TB-Profiler result

Run: SRR4034617
Summary

Run ID: SRR4034617

Sample name:

Date: 04-04-2023 06:55:31

Number of reads: 799894

Percentage reads mapped: 99.82

Strain: lineage4.3.3

Drug-resistance: Other

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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
lineage4.3.3 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
gid 4408100 c.102delG frameshift_variant 0.17 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 0.9
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9604 p.Val768Asp missense_variant 0.25
rpoB 760969 p.Ser388* stop_gained 0.18
rpoB 761213 c.1407G>A synonymous_variant 0.12
rpoB 761822 c.2016C>A synonymous_variant 0.29
rpoC 764649 p.Arg427Leu missense_variant 0.14
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765804 p.Thr812Ile missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776699 c.1782C>A synonymous_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781624 p.Ala22Val missense_variant 0.13
fbiC 1303388 p.Ala153Glu missense_variant 0.12
fbiC 1304072 p.Thr381Ile missense_variant 0.12
fbiC 1304502 c.1572G>T synonymous_variant 0.22
fbiC 1304527 p.Asp533Tyr missense_variant 0.17
fbiC 1305037 p.Arg703Trp missense_variant 0.25
Rv1258c 1406507 c.834T>C synonymous_variant 0.12
Rv1258c 1406558 c.782delG frameshift_variant 0.15
Rv1258c 1406935 p.Gly136Cys missense_variant 0.17
Rv1258c 1407169 p.Ala58Thr missense_variant 0.13
embR 1416289 c.1059G>A synonymous_variant 0.12
embR 1416344 p.Thr335Met missense_variant 0.15
embR 1416918 p.Glu144Lys missense_variant 0.11
embR 1417147 c.201C>T synonymous_variant 0.18
atpE 1461203 c.159C>T synonymous_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473265 n.1421delA non_coding_transcript_exon_variant 0.2
rrl 1476017 n.2360G>T non_coding_transcript_exon_variant 0.15
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 1.0
fabG1 1674140 p.Gly234Asp missense_variant 0.11
inhA 1674959 p.Thr253Ser missense_variant 0.29
rpsA 1833988 c.447C>A synonymous_variant 0.14
rpsA 1834720 c.1181_1182delAG frameshift_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102551 c.492G>T synonymous_variant 0.15
ndh 2103120 c.-78C>A upstream_gene_variant 0.12
katG 2155081 p.Thr344Lys missense_variant 0.12
katG 2155253 p.Glu287* stop_gained 0.22
PPE35 2168699 c.1914C>A synonymous_variant 0.12
PPE35 2170377 p.Ala79Val missense_variant 0.17
PPE35 2170698 c.-86G>T upstream_gene_variant 0.11
Rv1979c 2222683 p.Trp161Leu missense_variant 0.22
Rv1979c 2223051 p.Glu38Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518033 c.-82C>T upstream_gene_variant 0.17
kasA 2518919 p.Gly269Ser missense_variant 1.0
kasA 2519221 c.1107G>A synonymous_variant 0.5
eis 2714663 p.Ala224Thr missense_variant 0.25
eis 2715502 c.-170C>T upstream_gene_variant 0.25
pepQ 2860039 c.379delA frameshift_variant 0.15
ribD 2987131 c.296dupG frameshift_variant 0.15
Rv2752c 3065252 p.Ala314Thr missense_variant 0.15
Rv2752c 3065824 p.Pro123Leu missense_variant 0.9
Rv2752c 3065881 p.Gly104Val missense_variant 0.18
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074522 c.-51C>T upstream_gene_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087549 p.Ala244Thr missense_variant 0.15
ald 3087614 c.795G>T synonymous_variant 0.12
fbiD 3339170 p.Arg18Pro missense_variant 0.18
fbiD 3339338 p.Gly74Val missense_variant 0.22
fbiD 3339371 p.Pro85His missense_variant 0.17
fbiD 3339702 c.585G>T synonymous_variant 0.25
Rv3083 3449982 c.1479G>A synonymous_variant 0.4
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474548 p.His181Arg missense_variant 0.14
fprA 3474658 p.Leu218Ile missense_variant 0.2
fprA 3474673 c.668delT frameshift_variant 0.22
fprA 3474804 c.798C>A synonymous_variant 0.14
Rv3236c 3612903 p.Ala72Ser missense_variant 0.2
fbiB 3640776 c.-759C>A upstream_gene_variant 0.13
fbiB 3641982 c.451_452delAC frameshift_variant 0.18
fbiB 3642264 p.Gly244Trp missense_variant 0.17
fbiB 3642345 p.Val271Met missense_variant 0.18
fbiB 3642504 p.Asp324Tyr missense_variant 0.15
alr 3840282 p.Ala380Val missense_variant 0.18
alr 3840859 p.Val188Phe missense_variant 0.12
rpoA 3878497 p.Ser4* stop_gained 0.25
clpC1 4038285 p.Trp807Ser missense_variant 0.13
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039411 p.Arg432Ser missense_variant 0.12
embC 4240630 c.768C>A synonymous_variant 0.18
embC 4240658 p.Arg266Ser missense_variant 0.18
embC 4240698 p.Ala279Asp missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244850 c.1618C>A synonymous_variant 0.12
embB 4245848 c.-666C>T upstream_gene_variant 0.2
embB 4247966 p.Ala485Ser missense_variant 0.13
embB 4249028 p.Pro839Thr missense_variant 0.13
aftB 4267718 c.1119C>T synonymous_variant 0.12
ethA 4326144 p.Asp444Tyr missense_variant 0.14
ethA 4326540 p.Val312Leu missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408098 c.105G>A synonymous_variant 0.14
gid 4408156 p.Leu16Arg missense_variant 1.0