TB-Profiler result

Run: ERR2229155
Summary

Run ID: ERR2229155

Sample name:

Date: 31-03-2023 16:44:53

Number of reads: 555238

Percentage reads mapped: 99.42

Strain: lineage4.8

Drug-resistance: HR-TB

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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
tlyA 1918622 c.686delC frameshift_variant 0.15 capreomycin
katG 2153932 p.Ala727Asp missense_variant 0.13 isoniazid
thyA 3074201 p.Gly91Arg missense_variant 0.2 para-aminosalicylic_acid
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 7362 p.Glu21Gln missense_variant 1.0
fgd1 490846 p.Glu22* stop_gained 0.18
fgd1 491735 p.Arg318His missense_variant 0.17
mshA 575881 p.His178Gln missense_variant 0.4
mshA 576108 p.Ala254Gly missense_variant 0.33
ccsA 620024 p.Ala45Val missense_variant 0.29
ccsA 620130 c.240G>T synonymous_variant 0.33
ccsA 620862 c.972C>T synonymous_variant 0.15
rpoB 760115 c.309C>T synonymous_variant 0.15
rpoB 760510 p.Leu235Pro missense_variant 0.13
rpoB 762028 p.Leu741His missense_variant 0.15
rpoC 763241 c.-129G>A upstream_gene_variant 0.12
rpoC 766363 c.2994G>A synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776433 p.Ser683* stop_gained 0.5
mmpL5 778426 p.Ala19Ser missense_variant 0.15
mmpR5 779276 p.Arg96Leu missense_variant 0.29
mmpR5 779353 p.Leu122Met missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781860 p.Ser101Pro missense_variant 0.12
rplC 800731 c.-78A>G upstream_gene_variant 0.14
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475584 n.1927T>C non_coding_transcript_exon_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918391 p.Val151Glu missense_variant 0.14
tlyA 1918609 p.Gly224Cys missense_variant 0.18
katG 2153911 p.Leu734Pro missense_variant 0.15
katG 2156117 c.-6A>T upstream_gene_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169272 c.1341C>G synonymous_variant 0.13
PPE35 2169278 c.1335T>C synonymous_variant 0.13
PPE35 2169281 c.1332T>G synonymous_variant 0.19
PPE35 2169902 p.Leu237Phe missense_variant 0.3
PPE35 2169910 p.Asn235Tyr missense_variant 0.27
PPE35 2170048 p.Leu189Val missense_variant 0.26
PPE35 2170053 p.Thr187Ser missense_variant 0.35
PPE35 2170139 c.474G>A synonymous_variant 0.14
PPE35 2170147 p.Ser156Ala missense_variant 0.19
PPE35 2170159 p.Ala152Ser missense_variant 0.15
Rv1979c 2222962 p.Ala68Glu missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289163 c.79C>T synonymous_variant 0.13
eis 2714521 p.Pro271Gln missense_variant 0.14
folC 2746749 p.Gly284Trp missense_variant 0.2
folC 2746949 p.Ala217Glu missense_variant 0.18
folC 2747473 c.126C>T synonymous_variant 0.17
Rv2752c 3064895 p.Ala433Ser missense_variant 0.25
Rv2752c 3065556 c.636G>T synonymous_variant 0.33
ald 3086937 p.Gly40Arg missense_variant 0.12
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fprA 3474703 p.Ile233Val missense_variant 0.14
fbiA 3641378 p.Arg279Leu missense_variant 0.17
fbiB 3642219 p.Ala229Ser missense_variant 0.29
fbiB 3642512 p.Leu326Phe missense_variant 0.14
fbiB 3642595 p.Pro354Leu missense_variant 0.12
fbiB 3642749 c.1215T>C synonymous_variant 0.15
alr 3840502 p.Leu307Val missense_variant 0.2
alr 3841546 c.-126C>A upstream_gene_variant 0.28
rpoA 3877570 p.Pro313Leu missense_variant 0.15
rpoA 3878444 p.Val22Leu missense_variant 0.12
clpC1 4038859 c.1845delG frameshift_variant 0.18
clpC1 4039026 p.Thr560Asn missense_variant 0.17
clpC1 4040144 c.561G>C synonymous_variant 0.18
panD 4043921 p.Pro121Thr missense_variant 0.33
embC 4239994 c.132C>T synonymous_variant 0.22
embA 4242475 c.-758G>C upstream_gene_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243796 c.564C>A synonymous_variant 0.13
embA 4243893 p.Leu221Met missense_variant 0.29
embA 4245559 p.Gly776Val missense_variant 0.18
embB 4248937 c.2424G>A synonymous_variant 0.17
embB 4249490 p.Ala993Ser missense_variant 0.2
aftB 4267941 p.Gly299Val missense_variant 0.33
ubiA 4269864 c.-32delG upstream_gene_variant 0.13
ethA 4326532 c.942C>T synonymous_variant 0.14
ethA 4328435 c.-962C>A upstream_gene_variant 0.2
whiB6 4338327 p.Asp65Glu missense_variant 0.22
whiB6 4338354 p.Cys56* stop_gained 0.17
whiB6 4338413 p.Asp37Asn missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407551 p.Met218Leu missense_variant 0.29
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0