TB-Profiler result

Run: SRR9971339
Summary

Run ID: SRR9971339

Sample name:

Date: 04-04-2023 23:23:50

Number of reads: 4744312

Percentage reads mapped: 97.61

Strain: lineage4.3.3

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
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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.Ser450Trp missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.94 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.17 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289200 p.Cys14Trp missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.26
rpoC 764995 c.1626C>G 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 1472150 n.305T>A non_coding_transcript_exon_variant 0.16
rrs 1472351 n.506G>T non_coding_transcript_exon_variant 0.11
rrs 1472417 n.572G>T non_coding_transcript_exon_variant 0.11
rrs 1472452 n.607G>T non_coding_transcript_exon_variant 0.14
rrs 1472571 n.726G>T non_coding_transcript_exon_variant 0.33
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.29
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.25
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.25
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.33
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.36
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.36
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.36
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.33
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.36
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.36
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.36
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.36
rrs 1472687 n.842_843insC non_coding_transcript_exon_variant 0.31
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.31
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.31
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.25
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.22
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.17
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.17
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.11
rrl 1473965 n.308G>C non_coding_transcript_exon_variant 0.13
rrl 1475770 n.2113G>T non_coding_transcript_exon_variant 0.13
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.22
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.18
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.25
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.25
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.25
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.2
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.27
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.27
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.26
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.27
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.27
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.27
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.14
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.32
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.22
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.2
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.19
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.13
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.12
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.13
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.12
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.13
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.13
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.12
rpsA 1834836 p.Met432Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156196 c.-85C>T upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
folC 2746290 p.Arg437Cys missense_variant 1.0
folC 2746340 p.Ala420Val missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.43
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038968 c.1737G>A synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.16
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0