TB-Profiler result

Run: ERR7801181
Summary

Run ID: ERR7801181

Sample name:

Date: 02-04-2023 05:57:59

Number of reads: 771499

Percentage reads mapped: 99.65

Strain: lineage4.3.4.2

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 0.99
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.98
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 5629 c.390G>T synonymous_variant 0.13
gyrB 6088 c.849C>A synonymous_variant 0.15
gyrB 6140 p.Val301Leu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7703 c.402G>T synonymous_variant 0.15
gyrA 8007 p.Gly236* stop_gained 0.18
gyrA 9079 p.Gly593Glu missense_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490966 p.Gly62Cys missense_variant 0.17
fgd1 491180 p.Arg133His missense_variant 0.14
fgd1 491645 p.Ser288* stop_gained 0.23
fgd1 491754 p.Phe324Leu missense_variant 0.18
ccsA 620424 c.534G>T synonymous_variant 0.19
ccsA 620544 c.654G>T synonymous_variant 0.13
ccsA 620555 p.Ala222Asp missense_variant 0.13
rpoB 759860 c.54G>T synonymous_variant 0.15
rpoB 759887 c.81C>A synonymous_variant 0.15
rpoB 760649 c.843G>T synonymous_variant 0.29
rpoB 761882 c.2076C>A synonymous_variant 0.15
rpoB 762344 c.2538G>T synonymous_variant 0.13
rpoB 762506 p.Phe900Leu missense_variant 0.15
rpoC 762587 c.-783G>A upstream_gene_variant 0.13
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765521 p.Asp718Tyr missense_variant 0.17
rpoC 766504 c.3135G>T synonymous_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775937 c.2544G>T synonymous_variant 0.18
mmpL5 775940 c.2541C>T synonymous_variant 0.2
mmpL5 776183 p.Lys766Asn missense_variant 0.33
mmpL5 777547 p.Gly312Cys missense_variant 0.15
mmpL5 777634 p.Gly283Cys missense_variant 0.15
mmpL5 777698 p.Phe261Leu missense_variant 0.18
mmpR5 778442 c.-548G>T upstream_gene_variant 0.14
mmpS5 778669 p.Gln79His missense_variant 0.12
mmpL5 779190 c.-710G>T upstream_gene_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406530 p.Gly271Cys missense_variant 0.15
Rv1258c 1407071 c.270C>A synonymous_variant 0.13
embR 1416859 c.489C>A synonymous_variant 0.15
embR 1416865 c.483C>A synonymous_variant 0.14
embR 1417002 p.Val116Phe missense_variant 0.14
embR 1417507 c.-160A>T upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472128 n.283G>T non_coding_transcript_exon_variant 0.17
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.18
rrs 1472257 n.412G>T non_coding_transcript_exon_variant 0.18
rrs 1472343 n.498C>A non_coding_transcript_exon_variant 0.15
rrs 1473297 n.1452G>T non_coding_transcript_exon_variant 0.18
rrl 1473416 n.-242G>A upstream_gene_variant 0.18
rrl 1474477 n.820C>A non_coding_transcript_exon_variant 0.25
rrl 1476010 n.2353G>T non_coding_transcript_exon_variant 0.5
rrl 1476018 n.2361G>T non_coding_transcript_exon_variant 0.5
rrl 1476290 n.2633C>A non_coding_transcript_exon_variant 0.25
rrl 1476530 n.2873C>A non_coding_transcript_exon_variant 0.15
fabG1 1673504 p.Gly22Val missense_variant 0.2
inhA 1673865 c.-337C>A upstream_gene_variant 0.14
rpsA 1833599 p.Glu20* stop_gained 0.17
rpsA 1834181 p.Gly214Cys missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918681 p.Asp248Tyr missense_variant 0.17
ndh 2101973 p.Ala357Glu missense_variant 0.14
ndh 2102665 c.377dupT frameshift_variant 0.14
ndh 2102718 p.Gln109Glu missense_variant 0.14
katG 2155043 p.Asp357Tyr missense_variant 0.18
katG 2155122 c.990C>T synonymous_variant 0.29
katG 2155260 c.852C>A synonymous_variant 0.2
PPE35 2167760 c.2853G>T synonymous_variant 0.15
PPE35 2167998 p.Pro872Gln missense_variant 0.15
PPE35 2170405 p.Ala70Ser missense_variant 0.12
PPE35 2170731 c.-119C>A upstream_gene_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289488 c.-247G>A upstream_gene_variant 0.15
pncA 2289502 c.-261G>T upstream_gene_variant 0.15
kasA 2518104 c.-11G>A upstream_gene_variant 0.13
ahpC 2726557 p.Ala122Val missense_variant 0.15
ribD 2987020 p.Ala61Gly missense_variant 0.1
Rv2752c 3065646 c.546C>A synonymous_variant 0.2
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339366 c.249G>T synonymous_variant 0.2
Rv3083 3449461 p.Gln320Lys missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474317 p.Val104Asp missense_variant 0.22
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3613213 c.-97C>A upstream_gene_variant 0.13
fbiA 3640351 c.-192C>T upstream_gene_variant 0.22
fbiB 3642636 p.Ala368Ser missense_variant 0.14
fbiB 3642647 c.1113C>A synonymous_variant 0.14
rpoA 3877824 p.Glu228Asp missense_variant 0.14
rpoA 3877963 p.Arg182Leu missense_variant 0.14
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038985 p.Asp574Asn missense_variant 0.15
panD 4043879 c.403C>A synonymous_variant 0.14
embC 4241469 p.Ala536Asp missense_variant 0.12
embC 4242263 p.Glu801* stop_gained 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243092 p.Leu1077Arg missense_variant 0.13
embC 4243095 p.Gly1078Val missense_variant 0.13
embA 4243099 c.-134G>C upstream_gene_variant 0.14
embA 4243102 c.-131G>T upstream_gene_variant 0.14
embC 4243103 p.Thr1081Pro missense_variant 0.14
embC 4243106 p.Arg1082Ser missense_variant 0.15
embC 4243107 c.3245_3246insGTTCAGAT frameshift_variant 0.14
embA 4243385 c.153C>A synonymous_variant 0.2
aftB 4267406 p.Lys477Asn missense_variant 0.12
aftB 4267948 p.Asp297Asn missense_variant 0.17
ethA 4326066 p.Arg470Ser missense_variant 0.4
ethA 4326325 c.1149G>T synonymous_variant 0.14
ethA 4326498 c.976C>A synonymous_variant 0.15
ethA 4326611 p.Pro288His missense_variant 0.14
ethR 4327711 p.Gly55Ser missense_variant 0.14
ethR 4327895 p.Ser116* stop_gained 0.15
ethA 4328019 c.-546G>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407751 p.Pro151Gln missense_variant 0.18
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4408345 c.-143C>A upstream_gene_variant 0.12