TB-Profiler result

Run: SRR1140740
Summary

Run ID: SRR1140740

Sample name:

Date: 02-04-2023 20:58:19

Number of reads: 601681

Percentage reads mapped: 46.87

Strain: lineage4.6.1.2

Drug-resistance: RR-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
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.1 Euro-American (Uganda) T2 RD724 0.95
lineage4.6.1.2 Euro-American T2 RD724 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
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 6501 p.Arg421His missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7539 p.Thr80Ala missense_variant 1.0
gyrA 7912 p.Ala204Gly missense_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 619981 p.Leu31Met missense_variant 0.14
rpoC 762899 c.-471G>C upstream_gene_variant 0.4
rpoC 762917 c.-453C>G upstream_gene_variant 0.4
rpoC 762920 c.-450C>T upstream_gene_variant 0.5
rpoC 762923 c.-447C>G upstream_gene_variant 0.5
rpoB 762925 p.Thr1040Ile missense_variant 0.5
rpoB 762934 c.3129_3130insAGCC frameshift_variant 0.4
rpoB 762938 c.3133_3136delATGA frameshift_variant 0.4
rpoC 762989 c.-381G>C upstream_gene_variant 0.29
rpoC 764593 c.1224C>T synonymous_variant 0.22
rpoC 764605 c.1236G>C synonymous_variant 0.3
rpoC 764611 c.1242G>T synonymous_variant 0.36
rpoC 764632 c.1263T>C synonymous_variant 0.36
rpoC 764641 c.1272C>T synonymous_variant 0.4
rpoC 764650 c.1281G>T synonymous_variant 0.33
rpoC 764663 p.Val432Thr missense_variant 0.3
rpoC 764672 p.Gln435Glu missense_variant 0.29
rpoC 764677 c.1308C>G synonymous_variant 0.29
rpoC 764995 c.1626C>G synonymous_variant 0.2
rpoC 767001 p.Thr1211Met missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779230 p.Glu81Lys missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407350 c.-10C>T upstream_gene_variant 0.22
embR 1416410 p.Leu313Arg missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.43
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.5
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.44
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.46
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.43
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.43
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.38
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.38
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.38
rrs 1472264 n.419T>C non_coding_transcript_exon_variant 0.42
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.45
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.3
rrs 1472284 n.439C>T non_coding_transcript_exon_variant 0.25
rrs 1472349 n.504A>C non_coding_transcript_exon_variant 0.25
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.22
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.22
rrs 1472382 n.537G>T non_coding_transcript_exon_variant 0.2
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.2
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.22
rrs 1472415 n.570T>A non_coding_transcript_exon_variant 0.25
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.54
rrs 1472770 n.925C>T non_coding_transcript_exon_variant 0.47
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.53
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.7
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.67
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.57
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.4
rrs 1472826 n.981G>C non_coding_transcript_exon_variant 0.5
rrl 1475514 n.1857G>T non_coding_transcript_exon_variant 0.5
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.5
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.6
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.6
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.6
rrl 1476208 n.2551C>A non_coding_transcript_exon_variant 0.67
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.67
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.67
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.5
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.5
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.86
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.88
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.8
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.8
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.71
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.67
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.67
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.6
rrl 1476491 n.2834T>C non_coding_transcript_exon_variant 0.6
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.5
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.5
inhA 1674465 c.264C>T synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154874 p.Tyr413Cys missense_variant 0.88
PPE35 2167918 p.Phe899Leu missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714822 p.His171Asn missense_variant 0.22
fbiD 3338982 c.-136G>T upstream_gene_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474541 p.Ala179Ser missense_variant 0.25
alr 3840629 c.792C>T synonymous_variant 0.15
clpC1 4038341 c.2364G>A synonymous_variant 0.17
clpC1 4039697 c.1008C>G synonymous_variant 0.27
clpC1 4039711 p.Ile332Val missense_variant 0.33
clpC1 4039712 c.993C>T synonymous_variant 0.36
clpC1 4039715 c.990G>A synonymous_variant 0.4
clpC1 4039739 c.966C>G synonymous_variant 0.5
embC 4239943 c.81G>T synonymous_variant 0.33
embC 4240602 p.Ala247Gly missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245055 p.Thr608Asn missense_variant 1.0
embA 4245247 p.Gly672Ala missense_variant 0.18
embB 4246865 p.Val118Phe missense_variant 0.2
ubiA 4269730 p.Ala35Val missense_variant 0.2
ethR 4328183 p.Tyr212Cys missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338635 c.-114A>C upstream_gene_variant 1.0
gid 4407541 p.Gly221Val missense_variant 0.2