TB-Profiler result

Run: SRR4035746

Summary

Run ID: SRR4035746

Sample name:

Date: 04-04-2023 07:16:24

Number of reads: 965254

Percentage reads mapped: 99.51

Strain: lineage4.1.2

Drug-resistance: Sensitive


Download CSV Download TXT Download PDF Download JSON
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 0.99
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 6228 p.Lys330Met missense_variant 0.17
gyrA 7174 c.-128C>T upstream_gene_variant 0.25
gyrB 7262 p.Val675Phe missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8061 p.Arg254Cys missense_variant 0.87
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575404 c.57C>A synonymous_variant 0.12
mshA 576136 c.789T>C synonymous_variant 0.18
mshA 576402 p.Ser352Phe missense_variant 0.22
ccsA 620107 p.Asp73His missense_variant 0.15
ccsA 620493 c.603G>A synonymous_variant 0.14
ccsA 620516 p.Glu209Val missense_variant 0.14
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 762474 p.Gly890Arg missense_variant 0.12
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 764805 p.Gln479Leu missense_variant 0.13
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766048 c.2679C>A synonymous_variant 0.15
rpoC 766063 c.2694C>T synonymous_variant 0.12
rpoC 766485 p.Val1039Ala missense_variant 0.11
rpoC 766622 p.Arg1085Trp missense_variant 0.15
rpoC 767161 p.Ile1264Met missense_variant 0.17
rpoC 767189 p.Pro1274Ser missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775893 p.His863Arg missense_variant 0.12
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpL5 777372 p.Pro370Arg missense_variant 0.14
mmpL5 777764 c.717G>A synonymous_variant 0.12
mmpS5 779587 c.-682A>G upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781450 c.-110A>T upstream_gene_variant 0.22
fbiC 1304666 p.Leu579Pro missense_variant 0.13
fbiC 1305306 c.2376A>G synonymous_variant 0.11
fbiC 1305339 c.2409C>T synonymous_variant 0.13
Rv1258c 1406768 c.573G>A synonymous_variant 0.15
Rv1258c 1406803 p.Ala180Thr missense_variant 0.15
Rv1258c 1406977 p.Thr122Ser missense_variant 0.13
Rv1258c 1407293 c.48G>A synonymous_variant 0.15
embR 1416870 p.Glu160Lys missense_variant 0.18
atpE 1460979 c.-66G>C upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471664 n.-182C>G upstream_gene_variant 0.15
rrs 1472139 n.294C>T non_coding_transcript_exon_variant 0.25
rrl 1475885 n.2228C>T non_coding_transcript_exon_variant 0.25
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.2
rrl 1476381 n.2724G>A non_coding_transcript_exon_variant 0.18
inhA 1674936 c.735G>A synonymous_variant 0.18
inhA 1674951 c.750G>C synonymous_variant 0.2
rpsA 1834816 c.1275C>T synonymous_variant 0.14
rpsA 1834827 p.Thr429Ile missense_variant 0.15
rpsA 1834841 p.Lys434Glu missense_variant 0.17
tlyA 1917817 c.-122delC upstream_gene_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918172 p.Ala78Val missense_variant 0.13
tlyA 1918405 p.Ser156Pro missense_variant 0.12
tlyA 1918595 p.Gly219Asp missense_variant 0.17
ndh 2101668 p.Ala459Thr missense_variant 0.15
ndh 2101675 c.1368G>A synonymous_variant 0.17
ndh 2102342 p.Ala234Val missense_variant 0.14
ndh 2103237 c.-195C>T upstream_gene_variant 0.13
katG 2156328 c.-217C>A upstream_gene_variant 0.14
katG 2156423 c.-312A>G upstream_gene_variant 0.2
PPE35 2167690 p.Asn975Tyr missense_variant 0.29
PPE35 2168520 p.Gln698Arg missense_variant 0.12
PPE35 2168731 p.Pro628Ser missense_variant 0.15
PPE35 2170149 p.His155Leu missense_variant 0.17
Rv1979c 2221727 p.Thr480Ala missense_variant 0.14
Rv1979c 2222006 p.Ile387Val missense_variant 0.13
Rv1979c 2222016 p.Phe383Leu missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289689 c.-448A>T upstream_gene_variant 0.2
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2715411 c.-79A>T upstream_gene_variant 0.18
eis 2715439 c.-107G>A upstream_gene_variant 0.17
ahpC 2725913 c.-280T>C upstream_gene_variant 0.12
ahpC 2726441 c.249G>A synonymous_variant 0.13
folC 2746932 p.Ala223Ser missense_variant 0.15
folC 2747168 p.Lys144Arg missense_variant 0.2
folC 2747665 c.-67T>G upstream_gene_variant 0.1
pepQ 2859511 p.His303Arg missense_variant 0.11
ribD 2987587 p.Tyr250Ser missense_variant 0.12
Rv2752c 3065431 p.Ala254Gly missense_variant 0.12
Rv2752c 3065469 c.723C>T synonymous_variant 0.18
Rv2752c 3065545 p.Ser216Asn missense_variant 0.18
Rv2752c 3065688 c.502_503dupAC frameshift_variant 0.15
thyX 3067297 p.Arg217Cys missense_variant 0.2
thyX 3067696 p.Gly84Arg missense_variant 0.17
thyX 3068123 c.-178A>G upstream_gene_variant 0.17
thyA 3073769 p.Arg235Trp missense_variant 0.17
thyA 3073806 c.666C>G synonymous_variant 0.3
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449138 p.Arg212Gln missense_variant 0.12
Rv3083 3449195 p.Gly231Ala missense_variant 0.11
Rv3083 3449247 c.744C>T synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474295 p.Tyr97Asn missense_variant 0.13
fprA 3474549 p.His181Gln missense_variant 0.25
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
Rv3236c 3612513 p.Trp202Arg missense_variant 0.25
Rv3236c 3612761 p.Leu119His missense_variant 0.17
Rv3236c 3612766 c.351C>T synonymous_variant 0.14
fbiB 3642448 p.Ile305Thr missense_variant 0.12
fbiB 3642470 c.936G>A synonymous_variant 0.12
alr 3840844 c.576delG frameshift_variant 0.14
alr 3840915 p.Pro169Leu missense_variant 0.18
alr 3841478 c.-58C>T upstream_gene_variant 0.13
alr 3841498 c.-78A>G upstream_gene_variant 0.15
rpoA 3878443 p.Val22Ala missense_variant 0.18
clpC1 4038921 p.Phe595Ser missense_variant 0.13
clpC1 4038925 c.1780C>T synonymous_variant 0.13
clpC1 4040216 c.489C>G synonymous_variant 0.12
embC 4240456 c.594C>G synonymous_variant 0.14
embC 4240874 p.Ser338Arg missense_variant 0.11
embC 4242147 p.Asn762Ile missense_variant 0.12
embC 4242182 p.Ala774Thr missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244052 p.Asp274Asn missense_variant 0.13
embA 4244278 p.Pro349Leu missense_variant 0.18
embA 4244462 c.1230A>G synonymous_variant 0.14
embB 4246762 c.249G>A synonymous_variant 0.15
embB 4247715 p.Gly401Asp missense_variant 0.13
embB 4247964 p.Ala484Val missense_variant 0.12
embB 4248875 p.Phe788Leu missense_variant 0.17
embB 4248906 p.Val798Ala missense_variant 0.22
aftB 4268220 p.Thr206Ile missense_variant 0.12
ubiA 4269214 p.Arg207Pro missense_variant 0.11
ubiA 4269758 p.Trp26Arg missense_variant 0.17
ethA 4326702 p.Arg258Trp missense_variant 0.14
ethR 4327740 p.Tyr64* stop_gained 0.12
ethR 4327808 p.Leu87Pro missense_variant 0.1
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338703 c.-182T>C upstream_gene_variant 0.22
gid 4407577 p.Lys209Arg missense_variant 0.12