TB-Profiler result

Run: ERR2229410
Summary

Run ID: ERR2229410

Sample name:

Date: 31-03-2023 17:10:29

Number of reads: 698458

Percentage reads mapped: 99.22

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.99
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 5949 p.Ala237Glu missense_variant 0.15
gyrA 7286 c.-16T>A upstream_gene_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7624 p.Pro108Gln missense_variant 0.12
gyrA 7856 p.Met185Ile missense_variant 0.13
gyrA 8872 p.Gly524Glu missense_variant 0.12
mshA 575257 c.-91T>A upstream_gene_variant 0.15
mshA 575751 p.Gly135Val missense_variant 0.12
mshA 576108 p.Ala254Gly missense_variant 0.33
rpoB 762156 p.Val784Leu missense_variant 0.13
rpoC 765144 c.1779delC frameshift_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775741 c.2740C>T synonymous_variant 0.18
mmpL5 776425 p.Asp686Asn missense_variant 0.14
mmpL5 777128 c.1353A>G synonymous_variant 0.13
mmpL5 777164 c.1317C>T synonymous_variant 0.12
mmpL5 777503 c.978C>T synonymous_variant 0.18
mmpR5 779159 p.Ala57Glu missense_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800807 c.-2C>T upstream_gene_variant 0.15
rplC 801148 p.Val114Leu missense_variant 0.12
fbiC 1303445 p.Ser172Tyr missense_variant 0.12
fbiC 1303614 c.684C>A synonymous_variant 0.22
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304736 p.Gln602His missense_variant 0.33
fbiC 1304956 p.Val676Phe missense_variant 0.33
Rv1258c 1406358 p.Ile328Asn missense_variant 0.2
embR 1416773 p.Ala192Asp missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475735 n.2078T>C non_coding_transcript_exon_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.23
inhA 1674336 c.135G>A synonymous_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917995 p.Ser19* stop_gained 0.22
ndh 2103234 c.-192G>T upstream_gene_variant 0.18
katG 2155877 p.Asp79Tyr missense_variant 0.2
PPE35 2167833 p.Leu927Arg missense_variant 0.17
PPE35 2167955 c.2658A>C synonymous_variant 0.14
PPE35 2167965 p.Ala883Gly missense_variant 0.33
PPE35 2167967 c.2646A>C synonymous_variant 0.33
PPE35 2168140 p.Ala825Thr missense_variant 0.13
PPE35 2168143 p.Phe824Leu missense_variant 0.12
PPE35 2168150 c.2463T>C synonymous_variant 0.12
PPE35 2168573 c.2040T>C synonymous_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169009 p.Pro535Leu missense_variant 0.18
PPE35 2169879 p.Phe245Ser missense_variant 0.11
PPE35 2169882 p.Ser244Asn missense_variant 0.12
PPE35 2169890 c.723C>T synonymous_variant 0.12
PPE35 2169893 c.720C>A synonymous_variant 0.12
PPE35 2169902 p.Leu237Phe missense_variant 0.18
PPE35 2170048 p.Leu189Val missense_variant 0.29
PPE35 2170053 p.Thr187Ser missense_variant 0.33
PPE35 2170076 c.537G>A synonymous_variant 0.17
PPE35 2170147 p.Ser156Ala missense_variant 0.14
Rv1979c 2222842 c.322dupG frameshift_variant 0.12
Rv1979c 2222853 c.312C>T synonymous_variant 0.12
Rv1979c 2223016 p.Ala50Val missense_variant 0.15
Rv1979c 2223068 p.Phe33Leu missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518606 c.492G>C synonymous_variant 0.17
kasA 2518609 p.Met165Ile missense_variant 0.17
kasA 2518809 p.Lys232Arg missense_variant 0.17
kasA 2518854 p.Leu247Pro missense_variant 0.13
kasA 2518864 c.750G>C synonymous_variant 0.14
eis 2714562 c.771T>A synonymous_variant 0.13
eis 2714939 p.Gly132Trp missense_variant 0.5
eis 2715321 c.12C>A synonymous_variant 0.18
pepQ 2859566 p.Gly285Cys missense_variant 0.25
ribD 2986711 c.-128G>T upstream_gene_variant 0.13
Rv2752c 3065164 p.Gly343Asp missense_variant 0.17
Rv2752c 3065813 p.Glu127* stop_gained 0.25
thyX 3067818 p.Cys43Phe missense_variant 0.18
thyX 3068047 c.-102C>A upstream_gene_variant 0.15
fprA 3473907 c.-100G>T upstream_gene_variant 0.14
fprA 3474562 p.Leu186Ile missense_variant 0.18
fprA 3475191 c.1185C>T synonymous_variant 0.15
fprA 3475267 p.Ala421Ser missense_variant 0.18
Rv3236c 3612187 p.Met310Ile missense_variant 0.2
Rv3236c 3612726 p.Gly131Ser missense_variant 0.29
Rv3236c 3612762 p.Leu119Phe missense_variant 0.22
fbiA 3640846 p.Phe102Leu missense_variant 0.14
fbiA 3640880 p.Leu113Arg missense_variant 0.11
fbiA 3640888 c.349delC frameshift_variant 0.14
fbiB 3642564 p.Ala344Thr missense_variant 0.17
clpC1 4038443 c.2262G>A synonymous_variant 0.33
clpC1 4039256 p.Gln483His missense_variant 0.15
clpC1 4039638 p.Ile356Thr missense_variant 0.17
clpC1 4039691 c.1014G>C synonymous_variant 0.18
clpC1 4040144 c.561G>C synonymous_variant 0.15
clpC1 4040236 p.Gly157Cys missense_variant 0.29
embC 4240213 c.351C>A synonymous_variant 0.29
embC 4241231 p.Arg457Trp missense_variant 0.13
embC 4241841 p.Ser660* stop_gained 0.25
embC 4242281 p.Ser807Cys missense_variant 0.25
embC 4242528 p.Gly889Val missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243461 p.Ser77Ala missense_variant 0.11
embB 4246555 c.42G>C synonymous_variant 0.4
embB 4246556 p.Ala15Pro missense_variant 0.4
embB 4246563 p.Leu17Trp missense_variant 0.4
embB 4246567 c.54G>T synonymous_variant 0.4
embB 4247871 p.Ala453Val missense_variant 0.17
aftB 4267223 c.1614C>T synonymous_variant 0.12
aftB 4267982 c.855C>A synonymous_variant 0.29
aftB 4268750 c.87C>T synonymous_variant 0.2
ubiA 4269224 p.Ala204Thr missense_variant 0.29
ethA 4326104 p.Leu457Gln missense_variant 0.18
ethA 4326795 p.Arg227Cys missense_variant 0.15
ethR 4327814 p.Thr89Asn missense_variant 0.19
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407815 p.Gly130Ser missense_variant 0.14
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0