TB-Profiler result

Run: SRR11972193
Summary

Run ID: SRR11972193

Sample name:

Date: 03-04-2023 05:31:34

Number of reads: 229640

Percentage reads mapped: 99.15

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 2289207 p.Asp12Ala missense_variant 1.0 pyrazinamide
ahpC 2726145 c.-48G>A upstream_gene_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 5412 p.Met58Thr missense_variant 0.1
gyrB 6047 p.Ala270Thr missense_variant 0.29
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7752 p.Asp151Asn missense_variant 0.2
gyrA 9275 p.Glu658Asp missense_variant 0.12
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 620625 p.Ile245Met missense_variant 1.0
rpoB 761773 p.His656Pro missense_variant 1.0
rpoB 761815 p.Ala670Val missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763969 c.600C>T synonymous_variant 0.22
rpoC 764817 p.Val483Gly missense_variant 1.0
rpoC 766014 p.Gln882Arg missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
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 1.0
rplC 800808 c.-1A>T upstream_gene_variant 0.13
rplC 800921 p.Arg38His missense_variant 0.12
fbiC 1305442 p.Glu838Lys missense_variant 0.13
Rv1258c 1406506 p.Ala279Thr missense_variant 0.2
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473512 n.-146C>T upstream_gene_variant 0.33
rrl 1475714 n.2057G>A non_coding_transcript_exon_variant 0.25
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
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168026 p.Ala863Pro missense_variant 0.29
PPE35 2169003 c.1607_1609delCGT disruptive_inframe_deletion 0.15
PPE35 2170454 c.159C>G synonymous_variant 0.11
PPE35 2170457 c.156G>C synonymous_variant 0.11
PPE35 2170460 c.153G>A synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518230 p.Gly39Asp missense_variant 0.13
ahpC 2725960 c.-233A>G upstream_gene_variant 0.14
Rv2752c 3064653 c.1539A>T synonymous_variant 0.29
thyX 3067262 c.684C>A synonymous_variant 0.17
thyX 3067969 c.-24G>A upstream_gene_variant 0.2
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 3840356 c.1065T>C synonymous_variant 0.14
ddn 3987174 p.Ala111Thr missense_variant 0.17
clpC1 4038557 c.2148C>A synonymous_variant 0.2
clpC1 4039543 p.Arg388Cys missense_variant 0.12
clpC1 4040714 c.-10G>T upstream_gene_variant 0.13
embC 4241105 p.Arg415Trp missense_variant 0.17
embC 4241139 p.Ala426Val missense_variant 0.18
embC 4241457 p.Ala532Val missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.92
embB 4247717 p.Leu402Val missense_variant 1.0
embB 4247723 p.Pro404Ala missense_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4328463 c.-990G>T upstream_gene_variant 0.14
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