TB-Profiler result

Run: SRR1062857
Summary

Run ID: SRR1062857

Sample name:

Date: 02-04-2023 18:37:00

Number of reads: 4229466

Percentage reads mapped: 98.98

Strain: lineage4.3.2.1;lineage1.1.2

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 0.71
lineage1 Indo-Oceanic EAI RD239 0.33
lineage4.3 Euro-American (LAM) mainly-LAM None 0.63
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.36
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.33
lineage4.3.2 Euro-American (LAM) LAM3 None 0.66
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 0.68
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 0.58
gyrB 5764 c.525C>T synonymous_variant 0.33
gyrB 6112 p.Met291Ile missense_variant 0.29
gyrB 6124 c.885C>T synonymous_variant 0.29
gyrA 7222 c.-80C>T upstream_gene_variant 0.69
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.41
gyrA 9143 c.1842T>C synonymous_variant 0.33
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.32
rpoC 763031 c.-339T>C upstream_gene_variant 0.27
rpoC 763884 p.Ala172Val missense_variant 0.23
rpoC 763886 c.517C>A synonymous_variant 0.21
rpoC 764995 c.1626C>G synonymous_variant 0.67
rpoC 765171 p.Pro601Leu missense_variant 0.41
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.36
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.36
embR 1417481 c.-134G>A upstream_gene_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.67
rpsA 1834885 c.1344G>A synonymous_variant 0.73
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.39
PPE35 2167926 p.Leu896Ser missense_variant 0.27
PPE35 2167983 p.Gly877Asp missense_variant 0.27
Rv1979c 2222308 p.Asp286Gly missense_variant 0.32
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.33
ahpC 2726051 c.-142G>A upstream_gene_variant 0.31
Rv2752c 3064632 c.1560C>T synonymous_variant 0.31
thyA 3073868 p.Thr202Ala missense_variant 0.7
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.3
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.99
fprA 3474597 c.591C>A synonymous_variant 0.33
fprA 3474700 p.Gly232Ser missense_variant 0.28
fprA 3475159 p.Asn385Asp missense_variant 0.37
alr 3841369 p.Arg18Trp missense_variant 0.38
clpC1 4038287 c.2418C>T synonymous_variant 0.72
clpC1 4040517 p.Val63Ala missense_variant 0.28
embC 4240671 p.Thr270Ile missense_variant 0.32
embC 4241042 p.Asn394Asp missense_variant 0.39
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.29
embA 4245969 p.Pro913Ser missense_variant 0.36
embB 4247646 p.Glu378Ala missense_variant 0.26
embB 4249673 p.Ser1054Pro missense_variant 0.31
ubiA 4269387 p.Glu149Asp missense_variant 0.34
aftB 4269606 c.-770T>C upstream_gene_variant 0.34
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.33
whiB6 4338647 c.-126C>G upstream_gene_variant 0.68
gid 4407588 c.615A>G synonymous_variant 0.3
gid 4407873 c.330G>T synonymous_variant 0.18
gid 4407935 p.Leu90Val missense_variant 0.36
gid 4407944 p.Gln87Glu missense_variant 0.38
gid 4408156 p.Leu16Arg missense_variant 0.74