TB-Profiler result

Run: SRR1140750
Summary

Run ID: SRR1140750

Sample name:

Date: 02-04-2023 20:58:27

Number of reads: 3049508

Percentage reads mapped: 82.8

Strain: lineage4.3.4.2.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 1.0
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289054 p.Asp63Gly missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.99 ethambutol
embB 4247730 p.Gly406Asp missense_variant 1.0 ethambutol
ethA 4327033 p.Tyr147* stop_gained 1.0 ethionamide
ethA 4326694 c.440_779del frameshift_variant 1.0 ethionamide
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 6140 p.Val301Leu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 767083 c.3714C>T synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.17
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.18
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.16
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.15
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.15
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.14
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.11
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.19
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.15
rrs 1472382 n.537G>T non_coding_transcript_exon_variant 0.15
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.14
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.16
rrs 1472753 n.908A>C non_coding_transcript_exon_variant 0.83
rrs 1472770 n.925C>T non_coding_transcript_exon_variant 0.15
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.13
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.15
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.21
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.21
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.21
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.25
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.25
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.23
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.23
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.28
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.3
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.24
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.23
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.19
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.18
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.15
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.13
rrl 1476491 n.2834T>C non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
alr 3840719 c.702A>G synonymous_variant 1.0
alr 3840869 c.552C>G synonymous_variant 1.0
rpoA 3877964 p.Arg182Trp missense_variant 1.0
rpoA 3878590 c.-84_-83insC upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0