TB-Profiler result

Run: ERR3509865
Summary

Run ID: ERR3509865

Sample name:

Date: 01-04-2023 02:32:41

Number of reads: 358283

Percentage reads mapped: 99.8

Strain: lineage4.3.4.2.1

Drug-resistance: HR-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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 1.0
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
ahpC 2726141 c.-52C>T 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 6049 c.810G>T synonymous_variant 0.12
gyrB 6140 p.Val301Leu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7790 c.489G>T synonymous_variant 0.12
gyrA 8795 c.1494C>T synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491577 c.795G>T synonymous_variant 0.11
rpoB 760161 p.Lys119* stop_gained 0.18
rpoB 761385 p.Ala527Pro missense_variant 0.33
rpoB 763152 p.Lys1116Gln missense_variant 0.11
rpoC 764731 c.1362G>T synonymous_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765080 p.Gly571Trp missense_variant 0.14
rpoC 765499 c.2130C>A synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775644 p.Arg946Gln missense_variant 0.15
mmpL5 775856 c.2625T>C synonymous_variant 0.11
mmpS5 779609 c.-704C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781761 p.Pro68Thr missense_variant 0.11
rplC 801088 p.Glu94Lys missense_variant 0.29
fbiC 1303631 p.Pro234His missense_variant 0.11
fbiC 1304440 p.Arg504Ser missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471849 n.4T>A non_coding_transcript_exon_variant 0.18
rrs 1471989 n.144G>T non_coding_transcript_exon_variant 0.12
rrs 1472934 n.1089C>T non_coding_transcript_exon_variant 0.11
rrs 1473283 n.1440delA non_coding_transcript_exon_variant 0.14
rrl 1474329 n.672G>T non_coding_transcript_exon_variant 0.11
rrl 1476667 n.3010T>C non_coding_transcript_exon_variant 0.17
rrl 1476735 n.3078G>T non_coding_transcript_exon_variant 0.12
rpsA 1833877 c.336C>A synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154958 p.Arg385Leu missense_variant 0.11
PPE35 2167742 c.2871C>A synonymous_variant 0.14
PPE35 2169317 c.1296C>T synonymous_variant 0.22
PPE35 2170568 c.45C>A synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289173 c.69T>C synonymous_variant 0.11
pncA 2289909 c.-668G>A upstream_gene_variant 1.0
eis 2715465 c.-133G>T upstream_gene_variant 0.13
folC 2746238 p.Pro454Gln missense_variant 0.11
Rv2752c 3065178 c.1014G>A synonymous_variant 0.18
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074294 p.Leu60Met missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086891 c.72G>A synonymous_variant 0.17
Rv3083 3448316 c.-188C>T upstream_gene_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474842 p.Lys279Arg missense_variant 0.13
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
fbiB 3641755 p.Arg74Leu missense_variant 0.11
fbiB 3641958 p.Val142Ile missense_variant 0.18
alr 3840719 c.702A>G synonymous_variant 1.0
rpoA 3878582 c.-75C>A upstream_gene_variant 0.25
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4040857 c.-153C>A upstream_gene_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245455 c.2223C>A synonymous_variant 0.11
embB 4246655 p.Pro48Ser missense_variant 0.1
ubiA 4269610 p.Val75Ala missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0