRR5535709
Summary

Run ID: SRR5535709

Sample name:

Date: 04-04-2023 10:38:47

Number of reads: 1924687

Percentage reads mapped: 99.22

Strain: lineage4.1.2.1

Drug-resistance: Other

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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 0.99
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
pncA 2289192 p.Gly17Val missense_variant 0.33 pyrazinamide
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 5471 p.Ala78Ser missense_variant 0.18
gyrB 5492 p.Pro85Thr missense_variant 0.18
gyrA 7000 c.-302C>T upstream_gene_variant 0.14
gyrB 7195 p.Met652Ile missense_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8287 p.Asn329Thr missense_variant 0.25
gyrA 8578 p.Asp426Gly missense_variant 0.17
gyrA 8871 p.Gly524Arg missense_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9734 c.2433A>C synonymous_variant 0.17
fgd1 491353 p.Gly191Cys missense_variant 0.13
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
ccsA 620404 p.Leu172Met missense_variant 0.17
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760352 p.Asp182Glu missense_variant 0.29
rpoB 760555 p.Glu250Gly missense_variant 1.0
rpoB 762044 c.2238C>A synonymous_variant 0.15
rpoC 762377 c.-993C>A upstream_gene_variant 0.4
rpoC 763142 c.-228C>A upstream_gene_variant 0.18
rpoC 763669 c.300C>T synonymous_variant 0.22
rpoC 763676 p.His103Asn missense_variant 0.2
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765822 p.Ala818Asp missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775964 c.2517G>T synonymous_variant 0.2
mmpL5 776236 p.Thr749Ser missense_variant 0.25
mmpL5 778309 p.Gln58Lys missense_variant 0.17
mmpS5 778551 p.Asp119His missense_variant 0.14
mmpL5 778909 c.-429G>T upstream_gene_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781691 p.Lys44Asn missense_variant 0.12
rplC 801219 c.411C>T synonymous_variant 0.18
fbiC 1302920 c.-11G>A upstream_gene_variant 0.93
fbiC 1305019 p.Ala697Thr missense_variant 0.17
Rv1258c 1406599 p.Pro248Thr missense_variant 0.2
Rv1258c 1406603 c.738G>A synonymous_variant 0.18
Rv1258c 1406620 p.Pro241Thr missense_variant 0.17
Rv1258c 1407227 p.Glu38Asp missense_variant 0.2
embR 1416352 c.996C>A synonymous_variant 0.22
embR 1417044 p.Arg102Trp missense_variant 0.13
embR 1417150 c.198G>T synonymous_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.4
rpsA 1833868 p.Tyr109* stop_gained 0.13
rpsA 1834764 p.Glu408Gly missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101922 p.Ser374* stop_gained 0.25
ndh 2102358 p.Gly229Ser missense_variant 0.4
ndh 2102514 p.Gly177Trp missense_variant 0.29
ndh 2102776 c.267C>T synonymous_variant 0.22
katG 2154016 p.Gly699Val missense_variant 0.18
katG 2155243 p.Ala290Asp missense_variant 0.29
katG 2155635 c.477C>A synonymous_variant 0.33
PPE35 2167874 c.2739C>A synonymous_variant 0.25
PPE35 2167895 p.Asn906Lys missense_variant 0.25
PPE35 2168221 p.Ala798Ser missense_variant 0.5
PPE35 2168236 p.Ala793Ser missense_variant 0.5
PPE35 2169150 p.Pro488Gln missense_variant 1.0
PPE35 2170014 p.Gly200Val missense_variant 0.12
PPE35 2170628 c.-16C>G upstream_gene_variant 0.17
Rv1979c 2223249 c.-85G>A upstream_gene_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289522 c.-281T>G upstream_gene_variant 0.29
pncA 2289606 c.-365G>A upstream_gene_variant 0.25
pncA 2289811 c.-570C>A upstream_gene_variant 0.4
pncA 2289848 c.-607G>T upstream_gene_variant 0.2
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518166 p.Ala18Thr missense_variant 0.14
kasA 2518535 p.Ala141Ser missense_variant 0.17
eis 2714243 p.His364Asn missense_variant 0.22
folC 2746277 p.Asp441Gly missense_variant 1.0
pepQ 2860578 c.-160G>T upstream_gene_variant 0.12
ribD 2986649 c.-190G>T upstream_gene_variant 0.15
ribD 2986987 p.Asp50Ala missense_variant 0.13
Rv2752c 3065577 p.Asn205Lys missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087186 p.Ala123Thr missense_variant 0.22
ald 3087581 c.762T>C synonymous_variant 0.22
Rv3083 3449054 p.Gly184Asp missense_variant 0.14
Rv3083 3449069 p.Ala189Glu missense_variant 0.14
Rv3083 3449613 p.Lys370Asn missense_variant 0.29
Rv3083 3449660 p.Trp386Leu missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475141 p.Val379Ile missense_variant 0.22
Rv3236c 3611981 p.Ala379Asp missense_variant 0.15
Rv3236c 3613267 c.-151G>T upstream_gene_variant 0.33
fbiA 3640600 p.Gln20Lys missense_variant 0.18
fbiB 3641010 c.-525C>A upstream_gene_variant 0.27
alr 3840716 c.705G>T synonymous_variant 0.5
rpoA 3878037 c.471C>A synonymous_variant 0.17
ddn 3987214 p.Pro124Gln missense_variant 0.22
clpC1 4039160 p.His515Gln missense_variant 0.18
clpC1 4039815 p.Ala297Asp missense_variant 0.15
clpC1 4040496 p.Gly70Asp missense_variant 0.29
embC 4239886 c.24C>G synonymous_variant 0.14
embC 4240308 p.Gly149Val missense_variant 0.19
embC 4242022 c.2160G>T synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 0.97
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244034 p.Gly268Cys missense_variant 0.13
embA 4244833 p.Val534Ala missense_variant 0.17
embA 4245300 c.2068C>T synonymous_variant 0.17
embB 4245527 c.-987C>T upstream_gene_variant 0.2
embA 4245898 p.Gly889Ala missense_variant 0.2
embA 4246038 p.Ala936Ser missense_variant 0.17
embB 4247413 p.Asp300Glu missense_variant 0.33
embB 4248432 p.Trp640Leu missense_variant 0.22
embB 4249383 p.Pro957Gln missense_variant 0.14
aftB 4267383 p.Ala485Glu missense_variant 0.2
aftB 4267925 c.912G>T synonymous_variant 0.22
aftB 4268277 p.Pro187Leu missense_variant 0.17
aftB 4268279 c.558G>T synonymous_variant 0.14
aftB 4268427 c.409delT frameshift_variant 0.12
aftB 4268780 p.Trp19Cys missense_variant 0.18
aftB 4269582 c.-746C>T upstream_gene_variant 0.15
aftB 4269615 c.-779C>T upstream_gene_variant 0.18
ubiA 4269730 p.Ala35Glu missense_variant 0.22
ubiA 4269812 p.Gln8Lys missense_variant 0.23
ethA 4326064 c.1410C>T synonymous_variant 0.29
ethA 4326141 p.Glu445* stop_gained 0.17
ethA 4326497 p.Arg326Leu missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0