TB-Profiler result

Run: SRR2101497
Summary

Run ID: SRR2101497

Sample name:

Date: 03-04-2023 23:45:06

Number of reads: 698461

Percentage reads mapped: 99.64

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 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
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 6648 p.Gly470Asp missense_variant 0.22
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 7966 p.Arg222Leu missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 619973 c.94_96delCTG conservative_inframe_deletion 0.17
ccsA 620748 c.858T>G synonymous_variant 0.25
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1461183 p.Gly47Trp missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472067 n.222G>C non_coding_transcript_exon_variant 0.11
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.14
rrl 1475611 n.1954T>C non_coding_transcript_exon_variant 0.12
rpsA 1833343 c.-199G>T upstream_gene_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167810 p.Asn935Asp missense_variant 0.17
PPE35 2169377 p.Phe412Leu missense_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714352 c.981C>A synonymous_variant 0.1
folC 2746745 p.Val285Gly missense_variant 0.21
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074648 c.-177T>G upstream_gene_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087560 c.741C>A synonymous_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475255 c.1249C>T synonymous_variant 0.13
fprA 3475326 c.1320C>A synonymous_variant 0.17
fprA 3475329 c.1323G>T synonymous_variant 0.18
rpoA 3878436 c.72A>G synonymous_variant 0.12
rpoA 3878559 c.-53_-52insC upstream_gene_variant 0.67
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4239973 c.111T>G synonymous_variant 0.19
embC 4240286 p.Ala142Ser missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.12
embB 4246555 c.42G>C synonymous_variant 0.12
embB 4246556 p.Ala15Pro missense_variant 0.12
aftB 4268663 c.173delA frameshift_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407604 p.Ala200Gly missense_variant 0.11
gid 4408156 p.Leu16Arg missense_variant 1.0