TB-Profiler result

Run: SRR11972247
Summary

Run ID: SRR11972247

Sample name:

Date: 03-04-2023 05:33:23

Number of reads: 161600

Percentage reads mapped: 99.46

Strain:

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
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.93
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 761109 p.Asp435Tyr missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247574 p.Asp354Ala missense_variant 0.58 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
gyrB 5075 c.-165C>T upstream_gene_variant 0.22
gyrB 5172 c.-68C>T upstream_gene_variant 0.14
gyrB 5653 c.414G>A synonymous_variant 0.33
gyrB 5673 p.Glu145Val missense_variant 0.2
gyrB 5836 c.597C>T synonymous_variant 0.29
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7935 p.Glu212* stop_gained 0.13
gyrA 8039 c.740delG frameshift_variant 0.25
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491124 c.342C>T synonymous_variant 0.67
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759664 c.-143G>A upstream_gene_variant 0.22
rpoB 760519 p.Thr238Ile missense_variant 0.4
rpoB 760917 p.Arg371Gly missense_variant 0.5
rpoB 762311 c.2505C>T synonymous_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763151 c.-219C>T upstream_gene_variant 0.33
rpoC 764695 c.1326T>A synonymous_variant 0.67
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777757 p.Ala242Thr missense_variant 0.25
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801361 p.Val185Leu missense_variant 0.22
fbiC 1303836 c.906G>A synonymous_variant 0.5
fbiC 1304894 p.Gly655Asp missense_variant 1.0
fbiC 1305449 p.Ile840Thr missense_variant 0.18
Rv1258c 1406484 p.Pro286His missense_variant 0.29
embR 1417368 c.-21G>A upstream_gene_variant 0.18
embR 1417390 c.-43A>T upstream_gene_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471856 n.11A>G non_coding_transcript_exon_variant 0.13
rrs 1473216 n.1371C>T non_coding_transcript_exon_variant 0.12
rrs 1473228 n.1383T>A non_coding_transcript_exon_variant 0.12
rrl 1473514 n.-144C>T upstream_gene_variant 0.17
rrl 1473658 n.1T>C non_coding_transcript_exon_variant 0.18
rrl 1474553 n.896T>C non_coding_transcript_exon_variant 1.0
rrl 1476085 n.2428G>A non_coding_transcript_exon_variant 0.18
fabG1 1674044 p.Ala202Glu missense_variant 0.15
inhA 1674415 p.Ala72Thr missense_variant 0.4
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834423 c.882G>A synonymous_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102975 p.Gly23Glu missense_variant 0.33
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.5
PPE35 2169910 p.Asn235Tyr missense_variant 0.5
PPE35 2170198 p.Ala139Thr missense_variant 0.25
Rv1979c 2222838 c.327G>A synonymous_variant 0.29
Rv1979c 2222902 p.Arg88His missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289345 c.-104G>A upstream_gene_variant 0.5
eis 2714846 p.Val163Ile missense_variant 1.0
ribD 2986971 p.Phe45Ile missense_variant 0.4
ribD 2987021 c.183G>A synonymous_variant 0.4
thyA 3073857 c.615C>T synonymous_variant 0.4
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3841510 c.-90A>G upstream_gene_variant 0.25
alr 3841539 c.-119C>T upstream_gene_variant 0.2
alr 3841546 c.-126C>A upstream_gene_variant 0.43
alr 3841612 c.-193_-192insC upstream_gene_variant 0.17
ddn 3986944 p.Gly34Val missense_variant 0.25
clpC1 4040166 p.Ala180Val missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243269 p.Ala13Thr missense_variant 0.18
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243505 c.273C>G synonymous_variant 0.22
embA 4245116 c.1884C>T synonymous_variant 0.17
embA 4246143 p.Ile971Phe missense_variant 0.29
embB 4247137 c.624C>A synonymous_variant 0.2
embB 4248115 c.1602C>T synonymous_variant 1.0
embB 4249455 p.Thr981Met missense_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268267 c.570G>T synonymous_variant 0.17
aftB 4268487 p.Met117Thr missense_variant 0.17
whiB6 4338379 p.Glu48Gly missense_variant 0.22
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