TB-Profiler result

Run: SRR11972446
Summary

Run ID: SRR11972446

Sample name:

Date: 03-04-2023 05:42:39

Number of reads: 1320264

Percentage reads mapped: 88.56

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 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
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 2288805 p.Ala146Glu missense_variant 0.93 pyrazinamide
embA 4243221 c.-12C>T upstream_gene_variant 0.97 ethambutol
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 619867 c.-24C>G upstream_gene_variant 0.15
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761998 p.Leu731Pro missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764058 p.Ala230Val missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775955 p.Ile842Val missense_variant 0.12
mmpL5 776100 p.Thr794Ile missense_variant 0.94
mmpL5 776182 p.Asp767Asn missense_variant 0.96
mmpR5 779363 p.Leu125Arg missense_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 0.95
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.23
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102401 c.642T>C synonymous_variant 0.11
ndh 2102407 c.636T>C synonymous_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155354 p.Arg253Pro missense_variant 0.1
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.41
PPE35 2170053 p.Thr187Ser missense_variant 0.41
PPE35 2170066 p.Ala183Thr missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747437 p.Met54Ile missense_variant 1.0
ribD 2987151 p.His105Asn missense_variant 0.14
Rv2752c 3064860 c.1332G>A synonymous_variant 0.12
thyA 3074136 c.336C>T synonymous_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086997 p.Thr60Gly missense_variant 0.13
fbiD 3339050 c.-68C>T upstream_gene_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642201 p.Ser223Thr missense_variant 0.12
rpoA 3878641 c.-134C>G upstream_gene_variant 0.29
embC 4241114 p.Ala418Thr missense_variant 0.12
embC 4241958 p.Arg699Leu missense_variant 1.0
embC 4242414 p.Leu851Pro missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.2
embB 4246548 p.Pro12Gln missense_variant 0.18
embB 4246555 c.42G>C synonymous_variant 0.2
embB 4246556 p.Ala15Pro missense_variant 0.2
embB 4246563 p.Leu17Trp missense_variant 0.15
embB 4246567 c.54G>T synonymous_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 0.95
ethA 4327472 c.2T>G start_lost 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.95