TB-Profiler result

Run: SRR4034064
Summary

Run ID: SRR4034064

Sample name:

Date: 04-04-2023 06:33:05

Number of reads: 685756

Percentage reads mapped: 99.61

Strain: lineage4.3.2.1

Drug-resistance: Sensitive

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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 1.0
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 0.99
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
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 7184 p.Ser649Pro 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 7995 p.Gly232* stop_gained 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 762471 p.Ile889Val missense_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765046 p.Met559Ile missense_variant 0.1
rpoC 766048 c.2679C>A synonymous_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778191 p.Gly97Val missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800658 c.-151T>C upstream_gene_variant 0.11
fbiC 1303172 p.Arg81Met missense_variant 0.13
fbiC 1303536 c.606G>C synonymous_variant 1.0
Rv1258c 1406605 c.736C>T synonymous_variant 0.13
embR 1417175 p.Ala58Asp missense_variant 0.25
embR 1417369 c.-22C>A upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrs 1472612 n.767G>A non_coding_transcript_exon_variant 0.18
rrl 1476164 n.2509G>T non_coding_transcript_exon_variant 0.14
rrl 1476583 n.2926G>T non_coding_transcript_exon_variant 0.12
fabG1 1673246 c.-194G>T upstream_gene_variant 0.12
fabG1 1673452 p.Ala5Ser missense_variant 0.17
inhA 1674075 c.-127C>G upstream_gene_variant 0.14
inhA 1674670 p.Ala157Thr missense_variant 0.29
tlyA 1917953 p.Ala5Asp missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918479 c.540G>T synonymous_variant 0.2
tlyA 1918542 c.603G>A synonymous_variant 0.25
tlyA 1918638 c.699A>C synonymous_variant 0.33
katG 2154193 p.Arg640His missense_variant 0.29
katG 2154879 c.1233C>A synonymous_variant 0.12
katG 2156423 c.-312A>G upstream_gene_variant 0.12
PPE35 2169320 p.Leu431Phe missense_variant 0.13
Rv1979c 2223072 c.93T>C synonymous_variant 0.14
Rv1979c 2223206 c.-42T>C upstream_gene_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289371 c.-130C>A upstream_gene_variant 0.14
pncA 2289447 c.-206G>T upstream_gene_variant 0.11
pncA 2289877 c.-636C>A upstream_gene_variant 0.2
pncA 2290107 c.-866T>A upstream_gene_variant 1.0
pncA 2290237 c.-996G>T upstream_gene_variant 0.13
folC 2747320 c.279C>A synonymous_variant 0.25
pepQ 2859434 p.Tyr329His missense_variant 0.17
ribD 2986805 c.-34G>T upstream_gene_variant 0.14
ribD 2986850 c.12T>C synonymous_variant 0.11
Rv2752c 3064564 c.1627delG frameshift_variant 0.17
Rv2752c 3065394 p.Met266Ile missense_variant 0.15
Rv2752c 3065687 p.Gly169Ser missense_variant 0.14
Rv2752c 3065892 c.300C>A synonymous_variant 0.14
Rv2752c 3066302 c.-111C>G upstream_gene_variant 0.1
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086925 p.Gln36Lys missense_variant 0.11
Rv3083 3448798 p.His99Asn missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568726 c.-47C>A upstream_gene_variant 0.15
Rv3236c 3612213 p.Ala302Thr missense_variant 0.13
fbiB 3641610 p.Gly26Cys missense_variant 0.13
alr 3841603 c.-183C>A upstream_gene_variant 0.12
ddn 3986869 p.Leu9Arg missense_variant 0.15
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039486 p.Gly407Ser missense_variant 0.33
panD 4044171 p.Asp37Glu missense_variant 0.15
embC 4240250 p.Leu130Met missense_variant 0.22
embC 4240911 p.Ala350Glu missense_variant 0.17
embC 4242028 c.2166G>A synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4246339 p.Leu1036Pro missense_variant 0.15
embB 4248073 c.1560C>T synonymous_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0