TB-Profiler result

Run: ERR2229742
Summary

Run ID: ERR2229742

Sample name:

Date: 31-03-2023 17:31:11

Number of reads: 542399

Percentage reads mapped: 99.04

Strain: lineage4

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
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 1917946 p.Arg3* stop_gained 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
gyrA 6631 c.-671C>A upstream_gene_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576338 p.Gln331Lys missense_variant 0.4
ccsA 620263 p.Gly125Ser missense_variant 0.25
rpoB 760223 c.417T>C synonymous_variant 0.14
rpoB 762652 p.Trp949* stop_gained 0.29
rpoC 763874 c.507delA frameshift_variant 0.25
rpoC 765817 c.2448G>T synonymous_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777128 c.1353A>G synonymous_variant 0.22
mmpL5 777157 c.1324C>A synonymous_variant 0.2
mmpL5 777164 c.1317C>T synonymous_variant 0.22
mmpL5 777173 c.1308C>T synonymous_variant 0.2
mmpL5 777176 p.Glu435Asp missense_variant 0.2
mmpL5 778107 p.Ser125Tyr missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304137 p.Ala403Thr missense_variant 0.67
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471670 n.-176G>T upstream_gene_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474523 n.866C>A non_coding_transcript_exon_variant 0.25
rrl 1474988 n.1331C>A non_coding_transcript_exon_variant 0.22
rrl 1475031 n.1374G>T non_coding_transcript_exon_variant 0.33
fabG1 1673346 c.-94C>G upstream_gene_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.15
fabG1 1673887 p.Gln150Lys missense_variant 0.12
fabG1 1674047 p.Leu203Pro missense_variant 0.2
rpsA 1833460 c.-82G>C upstream_gene_variant 0.2
rpsA 1833787 c.246C>T synonymous_variant 0.17
rpsA 1833853 c.312G>A synonymous_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918246 p.Arg103Ser missense_variant 0.25
katG 2154145 p.Asp656Gly missense_variant 0.14
PPE35 2167955 c.2658A>C synonymous_variant 0.13
PPE35 2167965 p.Ala883Gly missense_variant 0.27
PPE35 2167967 c.2646A>C synonymous_variant 0.27
PPE35 2168174 p.Gln813His missense_variant 0.18
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169207 p.Gly469Val missense_variant 0.12
PPE35 2169351 p.Ala421Gly missense_variant 0.12
PPE35 2169902 c.711G>C synonymous_variant 0.12
PPE35 2169941 c.672C>T synonymous_variant 0.19
PPE35 2170048 p.Leu189Val missense_variant 0.53
PPE35 2170053 p.Thr187Ser missense_variant 0.53
PPE35 2170187 p.Glu142Gln missense_variant 0.16
PPE35 2170527 p.Ser29Val missense_variant 0.14
Rv1979c 2222193 c.972G>T synonymous_variant 0.14
Rv1979c 2222481 c.684G>T synonymous_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289157 p.Arg29Cys missense_variant 0.14
pncA 2289169 p.Ala25Thr missense_variant 0.12
pncA 2290084 c.-843T>C upstream_gene_variant 0.67
kasA 2518809 p.Lys232Arg missense_variant 0.2
kasA 2518839 p.Ala242Gly missense_variant 0.15
kasA 2518843 c.729T>C synonymous_variant 0.17
kasA 2518846 c.732G>C synonymous_variant 0.18
kasA 2518849 c.735G>T synonymous_variant 0.18
kasA 2518850 p.Met246Leu missense_variant 0.2
kasA 2518853 c.739_741delCTCinsTTG synonymous_variant 0.17
kasA 2518864 c.750G>C synonymous_variant 0.13
ahpC 2726215 p.Asp8Gly missense_variant 0.17
pepQ 2859456 c.962delT frameshift_variant 0.29
pepQ 2860441 c.-23C>T upstream_gene_variant 0.12
Rv2752c 3065824 p.Pro123Leu missense_variant 0.2
thyX 3067571 c.375C>T synonymous_variant 0.22
ald 3086649 c.-171C>A upstream_gene_variant 0.15
Rv3083 3448456 c.-48G>A upstream_gene_variant 0.4
whiB7 3568401 c.279G>T stop_lost&splice_region_variant 0.25
alr 3841030 p.Ala131Thr missense_variant 0.2
embC 4240723 c.865delG frameshift_variant 0.17
embC 4241069 p.Ala403Ser missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245012 p.Arg594Cys missense_variant 0.17
embB 4247970 c.1458dupC frameshift_variant 0.22
whiB6 4338301 p.Gly74Val missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407647 p.Val186Ile missense_variant 0.17
gid 4408210 c.-8A>G upstream_gene_variant 0.13
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0