TB-Profiler result

Run: SRR6982415
Summary

Run ID: SRR6982415

Sample name:

Date: 04-04-2023 18:36:41

Number of reads: 373222

Percentage reads mapped: 99.19

Strain: lineage4.9.1

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
lineage4.9 Euro-American (H37Rv-like) T1 None 1.0
lineage4.9.1 Euro-American (H37Rv-like) T1 None 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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
gid 4407851 c.351dupG frameshift_variant 1.0 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 5946 p.Arg236His missense_variant 0.17
gyrB 6939 p.Pro567Gln missense_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8978 c.1677C>T synonymous_variant 1.0
fgd1 491295 c.513C>A synonymous_variant 0.38
fgd1 491492 p.Pro237His missense_variant 0.3
mshA 576166 c.819C>A synonymous_variant 0.18
mshA 576186 p.Pro280His missense_variant 0.18
ccsA 619831 c.-60T>G upstream_gene_variant 0.23
rpoB 761254 p.Pro483His missense_variant 0.17
rpoB 762691 p.Pro962Gln missense_variant 0.18
rpoB 762828 p.Arg1008Ser missense_variant 0.22
rpoB 763046 p.Gln1080His missense_variant 0.15
rpoC 763274 c.-96G>T upstream_gene_variant 0.17
rpoC 763887 p.Arg173Leu missense_variant 0.21
rpoC 764918 p.Val517Leu missense_variant 0.12
rpoC 765564 p.Ser732* stop_gained 0.18
rpoC 766666 c.3297C>A synonymous_variant 0.18
rpoC 766800 p.Ala1144Asp missense_variant 0.22
rpoC 766867 c.3498C>A synonymous_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775745 p.Met912Ile missense_variant 0.25
mmpL5 775751 c.2730C>T synonymous_variant 0.18
mmpL5 775823 c.2658G>T synonymous_variant 0.17
mmpL5 776074 p.Val803Ile missense_variant 0.2
mmpL5 776534 p.Lys649Asn missense_variant 0.15
mmpL5 777161 p.Gln440His missense_variant 0.22
mmpL5 777880 p.Asp201Tyr missense_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781403 c.-157G>T upstream_gene_variant 0.2
fbiC 1303134 c.204G>T synonymous_variant 0.22
fbiC 1303848 p.Phe306Leu missense_variant 0.18
fbiC 1304658 c.1728C>A synonymous_variant 0.16
fbiC 1305387 p.Met819Ile missense_variant 0.17
Rv1258c 1406165 c.1176G>T synonymous_variant 0.17
Rv1258c 1406183 c.1158C>A synonymous_variant 0.18
Rv1258c 1406872 p.Gly157Cys missense_variant 0.22
embR 1416817 p.Lys177Asn missense_variant 0.25
embR 1416894 p.Asp152Tyr missense_variant 0.25
embR 1417477 c.-130C>A upstream_gene_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471764 n.-82C>A upstream_gene_variant 0.25
rrs 1473180 n.1335G>A non_coding_transcript_exon_variant 0.15
rrs 1473324 n.1479G>T non_coding_transcript_exon_variant 0.19
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.2
rrl 1475129 n.1472G>A non_coding_transcript_exon_variant 0.25
rrl 1475200 n.1546delG non_coding_transcript_exon_variant 0.33
rrl 1475279 n.1622G>T non_coding_transcript_exon_variant 0.33
rrl 1476119 n.2462G>T non_coding_transcript_exon_variant 0.14
rrl 1476433 n.2776C>A non_coding_transcript_exon_variant 0.5
rrl 1476541 n.2884C>A non_coding_transcript_exon_variant 0.4
rrl 1476563 n.2906G>T non_coding_transcript_exon_variant 0.29
rrl 1476603 n.2946G>T non_coding_transcript_exon_variant 0.4
rrl 1476612 n.2955G>T non_coding_transcript_exon_variant 0.4
rrl 1476626 n.2969G>T non_coding_transcript_exon_variant 0.4
inhA 1674377 p.Pro59Gln missense_variant 0.4
rpsA 1834043 p.Glu168* stop_gained 0.17
rpsA 1834234 c.693G>T synonymous_variant 0.25
rpsA 1834623 p.Ser361* stop_gained 0.2
rpsA 1834905 p.Pro455Gln missense_variant 0.18
tlyA 1917861 c.-79G>T upstream_gene_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102340 c.703C>A synonymous_variant 0.2
ndh 2102772 p.His91Asn missense_variant 0.22
ndh 2102848 p.Glu65Asp missense_variant 0.29
ndh 2102917 c.126G>T synonymous_variant 0.2
katG 2154026 p.Leu696Met missense_variant 0.18
katG 2154247 p.Pro622His missense_variant 0.22
katG 2154273 p.Lys613Asn missense_variant 0.2
katG 2154401 p.Arg571Ser missense_variant 0.25
katG 2154496 p.Ser539Tyr missense_variant 0.25
katG 2155134 c.978G>T synonymous_variant 0.33
katG 2155137 c.975G>A synonymous_variant 0.33
katG 2155194 c.918C>A synonymous_variant 0.29
katG 2155950 c.162C>A synonymous_variant 0.2
katG 2156299 c.-188G>T upstream_gene_variant 0.17
PPE35 2170082 c.531T>G synonymous_variant 0.29
PPE35 2170560 p.Gly18Val missense_variant 0.25
Rv1979c 2222232 c.933G>T synonymous_variant 0.2
Rv1979c 2222643 c.522C>A synonymous_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289138 p.Leu35Arg missense_variant 0.8
pncA 2289360 c.-119G>T upstream_gene_variant 0.33
pncA 2289513 c.-272G>T upstream_gene_variant 0.18
pncA 2289529 c.-288G>T upstream_gene_variant 0.2
eis 2715089 p.Leu82Ile missense_variant 0.2
ahpC 2726341 p.Val50Gly missense_variant 1.0
folC 2746173 p.Gly476Trp missense_variant 0.15
folC 2746948 c.651G>T synonymous_variant 0.23
folC 2747353 c.246C>A synonymous_variant 0.18
folC 2747723 c.-125G>A upstream_gene_variant 0.22
ribD 2986827 c.-12G>A upstream_gene_variant 1.0
Rv2752c 3065615 p.Asp193Tyr missense_variant 0.25
Rv2752c 3065840 p.Glu118* stop_gained 0.25
Rv2752c 3065983 p.Arg70Leu missense_variant 0.29
thyA 3074430 c.42G>T synonymous_variant 0.4
thyA 3074547 c.-76G>T upstream_gene_variant 0.22
ald 3086828 c.9C>A synonymous_variant 0.18
ald 3087246 p.Gln143Lys missense_variant 0.2
ald 3087305 c.486G>T synonymous_variant 0.17
ald 3087731 c.912G>T synonymous_variant 0.22
ald 3087746 c.927G>T synonymous_variant 0.2
ald 3087932 c.1113C>A synonymous_variant 0.22
fbiD 3339379 p.Asp88Tyr missense_variant 0.4
fbiD 3339385 p.Asp90Asn missense_variant 1.0
Rv3083 3449367 c.864G>T synonymous_variant 0.2
whiB7 3568793 c.-114C>A upstream_gene_variant 0.25
Rv3236c 3612625 c.492C>A synonymous_variant 0.4
Rv3236c 3613003 p.Leu38Phe missense_variant 0.3
fbiB 3642496 p.Leu321Pro missense_variant 0.17
rpoA 3877557 c.951C>A synonymous_variant 0.17
rpoA 3877601 p.Gln303Lys missense_variant 0.2
rpoA 3877666 p.Ser281Tyr missense_variant 0.2
rpoA 3878398 p.Ser37* stop_gained 0.18
rpoA 3878552 c.-45C>A upstream_gene_variant 0.67
rpoA 3878650 c.-143C>A upstream_gene_variant 1.0
clpC1 4038401 p.Leu768Phe missense_variant 0.18
clpC1 4038497 c.2203_2207dupATCAG frameshift_variant 0.18
clpC1 4040088 p.Arg206Leu missense_variant 0.2
embC 4241167 c.1305C>A synonymous_variant 0.18
embC 4241186 p.Gly442Cys missense_variant 0.17
embC 4241319 p.Pro486Gln missense_variant 0.18
embC 4241424 p.Arg521Leu missense_variant 0.25
embC 4241503 c.1641G>T synonymous_variant 0.18
embC 4242543 p.Arg894Leu missense_variant 0.15
embA 4244077 p.Arg282Leu missense_variant 0.25
embA 4244393 c.1161G>T synonymous_variant 0.22
embA 4245452 c.2220G>T synonymous_variant 0.29
embB 4245743 c.-771C>A upstream_gene_variant 0.23
embB 4247261 p.Gln250Lys missense_variant 0.2
embB 4247299 c.786G>T synonymous_variant 0.2
embB 4247403 p.Ser297* stop_gained 0.43
embB 4247499 p.Pro329His missense_variant 0.4
embB 4248453 p.Trp647Leu missense_variant 0.29
embB 4248919 c.2406C>A synonymous_variant 0.22
embB 4248940 c.2427C>A synonymous_variant 0.18
aftB 4267145 c.1692G>T synonymous_variant 0.22
aftB 4267494 p.Gly448Val missense_variant 0.33
aftB 4267687 p.Gly384Cys missense_variant 0.29
aftB 4268898 c.-62G>T upstream_gene_variant 0.25
ubiA 4269891 c.-58G>T upstream_gene_variant 0.15
ubiA 4269918 c.-85G>T upstream_gene_variant 0.2
ethA 4327275 p.Arg67Ser missense_variant 0.2
ethR 4327982 p.Trp145Leu missense_variant 0.2
whiB6 4338341 p.Leu61Met missense_variant 0.18
whiB6 4338586 c.-65C>A upstream_gene_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0