TB-Profiler result

Run: ERR4815257
Summary

Run ID: ERR4815257

Sample name:

Date: 01-04-2023 13:45:38

Number of reads: 199998

Percentage reads mapped: 72.43

Strain: lineage4.4.1.1

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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans None 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
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.18 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr 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
gyrB 5570 p.Ser111Thr missense_variant 0.29
gyrB 5826 p.Glu196Gly missense_variant 0.5
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8587 p.Glu429Ala missense_variant 0.29
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575582 c.236_237delTG frameshift_variant 0.22
rpoB 760907 c.1101C>T synonymous_variant 0.29
rpoC 763353 c.-17A>G upstream_gene_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775682 c.2799C>T synonymous_variant 0.2
mmpL5 777879 p.Asp201Gly missense_variant 0.29
mmpL5 778270 p.Ser71Thr missense_variant 0.22
mmpS5 778841 p.Gly22Asp missense_variant 0.4
rpsL 781379 c.-181G>T upstream_gene_variant 0.5
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303433 p.Asp168Val missense_variant 0.15
Rv1258c 1406973 p.Ala123Asp missense_variant 0.25
embR 1417338 p.Ser4Cys missense_variant 0.14
atpE 1461033 c.-12G>C upstream_gene_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471876 n.31G>A non_coding_transcript_exon_variant 0.14
rrs 1472171 n.326A>T non_coding_transcript_exon_variant 0.5
rrs 1472342 n.499delC non_coding_transcript_exon_variant 0.22
rrs 1473150 n.1305T>C non_coding_transcript_exon_variant 0.38
rrs 1473161 n.1316A>G non_coding_transcript_exon_variant 0.3
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.2
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.27
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.27
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.27
rrs 1473201 n.1356A>G non_coding_transcript_exon_variant 0.18
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.2
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.2
rrs 1473215 n.1370A>G non_coding_transcript_exon_variant 0.2
rrl 1473734 n.77C>T non_coding_transcript_exon_variant 0.29
rrl 1473993 n.336G>A non_coding_transcript_exon_variant 0.4
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.33
rrl 1474527 n.870T>C non_coding_transcript_exon_variant 0.33
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.33
rrl 1474542 n.885A>G non_coding_transcript_exon_variant 0.4
rrl 1474551 n.894G>C non_coding_transcript_exon_variant 0.4
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.4
rrl 1474558 n.901G>T non_coding_transcript_exon_variant 0.4
rrl 1474837 n.1180A>G non_coding_transcript_exon_variant 0.6
rrl 1474862 n.1205C>T non_coding_transcript_exon_variant 0.75
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.75
rrl 1475224 n.1567T>A non_coding_transcript_exon_variant 0.22
rrl 1475751 n.2094C>T non_coding_transcript_exon_variant 0.15
rrl 1475765 n.2108A>T non_coding_transcript_exon_variant 0.15
rrl 1475772 n.2115A>C non_coding_transcript_exon_variant 0.21
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.21
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.67
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.67
rrl 1475892 n.2235A>G non_coding_transcript_exon_variant 0.67
rrl 1475897 n.2240T>G non_coding_transcript_exon_variant 0.67
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.67
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.67
rrl 1475900 n.2243A>C non_coding_transcript_exon_variant 0.67
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 1.0
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 1.0
rrl 1475938 n.2281C>A non_coding_transcript_exon_variant 1.0
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 1.0
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 1.0
rrl 1476359 n.2702C>T non_coding_transcript_exon_variant 0.5
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.5
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.57
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.67
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.6
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.73
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.64
rrl 1476513 n.2856G>T non_coding_transcript_exon_variant 0.5
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.5
rrl 1476520 n.2863G>T non_coding_transcript_exon_variant 0.5
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.44
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.44
rrl 1476529 n.2872A>T non_coding_transcript_exon_variant 0.44
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.44
rrl 1476539 n.2882A>C non_coding_transcript_exon_variant 0.44
rrl 1476544 n.2887T>C non_coding_transcript_exon_variant 0.5
rrl 1476547 n.2890C>A non_coding_transcript_exon_variant 0.5
rrl 1476563 n.2906G>T non_coding_transcript_exon_variant 0.33
rrl 1476566 n.2909A>G non_coding_transcript_exon_variant 0.33
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.33
inhA 1673859 c.-343G>T upstream_gene_variant 0.29
fabG1 1673873 p.Trp145* stop_gained 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918092 c.153G>A synonymous_variant 0.25
ndh 2102326 c.717G>C synonymous_variant 0.33
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2154397 p.Thr572Met missense_variant 0.29
PPE35 2168928 p.Ser562* stop_gained 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714581 c.750_751delTG frameshift_variant 0.4
folC 2747603 c.-5C>A upstream_gene_variant 0.22
Rv2752c 3065404 p.Gly263Asp missense_variant 0.22
thyA 3074100 c.372T>C synonymous_variant 0.29
ald 3086694 c.-126C>A upstream_gene_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087288 c.473_474dupTG frameshift_variant 0.29
Rv3083 3448608 c.105G>A synonymous_variant 1.0
Rv3083 3449865 c.1362G>A synonymous_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474464 p.Ile153Thr missense_variant 0.25
fprA 3474643 p.Arg213Cys missense_variant 0.22
whiB7 3568689 c.-10G>T upstream_gene_variant 0.15
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
Rv3236c 3613114 c.3G>A synonymous_variant 0.22
fbiA 3641504 p.Arg321His missense_variant 0.5
alr 3840723 p.His233Leu missense_variant 0.2
alr 3841501 c.-81G>C upstream_gene_variant 0.22
rpoA 3878436 c.72A>G synonymous_variant 0.4
ddn 3986650 c.-194A>C upstream_gene_variant 0.4
clpC1 4040522 c.183T>C synonymous_variant 1.0
panD 4044223 p.Leu20Gln missense_variant 0.29
embC 4241717 p.Arg619Trp missense_variant 0.33
embC 4241972 p.Val704Ile missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243484 c.252C>T synonymous_variant 0.33
embB 4248647 p.Gly712Ser missense_variant 0.29
embB 4248840 p.Pro776His missense_variant 0.4
aftB 4268368 p.Cys157Ser missense_variant 0.67
whiB6 4338595 c.-75delG upstream_gene_variant 1.0