TB-Profiler result

Run: SRR4033447
Summary

Run ID: SRR4033447

Sample name:

Date: 04-04-2023 06:06:20

Number of reads: 1407980

Percentage reads mapped: 99.65

Strain: lineage4.3.2.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.99
lineage4.3.2 Euro-American (LAM) LAM3 None 1.0
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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
katG 2154581 c.1530delC frameshift_variant 0.11 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 5520 p.Pro94Leu missense_variant 1.0
gyrB 6773 p.Gly512Arg missense_variant 0.14
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7472 c.171T>C synonymous_variant 0.12
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7951 p.Ala217Gly missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491108 p.Glu109Val missense_variant 0.14
rpoB 759847 p.Ser14Thr missense_variant 0.15
rpoB 761382 p.Thr526Ala missense_variant 0.12
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766585 c.3217delG frameshift_variant 0.18
mmpL5 775621 c.2859delC frameshift_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775818 p.Phe888Tyr missense_variant 0.18
mmpS5 778746 p.Lys54Glu missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781469 c.-91C>A upstream_gene_variant 0.12
rplC 800760 c.-49C>A upstream_gene_variant 0.14
rplC 801331 c.523_524insA frameshift_variant 0.12
rplC 801431 p.Val208Ala missense_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472197 n.352A>T non_coding_transcript_exon_variant 0.2
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrs 1472449 n.604C>T non_coding_transcript_exon_variant 0.25
rrl 1473784 n.130delC non_coding_transcript_exon_variant 0.25
rrl 1474946 n.1289C>T non_coding_transcript_exon_variant 0.4
rpsA 1833440 c.-102G>C upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102463 p.Glu194* stop_gained 0.14
ndh 2102936 p.Ala36Gly missense_variant 0.17
ndh 2102969 p.Gly25Ala missense_variant 0.12
ndh 2103066 c.-24T>C upstream_gene_variant 0.12
katG 2154164 p.Ser650Pro missense_variant 0.12
PPE35 2168888 c.1725G>A synonymous_variant 0.22
PPE35 2168911 p.Ile568Val missense_variant 0.29
PPE35 2169999 p.Ala205Val missense_variant 0.12
PPE35 2170301 p.Met104Ile missense_variant 0.13
Rv1979c 2222436 c.729A>G synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223347 c.-183C>A upstream_gene_variant 0.17
Rv1979c 2223353 c.-189T>A upstream_gene_variant 0.17
eis 2714424 c.909C>G synonymous_variant 0.12
ahpC 2726003 c.-190C>T upstream_gene_variant 0.15
Rv2752c 3065646 c.546C>G synonymous_variant 0.11
thyX 3067384 p.Asn188Asp missense_variant 0.11
thyX 3067446 p.Ala167Gly missense_variant 0.11
thyA 3073868 p.Thr202Ala missense_variant 0.94
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087910 p.Thr364Asn missense_variant 0.13
Rv3083 3448465 c.-39T>C upstream_gene_variant 0.12
Rv3083 3448488 c.-16C>G upstream_gene_variant 0.12
Rv3083 3448494 c.-10T>A upstream_gene_variant 0.13
Rv3083 3448547 p.Ser15Cys missense_variant 0.1
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841135 p.Glu96Lys missense_variant 0.2
alr 3841360 p.Thr21Ala missense_variant 0.12
rpoA 3877670 p.Glu280Lys missense_variant 0.14
rpoA 3878199 c.309T>A synonymous_variant 0.14
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4241768 p.Ser636Gly missense_variant 0.14
embC 4242009 p.Val716Ala missense_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246864 c.351C>A synonymous_variant 0.15
embB 4249629 p.Ile1039Asn missense_variant 0.13
aftB 4268611 p.Pro76Ser missense_variant 0.2
ethA 4326188 p.Arg429Pro missense_variant 0.15
ethA 4327206 p.Ala90Thr missense_variant 0.12
ethA 4327725 c.-252C>A upstream_gene_variant 0.14
ethR 4327822 p.Glu92Lys missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4408289 c.-87T>A upstream_gene_variant 0.15