TB-Profiler result

Run: SRR4033190
Summary

Run ID: SRR4033190

Sample name:

Date: 04-04-2023 05:53:48

Number of reads: 1146276

Percentage reads mapped: 94.56

Strain: lineage4.9

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
lineage4.9 Euro-American (H37Rv-like) T1 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
kasA 2519274 p.Gly387Asp missense_variant 0.12 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
mshA 576457 c.1110G>A synonymous_variant 0.25
rpoB 759732 c.-75C>T upstream_gene_variant 0.13
rpoB 761385 p.Ala527Thr missense_variant 0.15
rpoC 763442 p.Tyr25His missense_variant 0.15
rpoC 764549 p.Pro394Thr missense_variant 0.25
rpoC 765022 c.1653G>A synonymous_variant 0.12
rpoC 765098 p.Pro577Ser missense_variant 0.11
mmpL5 776660 c.1821C>T synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472167 n.322T>C non_coding_transcript_exon_variant 0.2
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.29
rrs 1472518 n.673G>C non_coding_transcript_exon_variant 0.29
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.2
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.2
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.18
rrs 1472544 n.699C>G non_coding_transcript_exon_variant 0.18
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.18
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.29
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.27
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.27
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.24
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.2
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.14
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.2
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.18
rrs 1472779 n.934G>A non_coding_transcript_exon_variant 0.18
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.17
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.25
rrs 1473147 n.1302G>C non_coding_transcript_exon_variant 0.25
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.25
rrs 1473150 n.1305T>G non_coding_transcript_exon_variant 0.25
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 0.18
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.18
rrs 1473164 n.1319C>G non_coding_transcript_exon_variant 0.18
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.17
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.15
rrs 1473179 n.1334C>T non_coding_transcript_exon_variant 0.15
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.17
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.14
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.14
rrl 1474804 n.1147C>T non_coding_transcript_exon_variant 0.21
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.31
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.33
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.36
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.36
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.33
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.33
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.2
rrl 1475687 n.2030C>T non_coding_transcript_exon_variant 0.4
rrl 1475696 n.2039T>C non_coding_transcript_exon_variant 0.33
rrl 1475703 n.2046A>G non_coding_transcript_exon_variant 0.33
rrl 1475707 n.2050T>A non_coding_transcript_exon_variant 0.25
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.22
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 1476372 n.2715T>C non_coding_transcript_exon_variant 0.41
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.5
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.5
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.5
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.52
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.52
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.35
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.29
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.15
inhA 1674952 p.Pro251Ala missense_variant 0.18
rpsA 1834359 p.Ser273Leu missense_variant 0.11
ndh 2102144 p.Ala300Val missense_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 0.11
PPE35 2169732 p.Asn294Ser missense_variant 0.12
Rv1979c 2223148 p.Thr6Lys missense_variant 0.11
pepQ 2859652 p.Ala256Val missense_variant 0.14
Rv2752c 3064926 p.Leu422Phe missense_variant 0.11
fprA 3475329 c.1323G>A synonymous_variant 0.16
Rv3236c 3612554 p.Ala188Val missense_variant 0.14
Rv3236c 3613284 c.-169delC upstream_gene_variant 0.2
fbiA 3640520 c.-23G>A upstream_gene_variant 0.11
rpoA 3878280 p.Ile76Met missense_variant 0.17
rpoA 3878352 c.156C>T synonymous_variant 0.15
ddn 3987038 c.195C>T synonymous_variant 0.11
clpC1 4039385 c.1320C>T synonymous_variant 0.12
embC 4239946 c.84C>T synonymous_variant 0.2
embC 4241688 c.1829delG frameshift_variant 0.11
embA 4245432 p.Ala734Thr missense_variant 0.13
embB 4245761 c.-753C>T upstream_gene_variant 0.15
aftB 4267702 c.1134delC frameshift_variant 0.11
ethA 4326055 c.1419C>T synonymous_variant 0.12
ethA 4327896 c.-423C>T upstream_gene_variant 0.11