TB-Profiler result

Run: SRR4034796
Summary

Run ID: SRR4034796

Sample name:

Date: 04-04-2023 07:04:58

Number of reads: 570338

Percentage reads mapped: 99.47

Strain: lineage4.1.1

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
lineage4.1 Euro-American T;X;H None 0.99
lineage4.1.1 Euro-American (X-type) X1;X2;X3 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
ahpC 2726145 c.-48G>T upstream_gene_variant 0.13 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 6849 p.Gly537Asp missense_variant 0.29
gyrB 7019 p.Gly594Trp missense_variant 0.15
gyrA 7186 c.-116C>A upstream_gene_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491031 c.249C>A synonymous_variant 0.14
fgd1 491214 c.432C>T synonymous_variant 0.17
fgd1 491342 p.Arg187His missense_variant 1.0
fgd1 491520 c.738C>A synonymous_variant 0.17
fgd1 491572 p.Asp264Tyr missense_variant 0.2
mshA 576636 p.Trp430Leu missense_variant 0.12
ccsA 619790 c.-101G>A upstream_gene_variant 0.29
rpoB 760768 p.Pro321His missense_variant 0.13
rpoB 760848 p.Thr348Ala missense_variant 0.2
rpoB 761564 c.1758G>T synonymous_variant 0.13
rpoC 763142 c.-228C>A upstream_gene_variant 0.13
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775622 c.2859C>A synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776021 c.2460G>T synonymous_variant 0.25
mmpL5 777148 p.Pro445Thr missense_variant 0.25
mmpL5 778063 p.Gln140Lys missense_variant 0.14
mmpS5 778718 p.Ser63Tyr missense_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781417 c.-143G>T upstream_gene_variant 0.18
fbiC 1303416 c.486C>A synonymous_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473010 n.1165C>A non_coding_transcript_exon_variant 0.18
rrs 1473035 n.1190G>T non_coding_transcript_exon_variant 0.22
rrl 1475941 n.2284G>T non_coding_transcript_exon_variant 0.17
inhA 1674280 p.Arg27Trp missense_variant 0.17
inhA 1674336 c.135G>A synonymous_variant 0.18
inhA 1674829 p.Glu210* stop_gained 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917980 p.Arg14Leu missense_variant 0.18
ndh 2102311 c.732G>A synonymous_variant 0.18
ndh 2103054 c.-12G>T upstream_gene_variant 0.17
ndh 2103235 c.-193C>A upstream_gene_variant 0.4
katG 2154615 c.1497G>A synonymous_variant 0.22
katG 2154840 c.1272G>T synonymous_variant 0.22
katG 2155771 p.Arg114Leu missense_variant 0.14
Rv1979c 2222622 c.543G>T synonymous_variant 0.2
Rv1979c 2222638 p.Ala176Glu missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289160 p.Ala28Ser missense_variant 0.12
pncA 2289481 c.-240G>T upstream_gene_variant 0.2
pncA 2290236 c.-995G>T upstream_gene_variant 0.29
eis 2714503 c.829delC frameshift_variant 0.2
ahpC 2726338 p.Val49Gly missense_variant 0.4
pepQ 2859744 c.675G>T synonymous_variant 0.15
Rv2752c 3066333 c.-142G>T upstream_gene_variant 0.25
Rv2752c 3066999 c.-808C>G upstream_gene_variant 0.25
thyX 3067710 p.Ser79Leu missense_variant 0.18
thyX 3067727 c.219A>G synonymous_variant 0.15
thyX 3068070 c.-125T>C upstream_gene_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339480 c.367_368dupCA frameshift_variant 0.22
Rv3083 3449328 c.825C>A synonymous_variant 0.25
Rv3083 3449845 p.Gln448Lys missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474304 c.299delT frameshift_variant 0.13
fprA 3474778 p.Arg258Cys missense_variant 0.18
fbiA 3641447 p.Thr302Met missense_variant 0.88
fbiB 3642252 p.Leu240Met missense_variant 0.33
alr 3840319 p.Pro368Thr missense_variant 0.22
alr 3840836 c.584delC frameshift_variant 0.29
rpoA 3877553 p.Glu319Lys missense_variant 0.83
rpoA 3878657 c.-151delA upstream_gene_variant 0.14
clpC1 4038245 c.2460C>T synonymous_variant 1.0
clpC1 4039291 p.Asp472Tyr missense_variant 0.18
clpC1 4039392 p.Ala438Val missense_variant 0.22
clpC1 4040457 c.247delC frameshift_variant 0.22
embC 4239875 p.Ala5Ser missense_variant 0.14
embC 4240897 c.1035C>G synonymous_variant 1.0
embC 4242051 p.Gln730Arg missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243300 p.Ala23Val missense_variant 0.21
embA 4245461 c.2229C>A synonymous_variant 0.2
embB 4249007 p.Pro832Ser missense_variant 0.22
embB 4249408 c.2895G>A synonymous_variant 1.0
embB 4249766 p.Arg1085Ser missense_variant 0.17
aftB 4267100 c.1737C>A synonymous_variant 0.4
whiB6 4338433 p.Pro30Gln missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408068 p.Trp45Cys missense_variant 0.18