TB-Profiler result

Run: SRR3732584
Summary

Run ID: SRR3732584

Sample name:

Date: 04-04-2023 05:36:09

Number of reads: 683392

Percentage reads mapped: 99.42

Strain: lineage4.3.3

Drug-resistance: MDR-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
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
rpoB 761110 p.Asp435Val missense_variant 1.0 rifampicin
tlyA 1918634 p.Gly232Asp missense_variant 1.0 capreomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
katG 2155270 p.Ala281Val missense_variant 0.25 isoniazid
pncA 2289213 p.Gln10Arg missense_variant 1.0 pyrazinamide
embB 4247469 p.Tyr319Ser missense_variant 1.0 ethambutol
gid 4407952 p.Pro84Leu missense_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 6082 p.Lys281Asn missense_variant 0.33
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7947 p.Leu216Met missense_variant 0.4
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490674 c.-109G>T upstream_gene_variant 0.14
fgd1 490698 c.-85G>A upstream_gene_variant 0.17
fgd1 491289 c.507C>A synonymous_variant 0.33
mshA 575322 c.-26C>A upstream_gene_variant 0.2
rpoB 760152 p.Cys116Ser missense_variant 0.67
rpoB 760480 p.Arg225Leu missense_variant 0.2
rpoB 760556 p.Glu250Asp missense_variant 0.22
rpoB 762276 p.Arg824Ser missense_variant 0.25
rpoB 762639 p.Gly945Trp missense_variant 0.29
rpoC 764602 c.1233C>T synonymous_variant 0.5
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765072 p.Pro568Leu missense_variant 0.18
rpoC 765621 c.2258_2259delCG frameshift_variant 0.67
rpoC 766520 p.Gly1051Ser missense_variant 0.22
rpoC 766720 c.3351C>T synonymous_variant 0.4
mmpL5 776565 p.Pro639His missense_variant 0.5
mmpR5 778406 c.-584G>T upstream_gene_variant 0.25
mmpS5 778748 p.Pro53His missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801054 c.246G>T synonymous_variant 0.67
rplC 801188 p.Met127Thr missense_variant 0.22
rplC 801198 c.390C>T synonymous_variant 0.2
fbiC 1303161 c.231G>A synonymous_variant 0.33
fbiC 1305129 c.2199C>A synonymous_variant 0.33
Rv1258c 1406924 c.416delT frameshift_variant 0.29
Rv1258c 1407517 c.-177G>T upstream_gene_variant 0.33
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.5
rrl 1473969 n.312G>T non_coding_transcript_exon_variant 1.0
rpsA 1834772 p.Arg411Ser missense_variant 0.5
rpsA 1834921 c.1380G>A synonymous_variant 0.4
rpsA 1834985 c.1445dupG frameshift_variant&stop_lost&splice_region_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102593 c.450C>T synonymous_variant 0.33
katG 2156354 c.-243G>T upstream_gene_variant 1.0
katG 2156449 c.-338G>T upstream_gene_variant 0.5
PPE35 2167824 p.Gly930Val missense_variant 0.5
PPE35 2168506 p.Gly703Ser missense_variant 0.5
Rv1979c 2222820 c.345G>T synonymous_variant 0.4
Rv1979c 2222970 c.195C>T synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289671 c.-430G>T upstream_gene_variant 0.25
kasA 2518919 p.Gly269Ser missense_variant 1.0
eis 2714871 c.462G>T synonymous_variant 0.33
eis 2715218 p.Leu39Met missense_variant 0.2
eis 2715471 c.-139C>A upstream_gene_variant 0.33
eis 2715550 c.-218G>T upstream_gene_variant 0.25
eis 2715578 c.-247delG upstream_gene_variant 0.25
folC 2747262 p.Lys113* stop_gained 0.33
ribD 2986772 c.-67C>T upstream_gene_variant 0.29
Rv2752c 3065376 c.816C>A synonymous_variant 0.5
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3073977 c.490_494delTACCA frameshift_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339058 c.-60G>T upstream_gene_variant 0.2
Rv3083 3448319 c.-185_-184insG upstream_gene_variant 0.33
Rv3083 3448850 p.Trp116Leu missense_variant 0.4
Rv3083 3449403 c.900G>A synonymous_variant 0.4
Rv3083 3449745 c.1242C>T synonymous_variant 0.4
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568532 p.Arg50Trp missense_variant 0.4
Rv3236c 3612298 c.819C>A synonymous_variant 0.2
Rv3236c 3612345 p.Arg258Trp missense_variant 0.4
fbiA 3640705 p.Gly55Trp missense_variant 0.4
fbiA 3641297 p.Leu252Ser missense_variant 0.22
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4040494 p.Gln71Lys missense_variant 0.5
embC 4240255 c.393G>T synonymous_variant 0.4
embC 4241658 p.Ser599* stop_gained 0.33
embC 4242182 p.Ala774Ser missense_variant 1.0
embA 4244364 p.Gly378Ser missense_variant 0.29
embA 4244506 p.Gly425Val missense_variant 0.29
embA 4244568 p.Arg446Cys missense_variant 0.22
embA 4245312 p.Ala694Thr missense_variant 0.67
embB 4246499 c.-15G>A upstream_gene_variant 0.29
embB 4246642 c.129G>T synonymous_variant 0.5
aftB 4267312 p.Gly509Trp missense_variant 0.29
aftB 4268190 p.Ala216Val missense_variant 0.5
aftB 4268735 c.102C>A synonymous_variant 0.67
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0