TB-Profiler result

Run: SRR11972318
Summary

Run ID: SRR11972318

Sample name:

Date: 03-04-2023 05:36:56

Number of reads: 1659797

Percentage reads mapped: 98.44

Strain: lineage2.2.1

Drug-resistance: MDR-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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288752 p.Ser164Pro missense_variant 0.11 pyrazinamide
pncA 2288887 p.Trp119Gly missense_variant 1.0 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7926 p.Asp209Asn missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575525 p.Pro60Ser missense_variant 0.13
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761773 p.His656Pro missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776009 c.2472A>G synonymous_variant 0.1
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 0.96
fbiC 1303771 p.His281Asn missense_variant 0.17
fbiC 1304373 c.1443C>T synonymous_variant 0.12
Rv1258c 1406162 c.1179C>T synonymous_variant 0.13
Rv1258c 1406229 p.Thr371Ile missense_variant 0.15
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474946 n.1289C>A non_coding_transcript_exon_variant 0.18
inhA 1674487 p.Gly96Arg missense_variant 0.11
rpsA 1834047 p.Ile169Ser missense_variant 0.74
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155378 p.Ala245Val missense_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726213 c.21C>T synonymous_variant 0.12
pepQ 2860186 p.Ala78Val missense_variant 0.15
Rv2752c 3065193 c.998delT frameshift_variant 1.0
thyX 3067629 c.316delC frameshift_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339072 c.-46T>C upstream_gene_variant 0.12
Rv3083 3449052 c.549C>T synonymous_variant 0.14
Rv3083 3449255 p.Gln251Leu missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474773 p.Ala256Val missense_variant 0.22
fprA 3475077 c.1074delG frameshift_variant 0.12
Rv3236c 3612527 p.Ala197Val missense_variant 0.15
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3641303 p.Gly254Asp missense_variant 0.22
alr 3841154 c.267C>G synonymous_variant 0.17
embC 4240578 p.Ala239Val missense_variant 0.15
embC 4241218 c.1356G>A synonymous_variant 0.15
embC 4241305 c.1443C>T synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242741 p.Leu960Pro missense_variant 0.17
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246936 c.423G>A synonymous_variant 0.12
embB 4247197 c.685delA frameshift_variant 0.15
embB 4247717 p.Leu402Val missense_variant 1.0
aftB 4267086 p.Leu584Arg missense_variant 0.12
aftB 4267405 p.Pro478Ser missense_variant 0.12
aftB 4267408 p.Lys477Glu missense_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268537 c.300G>A synonymous_variant 0.15
aftB 4269558 c.-722C>T upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0