TB-Profiler result

Run: SRR4034223

Summary

Run ID: SRR4034223

Sample name:

Date: 04-04-2023 06:38:48

Number of reads: 851509

Percentage reads mapped: 99.58

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 1.0
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 2154312 c.1799delA frameshift_variant 0.15 isoniazid
pncA 2289151 c.90delC frameshift_variant 0.18 pyrazinamide
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 5465 p.Glu76Lys missense_variant 0.14
gyrB 5520 p.Pro94Leu missense_variant 1.0
gyrB 7029 p.Ala597Val missense_variant 0.25
gyrA 7162 c.-140C>A upstream_gene_variant 0.13
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9181 p.Thr627Asn missense_variant 0.25
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 760201 p.Glu132Val missense_variant 0.12
rpoB 761947 p.Leu714Gln missense_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765140 p.Glu591* stop_gained 0.12
rpoC 765148 c.1783delG frameshift_variant 0.1
rpoC 765877 c.2508C>A synonymous_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778359 p.Val41Ala missense_variant 0.12
mmpS5 779587 c.-683delC upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801276 c.468G>A synonymous_variant 0.14
fbiC 1303127 p.Arg66Pro missense_variant 0.25
atpE 1461182 c.138A>G synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrs 1473097 n.1252G>A non_coding_transcript_exon_variant 0.25
rrl 1474220 n.563G>A non_coding_transcript_exon_variant 0.17
rrl 1475336 n.1679C>T non_coding_transcript_exon_variant 0.18
rrl 1475417 n.1761delA non_coding_transcript_exon_variant 0.14
fabG1 1673524 p.Leu29Met missense_variant 0.13
fabG1 1674017 p.Ala193Val missense_variant 0.5
inhA 1674277 p.Ala26Thr missense_variant 0.15
rpsA 1833576 p.Ala12Val missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918726 p.Ala263Thr missense_variant 0.25
katG 2154936 c.1176G>A synonymous_variant 0.33
PPE35 2167799 c.2813delG frameshift_variant 0.13
PPE35 2168000 c.2612delT frameshift_variant 0.13
PPE35 2168997 p.Ile539Thr missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289815 c.-574C>G upstream_gene_variant 0.25
eis 2714301 c.1032T>C synonymous_variant 0.2
eis 2714309 p.Pro342Thr missense_variant 0.15
eis 2715058 p.Arg92His missense_variant 0.12
folC 2746221 p.Ala460Thr missense_variant 0.17
folC 2747431 c.168G>A synonymous_variant 0.12
pepQ 2859438 c.981T>G synonymous_variant 0.33
pepQ 2859804 c.615C>T synonymous_variant 0.17
Rv2752c 3064683 c.1509G>A synonymous_variant 0.13
Rv2752c 3067104 c.-913C>T upstream_gene_variant 0.33
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087466 p.His216Leu missense_variant 0.14
fbiD 3339273 c.156T>G synonymous_variant 0.25
Rv3083 3448840 p.Gln113* stop_gained 0.15
fprA 3473923 c.-84G>T upstream_gene_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474779 p.Arg258His missense_variant 0.12
whiB7 3568583 p.Pro33Thr missense_variant 0.13
Rv3236c 3612149 p.Gln323Pro missense_variant 0.15
Rv3236c 3613272 c.-156G>A upstream_gene_variant 0.2
fbiB 3642414 p.Pro294Ser missense_variant 0.12
alr 3840547 p.Gly292Cys missense_variant 0.2
alr 3840988 p.Val145Met missense_variant 0.12
alr 3841032 c.388delG frameshift_variant 0.2
alr 3841292 c.128delG frameshift_variant 0.11
alr 3841504 c.-84C>A upstream_gene_variant 0.15
rpoA 3877707 p.Glu267Asp missense_variant 0.22
rpoA 3878217 c.290delT frameshift_variant 0.15
rpoA 3878383 c.124dupC frameshift_variant 0.25
ddn 3986947 p.Glu35Gly missense_variant 0.18
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039684 p.Arg341Cys missense_variant 0.15
clpC1 4040205 p.Thr167Met missense_variant 0.18
clpC1 4040831 c.-127C>A upstream_gene_variant 0.33
panD 4044312 c.-32delC upstream_gene_variant 0.15
embC 4240693 c.831T>C synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244453 c.1221G>A synonymous_variant 0.25
embB 4247635 c.1122G>T synonymous_variant 0.13
embB 4248734 p.Arg741Trp missense_variant 0.13
embB 4248993 p.Asn827Ser missense_variant 0.17
ubiA 4269896 c.-63G>A upstream_gene_variant 0.17
ethA 4328148 c.-675C>G upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407627 c.576C>T synonymous_variant 0.13
gid 4407629 c.573delT frameshift_variant 0.13
gid 4408156 p.Leu16Arg missense_variant 1.0