TB-Profiler result

Run: SRR4035796
Summary

Run ID: SRR4035796

Sample name:

Date: 04-04-2023 07:18:14

Number of reads: 1403238

Percentage reads mapped: 99.43

Strain: lineage4.1.2

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 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
ethA 4326609 c.864delC frameshift_variant 0.18 ethionamide, ethionamide
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 5540 p.Thr101Ala missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7774 p.Gly158Asp missense_variant 0.15
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490968 c.186C>G synonymous_variant 0.14
fgd1 491283 p.Asp167Glu missense_variant 0.12
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575925 p.Gly193Glu missense_variant 0.17
mshA 575932 c.585G>A synonymous_variant 0.15
mshA 576576 p.Ala410Val missense_variant 0.14
ccsA 620038 p.Pro50Ser missense_variant 0.14
ccsA 620043 c.153C>T synonymous_variant 0.12
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760418 c.612G>C synonymous_variant 0.12
rpoB 760425 p.Glu207Lys missense_variant 0.12
rpoB 761486 c.1680C>G synonymous_variant 0.11
rpoB 761537 c.1731C>G synonymous_variant 0.17
rpoB 762196 p.Val797Ala missense_variant 0.11
rpoB 762756 p.Ser984Thr missense_variant 0.15
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766024 c.2655C>T synonymous_variant 0.12
rpoC 766371 p.Gln1001Leu missense_variant 0.15
rpoC 766380 p.Gly1004Asp missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777166 p.Ser439Thr missense_variant 0.12
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpL5 777557 c.923delA frameshift_variant 0.2
mmpL5 779097 c.-617C>A upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304981 p.Lys684Met missense_variant 0.17
fbiC 1305014 p.Thr695Met missense_variant 0.13
Rv1258c 1406207 c.1134C>A synonymous_variant 0.12
embR 1417340 p.Gly3Val missense_variant 0.13
embR 1417487 c.-140T>C upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475460 n.1803A>G non_coding_transcript_exon_variant 0.11
rrl 1475476 n.1819G>A non_coding_transcript_exon_variant 0.14
rrl 1476748 n.3091A>G non_coding_transcript_exon_variant 0.13
fabG1 1673806 p.Ala123Pro missense_variant 0.1
fabG1 1673882 p.Gly148Asp missense_variant 0.12
rpsA 1833649 c.108C>T synonymous_variant 0.13
rpsA 1834492 c.951C>T synonymous_variant 0.13
rpsA 1834859 p.Ala440Ser missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918232 p.Glu98Gly missense_variant 0.15
tlyA 1918271 p.Ala111Val missense_variant 0.13
ndh 2102471 p.Glu191Gly missense_variant 0.1
katG 2154170 p.Glu648* stop_gained 0.13
katG 2154210 c.1902C>T synonymous_variant 0.15
katG 2155124 p.Asn330Tyr missense_variant 0.13
katG 2155283 p.Gly277Arg missense_variant 0.11
katG 2155307 p.Gly269Ser missense_variant 0.15
PPE35 2170380 p.Ala78Val missense_variant 0.2
PPE35 2170414 p.Ala67Ser missense_variant 0.17
PPE35 2170572 p.Leu14Ser missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289571 c.-330T>A upstream_gene_variant 0.14
pncA 2289599 c.-358A>T upstream_gene_variant 0.14
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2519188 c.1074G>A synonymous_variant 0.18
eis 2714967 c.365delA frameshift_variant 0.17
eis 2714970 c.363C>T synonymous_variant 0.15
eis 2715049 p.Gly95Ala missense_variant 0.11
eis 2715134 p.Leu67Met missense_variant 0.17
folC 2746842 p.Asp253Asn missense_variant 0.25
folC 2747081 p.Val173Asp missense_variant 0.13
ribD 2987242 p.Arg135Leu missense_variant 0.18
Rv2752c 3065885 p.Val103Leu missense_variant 0.13
thyX 3067440 p.Gln169Leu missense_variant 0.13
thyX 3067445 c.501C>T synonymous_variant 0.13
thyX 3067448 p.Gln166His missense_variant 0.13
thyA 3074659 c.-188G>C upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087025 p.Asp69Gly missense_variant 0.11
ald 3087168 p.Tyr117His missense_variant 0.11
fbiD 3339356 p.Leu80Arg missense_variant 0.12
fbiD 3339394 p.Asn93Asp missense_variant 0.1
fbiD 3339586 p.Ala157Thr missense_variant 0.15
Rv3083 3449107 p.Gly202Arg missense_variant 0.14
fprA 3473884 c.-123A>T upstream_gene_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474123 c.117G>C synonymous_variant 0.11
fprA 3474304 c.299delT frameshift_variant 0.18
fprA 3475211 p.His402Arg missense_variant 0.1
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
fbiA 3641128 p.Ala196Thr missense_variant 0.17
fbiB 3642159 p.Leu209Met missense_variant 0.15
fbiB 3642171 p.Pro213Ser missense_variant 0.17
alr 3840731 p.Glu230Asp missense_variant 0.12
alr 3840736 p.Phe229Leu missense_variant 0.12
alr 3840858 p.Val188Ala missense_variant 0.12
alr 3841313 c.108C>A synonymous_variant 0.14
alr 3841551 c.-131G>C upstream_gene_variant 0.11
rpoA 3878495 p.Gln5* stop_gained 0.13
clpC1 4039534 p.Asn391Asp missense_variant 0.11
clpC1 4039692 p.Leu338Pro missense_variant 0.15
embC 4240932 p.Trp357Ser missense_variant 0.12
embC 4241975 p.Gln705Lys missense_variant 0.33
embC 4242020 p.Val720Met missense_variant 0.15
embC 4242042 p.Met727Lys missense_variant 0.15
embA 4242577 c.-656A>G upstream_gene_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4243134 p.Leu1091Ser missense_variant 0.13
embA 4244002 p.Val257Ala missense_variant 0.17
embA 4244509 p.Leu426Ser missense_variant 0.12
embA 4244611 p.Ala460Val missense_variant 0.12
embA 4245064 p.Leu611Pro missense_variant 0.12
embA 4245802 p.Tyr857Phe missense_variant 0.12
embB 4246541 c.29delG frameshift_variant 0.18
embB 4246557 p.Ala15Val missense_variant 0.17
embB 4247207 p.Ala232Ser missense_variant 0.12
embB 4248606 p.Leu698Arg missense_variant 0.11
aftB 4267577 c.1260C>T synonymous_variant 0.18
aftB 4267821 p.Leu339* stop_gained 0.25
ethA 4327058 p.Gly139Ala missense_variant 0.12
ethA 4327398 p.Arg26Cys missense_variant 0.14
ethR 4327653 p.Asn35Lys missense_variant 0.13
ethR 4327691 p.Asp48Gly missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408352 c.-150C>T upstream_gene_variant 0.14