TB-Profiler result

Run: SRR1180972
Summary

Run ID: SRR1180972

Sample name:

Date: 03-04-2023 04:18:40

Number of reads: 978496

Percentage reads mapped: 86.05

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 2288818 p.Thr142Ala missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326120 c.1353delG frameshift_variant 0.12 ethionamide
ethA 4326159 c.1305_1314delCCCAGGTTAC frameshift_variant 0.12 ethionamide
ethA 4327441 c.32delG frameshift_variant 0.21 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
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 491452 p.Gly224Cys missense_variant 0.12
fgd1 491481 c.699C>A synonymous_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 1.0
fgd1 491756 p.Gln325Pro missense_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 762888 p.His1028Asn missense_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765618 p.Glu750Gly missense_variant 1.0
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 778300 p.Ala61Ser missense_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304055 p.Asp375Glu missense_variant 0.11
fbiC 1304813 p.Met628Thr missense_variant 0.11
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407424 c.-84C>T upstream_gene_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.15
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.16
rrs 1472129 n.284G>A non_coding_transcript_exon_variant 0.16
rrs 1472135 n.290C>T non_coding_transcript_exon_variant 0.17
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.17
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.18
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.18
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.18
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.19
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.18
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.28
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.19
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.19
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.17
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.16
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.16
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.16
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.15
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.13
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.14
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.15
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.12
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917880 c.-60C>A upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156311 c.-200C>A upstream_gene_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714526 c.805_806delAC frameshift_variant 1.0
eis 2714787 p.Trp182Cys missense_variant 0.12
pepQ 2859480 c.939C>T synonymous_variant 0.12
Rv2752c 3067014 c.-823G>A upstream_gene_variant 0.12
thyX 3067508 c.438G>T synonymous_variant 0.14
thyX 3068060 c.-115T>G upstream_gene_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087760 p.Thr314Asn missense_variant 0.12
fbiD 3339128 p.Thr4Arg missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474240 p.Phe78Leu missense_variant 0.11
whiB7 3568520 p.Ala54Pro missense_variant 0.11
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243136 p.Arg1092Gly missense_variant 0.14
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269304 p.Leu177Trp missense_variant 1.0
ethA 4326300 p.Thr392Pro missense_variant 0.1
whiB6 4338365 p.Cys53Arg missense_variant 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 1.0
gid 4407998 p.Gly69Cys missense_variant 0.14