TB-Profiler result

Run: SRR11972348
Summary

Run ID: SRR11972348

Sample name:

Date: 03-04-2023 05:38:09

Number of reads: 1611075

Percentage reads mapped: 99.19

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 761095 p.Leu430Pro missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 5900 p.Glu221Lys missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491361 c.579C>A synonymous_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761684 c.1878G>A synonymous_variant 0.14
rpoB 761701 p.Ala632Val missense_variant 0.12
rpoB 761879 c.2073G>A synonymous_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764012 p.Glu215Lys missense_variant 0.11
rpoC 767203 c.3834C>A synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406306 c.1035C>A synonymous_variant 0.13
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.17
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.2
rrs 1472195 n.350G>A non_coding_transcript_exon_variant 0.14
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.18
rrs 1472378 n.533G>T non_coding_transcript_exon_variant 0.22
rrs 1472379 n.534T>C non_coding_transcript_exon_variant 0.25
rrs 1472380 n.535G>C non_coding_transcript_exon_variant 0.25
rrs 1472396 n.551A>T non_coding_transcript_exon_variant 0.13
rrl 1474967 n.1313delG non_coding_transcript_exon_variant 0.2
rrl 1475397 n.1740G>A non_coding_transcript_exon_variant 0.12
inhA 1674687 c.486G>T synonymous_variant 0.11
rpsA 1833706 c.165C>T synonymous_variant 0.11
rpsA 1834125 p.Gln195Arg missense_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918362 c.423G>A synonymous_variant 0.11
katG 2154424 p.Ile563Thr missense_variant 0.1
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156019 c.93G>A synonymous_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223337 c.-173C>A upstream_gene_variant 0.11
ahpC 2726260 p.Leu23Pro missense_variant 0.11
folC 2747426 p.Gly58Asp missense_variant 0.11
Rv2752c 3067046 c.-855G>T upstream_gene_variant 0.12
thyX 3067286 c.660C>T synonymous_variant 1.0
thyA 3073721 p.Tyr251His missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339614 c.498delG frameshift_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474353 p.Gly116Asp missense_variant 0.13
fprA 3474359 c.355delC frameshift_variant 0.25
whiB7 3568582 p.Pro33Gln missense_variant 1.0
Rv3236c 3612113 c.1002_1003dupGG frameshift_variant 0.12
Rv3236c 3612601 c.516C>T synonymous_variant 0.12
Rv3236c 3612644 p.Glu158Val missense_variant 0.13
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613154 c.-38C>T upstream_gene_variant 0.12
fbiA 3641006 p.Val155Ala missense_variant 0.12
fbiB 3641196 c.-339C>A upstream_gene_variant 0.12
alr 3840911 c.510A>G synonymous_variant 0.1
clpC1 4039221 p.Pro495Leu missense_variant 0.13
clpC1 4040104 p.Met201Val missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243372 p.Gln47Arg missense_variant 0.11
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244061 c.831delT frameshift_variant 0.11
embA 4246507 p.Ala1092Val missense_variant 0.12
embB 4246567 c.54_55insT frameshift_variant 0.17
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267775 c.1062T>A synonymous_variant 0.17
aftB 4267886 c.951C>T synonymous_variant 0.25
aftB 4268456 c.381G>T synonymous_variant 0.18
ethA 4326676 p.Ser266Arg missense_variant 1.0
whiB6 4338393 c.129G>A synonymous_variant 0.11
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