TB-Profiler result

Run: SRR4035792
Summary

Run ID: SRR4035792

Sample name:

Date: 04-04-2023 07:17:59

Number of reads: 489787

Percentage reads mapped: 99.43

Strain: lineage4.1.2

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H 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
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 5194 c.-46G>A upstream_gene_variant 0.12
gyrB 5897 p.Asp220Asn missense_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 8754 p.Glu485Lys missense_variant 0.4
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490635 c.-148A>T upstream_gene_variant 0.25
fgd1 491591 p.Lys270Met missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 762831 p.Ser1009Gly missense_variant 0.15
rpoC 762851 c.-519C>T upstream_gene_variant 0.17
rpoC 763492 c.123G>A synonymous_variant 0.33
rpoC 764173 p.Phe268Leu missense_variant 0.14
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 764644 c.1275G>T synonymous_variant 0.33
rpoC 765061 p.Asn564Lys missense_variant 0.18
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765669 p.His767Arg missense_variant 0.18
rpoC 766370 p.Gln1001Lys missense_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776671 p.Phe604Leu missense_variant 0.29
mmpL5 777186 p.Ala432Glu missense_variant 0.18
mmpL5 777320 c.1161C>G synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801281 p.Ala158Val missense_variant 0.13
fbiC 1303573 p.Leu215Met missense_variant 0.25
fbiC 1304116 p.Pro396Thr missense_variant 0.2
fbiC 1304470 p.Tyr514Asn missense_variant 0.2
fbiC 1304485 p.Thr519Ser missense_variant 0.25
fbiC 1304539 p.Arg537Ser missense_variant 0.22
Rv1258c 1406370 p.Val324Gly missense_variant 0.25
embR 1416360 p.Ala330Ser missense_variant 0.33
embR 1416780 p.Val190Met missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472875 n.1030T>C non_coding_transcript_exon_variant 0.13
rrs 1472891 n.1046A>T non_coding_transcript_exon_variant 0.15
rrs 1473122 n.1277T>C non_coding_transcript_exon_variant 0.15
rrl 1474810 n.1153G>A non_coding_transcript_exon_variant 0.14
rrl 1475242 n.1585G>T non_coding_transcript_exon_variant 0.22
rrl 1475248 n.1591A>T non_coding_transcript_exon_variant 0.18
rrl 1476046 n.2389G>T non_coding_transcript_exon_variant 0.14
fabG1 1673825 p.Arg129His missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918587 p.Gln216His missense_variant 0.33
ndh 2101844 p.His400Arg missense_variant 0.13
ndh 2102712 p.Pro111Thr missense_variant 0.22
PPE35 2167702 p.Ala971Thr missense_variant 0.17
PPE35 2168485 p.Asn710Tyr missense_variant 0.17
PPE35 2169592 p.Ile341Phe missense_variant 0.29
PPE35 2169647 p.Phe322Leu missense_variant 0.13
PPE35 2169742 p.Asn291Asp missense_variant 0.25
PPE35 2169827 c.785delC frameshift_variant 0.14
PPE35 2170256 c.357G>A synonymous_variant 0.15
PPE35 2170809 c.-197C>T upstream_gene_variant 0.13
Rv1979c 2221813 p.Leu451* stop_gained 0.29
Rv1979c 2222064 c.1101G>A synonymous_variant 0.25
Rv1979c 2222211 c.954G>A synonymous_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290061 c.-820C>T upstream_gene_variant 0.22
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2714329 p.Asp335Gly missense_variant 0.33
ahpC 2726412 p.Glu74* stop_gained 0.25
folC 2746484 p.Phe372Tyr missense_variant 0.22
folC 2747346 c.253C>T synonymous_variant 0.25
pepQ 2860083 c.336C>T synonymous_variant 0.25
pepQ 2860111 p.Thr103Met missense_variant 0.25
pepQ 2860243 p.Arg59Gln missense_variant 0.22
pepQ 2860258 p.Leu54Ser missense_variant 0.22
ribD 2987150 p.Gln104His missense_variant 0.29
Rv2752c 3065495 p.Val233Met missense_variant 0.15
Rv2752c 3065857 p.Val112Ala missense_variant 0.17
thyX 3067402 p.Arg182Ser missense_variant 0.5
thyA 3074559 c.-88C>A upstream_gene_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449058 p.Ser185Arg missense_variant 0.22
Rv3083 3449064 c.561A>G synonymous_variant 0.22
Rv3083 3449083 p.Pro194Thr missense_variant 0.25
Rv3083 3449236 p.Arg245Trp missense_variant 0.17
Rv3083 3449940 p.Asp479Glu missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475000 c.994C>T synonymous_variant 0.33
fprA 3475041 c.1035C>T synonymous_variant 0.22
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
Rv3236c 3612317 p.Arg267His missense_variant 0.2
Rv3236c 3612618 p.Pro167Thr missense_variant 0.29
Rv3236c 3613274 c.-158C>T upstream_gene_variant 0.29
fbiA 3640621 p.Gln27* stop_gained 0.2
fbiA 3640631 p.Ala30Gly missense_variant 0.22
fbiA 3640640 p.Ala33Asp missense_variant 0.22
fbiB 3642377 c.843C>A synonymous_variant 0.25
fbiB 3642473 c.942delA frameshift_variant 0.25
alr 3840402 p.Arg340Gln missense_variant 0.4
alr 3840613 p.Gly270Arg missense_variant 0.25
alr 3841378 p.Thr15Ala missense_variant 0.18
alr 3841415 c.6A>G synonymous_variant 0.2
alr 3841508 c.-88C>T upstream_gene_variant 0.25
rpoA 3877948 p.Thr187Ile missense_variant 0.29
rpoA 3878143 p.Gly122Asp missense_variant 0.25
ddn 3986652 c.-192C>T upstream_gene_variant 0.33
ddn 3987054 p.Gly71Trp missense_variant 0.33
clpC1 4038700 p.Gly669Ser missense_variant 0.22
clpC1 4040138 c.567G>T synonymous_variant 0.29
clpC1 4040619 p.Gly29Asp missense_variant 0.29
panD 4044373 c.-92C>A upstream_gene_variant 0.2
embC 4239960 p.Ala33Asp missense_variant 0.29
embC 4240946 p.Glu362* stop_gained 0.17
embC 4241702 p.Arg614Cys missense_variant 0.22
embC 4241884 c.2022G>A synonymous_variant 0.22
embC 4242572 p.Glu904* stop_gained 0.17
embC 4242600 p.Gly913Ala missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242767 p.Arg969Cys missense_variant 0.25
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243482 p.Ala84Pro missense_variant 0.15
embA 4243532 c.300C>T synonymous_variant 0.17
embA 4243595 c.363G>A synonymous_variant 0.17
embA 4245372 p.Pro714Thr missense_variant 0.25
embA 4246435 p.Gln1068Arg missense_variant 0.22
embB 4247558 p.Trp349Arg missense_variant 0.13
embB 4247927 p.Leu472Met missense_variant 0.14
embB 4248919 c.2406C>T synonymous_variant 0.14
embB 4249182 p.His890Arg missense_variant 0.22
embB 4249298 p.Trp929Arg missense_variant 0.33
embB 4249314 p.Phe934Ser missense_variant 0.25
embB 4249534 c.3021C>T synonymous_variant 0.22
aftB 4267230 p.Trp536Leu missense_variant 0.25
ethA 4326142 c.1332C>T synonymous_variant 0.22
ethA 4326173 p.Phe434Tyr missense_variant 0.29
ethR 4328134 p.Glu196* stop_gained 0.33
whiB6 4338177 c.345G>A synonymous_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407778 p.Leu142Ser missense_variant 0.25