TB-Profiler result

Run: SRR6896199

Summary

Run ID: SRR6896199

Sample name:

Date: 04-04-2023 17:58:34

Number of reads: 486223

Percentage reads mapped: 99.29

Strain: lineage4.3.2.1

Drug-resistance: Other


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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
lineage4.3.2 Euro-American (LAM) LAM3 None 0.99
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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
tlyA 1918634 p.Gly232Asp missense_variant 0.12 capreomycin
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 5520 p.Pro94Leu missense_variant 1.0
gyrB 5553 p.Ala105Asp missense_variant 0.12
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9148 p.Gly616Val missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575419 c.72C>A synonymous_variant 0.13
mshA 575558 p.Tyr71His missense_variant 0.11
rpoB 759611 c.-195delC upstream_gene_variant 0.11
rpoB 761547 p.Val581Met missense_variant 0.12
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776497 p.Leu662Met missense_variant 0.12
mmpL5 777355 p.Val376Leu missense_variant 0.11
mmpL5 778197 p.Leu95Pro missense_variant 0.12
mmpS5 778860 p.Val16Phe missense_variant 0.12
mmpR5 779467 c.479delG frameshift_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416677 p.Ala224Val missense_variant 0.13
embR 1416691 p.Asp219Glu missense_variant 0.14
embR 1417212 p.Arg46Ser missense_variant 0.12
embR 1417355 c.-8G>C upstream_gene_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1474053 n.396G>T non_coding_transcript_exon_variant 0.12
rrl 1475080 n.1423G>T non_coding_transcript_exon_variant 0.12
rrl 1475159 n.1503delT non_coding_transcript_exon_variant 0.12
rrl 1475837 n.2180C>A non_coding_transcript_exon_variant 0.11
rrl 1476109 n.2452C>A non_coding_transcript_exon_variant 0.12
inhA 1674247 p.Ile16Val missense_variant 0.11
inhA 1674408 p.Glu69Asp missense_variant 0.12
rpsA 1833477 c.-65C>G upstream_gene_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918442 p.Val168Ala missense_variant 0.12
tlyA 1918614 c.675C>T synonymous_variant 0.14
tlyA 1918623 c.684C>T synonymous_variant 0.14
katG 2154432 c.1680C>A synonymous_variant 0.11
katG 2154870 c.1242G>A synonymous_variant 0.11
katG 2155851 c.261G>A synonymous_variant 0.17
katG 2156013 c.99C>G synonymous_variant 0.11
katG 2156362 c.-251C>A upstream_gene_variant 0.12
PPE35 2168521 p.Gln698Lys missense_variant 0.15
PPE35 2170519 p.Asp32Asn missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288741 c.501C>A synonymous_variant 0.14
pncA 2290070 c.-829G>A upstream_gene_variant 0.17
kasA 2518106 c.-9C>A upstream_gene_variant 0.13
kasA 2518348 c.234A>T synonymous_variant 0.33
kasA 2518809 p.Lys232Met missense_variant 0.12
kasA 2518812 p.Asp233Ala missense_variant 0.11
kasA 2518814 c.703_708delGACGGC conservative_inframe_deletion 0.12
kasA 2518823 p.Phe237Ile missense_variant 0.12
kasA 2518826 p.Val238Met missense_variant 0.12
kasA 2518829 p.Phe239Val missense_variant 0.12
ahpC 2726174 c.-19T>C upstream_gene_variant 0.1
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086878 p.Pro20Gln missense_variant 0.11
fbiD 3339529 p.Ser138Gly missense_variant 0.11
Rv3083 3449845 c.1343delA frameshift_variant 0.1
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3611961 c.1156T>C stop_lost&splice_region_variant 0.1
Rv3236c 3612975 p.Ile48Val missense_variant 0.1
Rv3236c 3613255 c.-139G>T upstream_gene_variant 0.11
fbiA 3640386 c.-157A>G upstream_gene_variant 0.11
fbiB 3641948 c.414G>A synonymous_variant 0.11
fbiB 3642424 p.Phe297Ser missense_variant 0.1
rpoA 3877862 p.Val216Phe missense_variant 0.11
rpoA 3877974 c.534G>T synonymous_variant 0.12
ddn 3986983 p.Ala47Glu missense_variant 0.12
ddn 3987024 p.Val61Ile missense_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039310 p.Glu465Asp missense_variant 0.12
clpC1 4039528 c.1177C>A synonymous_variant 0.13
panD 4044299 c.-18A>T upstream_gene_variant 0.12
embC 4242447 p.Ala862Asp missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244672 c.1440C>A synonymous_variant 0.12
embA 4246002 p.Asn924Asp missense_variant 0.14
embB 4246070 c.-444G>T upstream_gene_variant 0.18
embB 4246331 c.-183C>A upstream_gene_variant 0.12
embB 4247638 c.1125G>A synonymous_variant 0.17
embB 4247710 p.Asn399Lys missense_variant 0.14
embB 4248251 p.Gly580Cys missense_variant 0.13
embB 4248985 c.2472T>C synonymous_variant 0.15
embB 4249554 p.Ile1014Thr missense_variant 0.17
ubiA 4269675 p.Ser53Arg missense_variant 0.1
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407879 c.324G>T synonymous_variant 0.11
gid 4407969 c.234A>G synonymous_variant 0.11
gid 4408156 p.Leu16Arg missense_variant 1.0