TB-Profiler result

Run: ERR2229092
Summary

Run ID: ERR2229092

Sample name:

Date: 31-03-2023 16:38:12

Number of reads: 507448

Percentage reads mapped: 99.35

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
gid 4407967 p.Leu79* stop_gained 0.2 streptomycin
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 7005 p.Gly589Asp missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 491687 c.906delA frameshift_variant 0.29
rpoB 762370 p.Leu855Ser missense_variant 0.2
rpoC 765120 p.Gly584Val missense_variant 0.14
rpoC 765993 p.Arg875Gln missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777718 p.Ile255Phe missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781934 c.375A>T stop_lost&splice_region_variant 0.2
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1305344 p.Asn805Ser missense_variant 0.12
embR 1416232 c.1116T>C synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476575 n.2918C>A non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918616 p.Lys226Thr missense_variant 0.25
katG 2155670 p.Leu148Met missense_variant 0.25
PPE35 2167865 c.2748G>C synonymous_variant 0.18
PPE35 2167868 c.2745A>C synonymous_variant 0.17
PPE35 2167965 p.Ala883Gly missense_variant 0.18
PPE35 2167967 c.2646A>C synonymous_variant 0.17
PPE35 2168140 p.Ala825Thr missense_variant 0.25
PPE35 2168143 p.Phe824Leu missense_variant 0.25
PPE35 2168150 c.2463T>C synonymous_variant 0.5
PPE35 2168298 p.Pro772Gln missense_variant 0.25
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.12
PPE35 2169272 c.1341C>G synonymous_variant 0.13
PPE35 2169278 c.1335T>C synonymous_variant 0.21
PPE35 2169281 c.1332T>G synonymous_variant 0.23
PPE35 2169287 c.1326T>C synonymous_variant 0.36
PPE35 2169293 c.1320T>C synonymous_variant 0.15
PPE35 2169902 c.711G>C synonymous_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.63
PPE35 2170053 p.Thr187Ser missense_variant 0.7
PPE35 2170065 p.Ala183Gly missense_variant 0.21
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288897 c.345A>G synonymous_variant 0.12
eis 2714998 p.Gly112Asp missense_variant 0.5
pepQ 2860159 p.Ala87Gly missense_variant 0.25
Rv2752c 3065256 p.Met312Ile missense_variant 0.14
Rv2752c 3065933 p.Ile87Phe missense_variant 0.2
Rv3236c 3611964 p.Asn385Asp missense_variant 0.33
alr 3841349 c.72C>T synonymous_variant 0.18
alr 3841546 c.-126C>A upstream_gene_variant 0.31
rpoA 3877544 p.Gly322Ser missense_variant 0.17
rpoA 3877954 p.Gln185Arg missense_variant 0.33
rpoA 3878704 c.-197C>A upstream_gene_variant 0.22
clpC1 4039153 p.Ile518Val missense_variant 0.17
clpC1 4039161 p.His515Gly missense_variant 0.33
clpC1 4039169 p.Glu512Asp missense_variant 0.3
clpC1 4039178 c.1527G>C synonymous_variant 0.2
clpC1 4039526 c.1179G>C synonymous_variant 0.5
clpC1 4039530 p.Asp392Ala missense_variant 0.5
clpC1 4039730 c.975C>G synonymous_variant 0.25
clpC1 4039829 p.Leu292Ile missense_variant 0.29
panD 4043927 p.His119Tyr missense_variant 0.15
embC 4240843 c.981C>T synonymous_variant 0.14
embC 4240847 p.Asp329Asn missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244272 p.Leu347Gln missense_variant 0.4
embB 4246555 c.42G>C synonymous_variant 1.0
embB 4246556 p.Ala15Pro missense_variant 1.0
embB 4246563 p.Leu17Trp missense_variant 0.67
embB 4246567 c.54G>T synonymous_variant 0.33
embB 4247470 c.957T>C synonymous_variant 0.15
embB 4247472 p.Phe320Tyr missense_variant 0.15
embB 4249363 c.2850C>T synonymous_variant 0.14
ubiA 4269103 p.Ser244Ile missense_variant 0.25
ubiA 4269550 p.Gly95Asp missense_variant 0.18
ethA 4326786 p.Pro230Thr missense_variant 0.13
whiB6 4338195 c.305_326delACGGTTACCCGGTGCGCGACCA frameshift_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0