TB-Profiler result

Run: SRR6046851
Summary

Run ID: SRR6046851

Sample name:

Date: 04-04-2023 12:24:20

Number of reads: 160687

Percentage reads mapped: 51.31

Strain: lineage4

Drug-resistance: Other

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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 0.95
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 1472733 n.888G>A non_coding_transcript_exon_variant 1.0 streptomycin
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 5837 p.Leu200Ile missense_variant 0.5
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9306 p.Asp669Tyr missense_variant 0.67
gyrA 9484 c.2184delA frameshift_variant 0.5
fgd1 490723 c.-60C>T upstream_gene_variant 0.29
fgd1 490751 c.-32T>G upstream_gene_variant 0.33
fgd1 491363 p.Cys194Phe missense_variant 0.33
fgd1 491477 p.Lys232Arg missense_variant 0.33
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576001 p.Asp218Glu missense_variant 0.4
ccsA 619787 c.-104T>A upstream_gene_variant 0.67
ccsA 619848 c.-43C>A upstream_gene_variant 0.25
ccsA 620348 p.Gly153Glu missense_variant 0.25
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761003 c.1197C>A synonymous_variant 1.0
rpoB 761659 p.Pro618Leu missense_variant 0.67
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764762 p.His465Asn missense_variant 0.25
rpoC 766645 p.Glu1092Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776126 p.Cys785* stop_gained 0.29
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpR5 779315 p.Arg109Gln missense_variant 0.25
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801426 c.618C>T synonymous_variant 0.29
fbiC 1303016 p.Val29Gly missense_variant 0.5
fbiC 1303194 c.264C>T synonymous_variant 0.5
Rv1258c 1407019 p.Val108Leu missense_variant 0.5
Rv1258c 1407285 p.Ala19Val missense_variant 0.5
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 1.0
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 1.0
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.5
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.33
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.33
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.33
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.33
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.33
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.33
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.33
rrs 1473281 n.1436C>A non_coding_transcript_exon_variant 0.33
rrs 1473282 n.1437C>G non_coding_transcript_exon_variant 0.33
rrs 1473288 n.1443C>A non_coding_transcript_exon_variant 0.33
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.33
rrs 1473291 n.1446G>T non_coding_transcript_exon_variant 0.33
rrs 1473296 n.1451G>C non_coding_transcript_exon_variant 0.33
rrs 1473297 n.1452G>T non_coding_transcript_exon_variant 0.33
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.33
rrs 1473327 n.1482A>G non_coding_transcript_exon_variant 0.5
rrs 1473328 n.1483C>T non_coding_transcript_exon_variant 0.5
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.67
rrl 1473769 n.112T>C non_coding_transcript_exon_variant 0.67
inhA 1673574 c.-628C>A upstream_gene_variant 0.5
inhA 1673676 c.-526G>T upstream_gene_variant 0.5
rpsA 1833865 p.Gln108His missense_variant 0.25
rpsA 1834099 c.558C>T synonymous_variant 0.5
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1918068 c.129C>A synonymous_variant 0.5
ndh 2103225 c.-183A>C upstream_gene_variant 0.43
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155998 p.Trp38Cys missense_variant 1.0
PPE35 2167975 p.Ala880Ser missense_variant 0.5
Rv1979c 2221779 p.Met462Ile missense_variant 0.33
Rv1979c 2221917 c.1248G>T synonymous_variant 0.67
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289830 c.-589G>A upstream_gene_variant 1.0
ahpC 2726418 p.Glu76Lys missense_variant 1.0
folC 2746390 c.1209G>T synonymous_variant 0.5
folC 2747152 p.Met149Ile missense_variant 0.5
folC 2747215 p.Glu128Asp missense_variant 0.4
pepQ 2859751 p.Gly223Val missense_variant 0.5
ribD 2987183 c.345G>T synonymous_variant 1.0
ribD 2987599 p.Arg254Leu missense_variant 0.25
Rv2752c 3064589 p.Arg535Ser missense_variant 0.5
thyX 3067339 p.His203Asn missense_variant 0.4
thyX 3067481 c.465C>A synonymous_variant 0.33
thyA 3073815 p.Gln219His missense_variant 0.67
ald 3086766 c.-54C>A upstream_gene_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339707 p.Ala197Val missense_variant 0.18
Rv3083 3448368 c.-136C>T upstream_gene_variant 0.5
Rv3083 3448650 c.147C>A synonymous_variant 0.33
Rv3083 3449389 p.Arg296Trp missense_variant 0.18
Rv3083 3449823 p.Asn440Lys missense_variant 0.4
Rv3083 3449907 p.Lys468Asn missense_variant 0.5
fprA 3474750 p.Asn248Lys missense_variant 0.2
Rv3236c 3612799 c.318G>T synonymous_variant 0.33
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640764 p.Asp74Glu missense_variant 0.29
fbiB 3641343 c.-192C>G upstream_gene_variant 0.4
fbiB 3641790 c.256T>C synonymous_variant 0.4
alr 3840797 c.624C>T synonymous_variant 0.33
alr 3841612 c.-193_-192insC upstream_gene_variant 0.14
rpoA 3878078 p.Arg144Cys missense_variant 0.5
clpC1 4038494 c.2211G>T synonymous_variant 0.22
panD 4044478 c.-197G>T upstream_gene_variant 0.5
embC 4241188 c.1326C>A synonymous_variant 0.4
embC 4242639 p.Trp926Leu missense_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243032 p.Trp1057Leu missense_variant 0.5
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245187 p.Thr652Lys missense_variant 0.5
embA 4245227 p.His665Gln missense_variant 0.29
embA 4245637 p.Pro802Leu missense_variant 1.0
embA 4246048 p.Ala939Glu missense_variant 1.0
embB 4248252 p.Gly580Val missense_variant 1.0
aftB 4267132 p.Pro569Thr missense_variant 0.25
aftB 4267412 c.1425T>A synonymous_variant 0.22
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethR 4327687 p.Val47Ile missense_variant 0.4
ethA 4327863 c.-390G>C upstream_gene_variant 0.5
ethA 4328298 c.-825G>A upstream_gene_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0