TB-Profiler result

Run: SRR11972170
Summary

Run ID: SRR11972170

Sample name:

Date: 03-04-2023 05:30:52

Number of reads: 395522

Percentage reads mapped: 98.78

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 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 2155555 p.Gly186Val missense_variant 0.22 isoniazid
ethA 4326217 c.1256delT frameshift_variant 0.2 ethionamide
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 6414 p.Leu392Pro missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8504 c.1203G>T synonymous_variant 0.29
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760300 p.Thr165Asn missense_variant 0.13
rpoB 760513 p.Gly236Val missense_variant 0.25
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765478 c.2109T>C synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777157 c.1324C>A synonymous_variant 0.4
mmpL5 777164 c.1317C>T synonymous_variant 0.4
mmpL5 779280 c.-800G>A upstream_gene_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303835 p.Ala302Val missense_variant 0.33
Rv1258c 1406368 p.Tyr325Asp missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472193 n.348A>G non_coding_transcript_exon_variant 0.19
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.24
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.17
rrs 1472373 n.528G>A non_coding_transcript_exon_variant 0.21
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.23
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.25
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.23
rrs 1472390 n.545T>A non_coding_transcript_exon_variant 0.25
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.25
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.22
rrs 1472415 n.570T>G non_coding_transcript_exon_variant 0.22
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.17
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.17
fabG1 1673357 c.-83G>A upstream_gene_variant 0.14
fabG1 1673359 c.-81T>C upstream_gene_variant 0.14
fabG1 1673361 c.-79C>G upstream_gene_variant 0.14
fabG1 1673983 c.548delC frameshift_variant 0.33
rpsA 1834845 c.1313_1315delCCG disruptive_inframe_deletion 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155147 p.Thr322Met missense_variant 0.22
PPE35 2167814 c.2799C>T synonymous_variant 0.18
PPE35 2167868 c.2745A>C synonymous_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167955 c.2658A>C synonymous_variant 0.14
PPE35 2169902 c.711G>C synonymous_variant 0.13
PPE35 2170147 p.Ser156Ala missense_variant 0.22
PPE35 2170157 p.Ala152Ser missense_variant 0.21
PPE35 2170247 p.Ile122Met missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2518864 c.750G>C synonymous_variant 0.33
ahpC 2726037 c.-156G>T upstream_gene_variant 0.18
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ribD 2986863 p.Ala9Thr missense_variant 0.29
Rv2752c 3064662 c.1529delA frameshift_variant 0.18
Rv2752c 3065000 p.Gly398Arg missense_variant 0.2
thyX 3067882 p.Asp22Asn missense_variant 0.4
thyA 3074210 p.Gly88Ser missense_variant 0.18
thyA 3074641 c.-170C>T upstream_gene_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087421 p.Ile201Thr missense_variant 0.22
fbiD 3339661 p.Trp182Gly missense_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475224 c.1218G>A synonymous_variant 0.33
whiB7 3568797 c.-118G>C upstream_gene_variant 0.13
Rv3236c 3612070 c.1047G>A synonymous_variant 0.5
alr 3841473 c.-53G>A upstream_gene_variant 1.0
clpC1 4038768 p.Arg646Pro missense_variant 0.33
clpC1 4039334 c.1371G>T synonymous_variant 0.29
embC 4241855 p.Leu665Phe missense_variant 0.18
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242648 p.Leu929Arg missense_variant 0.5
embB 4247835 p.Thr441Lys missense_variant 0.29
embB 4248751 c.2238C>A synonymous_variant 0.5
aftB 4267148 c.1689A>G synonymous_variant 0.12
ubiA 4268941 p.Ala298Val missense_variant 0.18
ethA 4328215 c.-742C>A upstream_gene_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0