TB-Profiler result

Run: SRR11342635
Summary

Run ID: SRR11342635

Sample name:

Date: 02-04-2023 20:46:52

Number of reads: 2534285

Percentage reads mapped: 36.81

Strain: lineage4.8

Drug-resistance: MDR-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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoC 764363 p.Gly332Arg missense_variant 0.78 rifampicin
katG 2154857 p.Asp419His missense_variant 1.0 isoniazid
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
mshA 576113 p.Arg256Gly missense_variant 0.27
rpoC 764916 p.Leu516Pro missense_variant 0.14
rpoC 766487 p.Pro1040Ser missense_variant 0.23
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302983 p.Pro18Leu missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472204 n.359G>A non_coding_transcript_exon_variant 0.15
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.13
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.12
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.12
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.12
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.12
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.15
rrs 1472719 n.874G>A non_coding_transcript_exon_variant 0.18
rrs 1472733 n.888G>C non_coding_transcript_exon_variant 0.21
rrs 1472734 n.889C>A non_coding_transcript_exon_variant 0.2
rrs 1472741 n.896G>T non_coding_transcript_exon_variant 0.2
rrs 1472742 n.897C>G non_coding_transcript_exon_variant 0.23
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.32
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.31
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.29
rrs 1472805 n.960C>A non_coding_transcript_exon_variant 0.18
rrs 1472806 n.961A>T non_coding_transcript_exon_variant 0.18
rrs 1472813 n.968A>G non_coding_transcript_exon_variant 0.2
rrs 1473128 n.1283C>A non_coding_transcript_exon_variant 0.16
rrs 1473134 n.1289T>A non_coding_transcript_exon_variant 0.26
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.31
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.32
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 0.32
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.33
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.31
rrs 1473191 n.1346C>G non_coding_transcript_exon_variant 0.3
rrs 1473193 n.1348G>T non_coding_transcript_exon_variant 0.3
rrs 1473200 n.1355A>C non_coding_transcript_exon_variant 0.3
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.3
rrs 1473204 n.1359C>A non_coding_transcript_exon_variant 0.32
rrs 1473206 n.1361G>C non_coding_transcript_exon_variant 0.32
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.12
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.12
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.14
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.15
rrl 1475869 n.2212C>T non_coding_transcript_exon_variant 0.13
rrl 1476322 n.2665C>A non_coding_transcript_exon_variant 0.43
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.68
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.79
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.78
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.79
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.8
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.81
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.81
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.82
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.81
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.74
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.66
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.15
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
rpoA 3878613 c.-106A>C upstream_gene_variant 0.25
rpoA 3878618 c.-111A>C upstream_gene_variant 0.13
clpC1 4039729 p.Asp326Asn missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247028 p.Leu172Arg missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0