TB-Profiler result

Run: SRR3743189
Summary

Run ID: SRR3743189

Sample name:

Date: 04-04-2023 05:40:28

Number of reads: 1811621

Percentage reads mapped: 99.01

Strain: lineage4.2.1

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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 None 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
gyrA 7582 p.Asp94Gly missense_variant 0.18 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
embA 4243221 c.-12C>T upstream_gene_variant 0.11 ethambutol
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 7156 p.Asp639Glu missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8461 c.1161delA frameshift_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491123 p.Ile114Thr missense_variant 0.12
mshA 575865 p.Leu173Ser missense_variant 0.18
mshA 576766 c.1419G>T synonymous_variant 0.12
rpoB 759930 p.Leu42Ile missense_variant 0.1
rpoC 763616 c.250delC frameshift_variant 0.12
rpoC 763735 c.366G>T synonymous_variant 1.0
rpoC 764220 p.Gly284Val missense_variant 0.12
rpoC 764725 p.Phe452Leu missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775968 p.Met838Thr missense_variant 0.12
mmpL5 778960 c.-480G>T upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781414 c.-146G>A upstream_gene_variant 0.11
fbiC 1303537 c.607C>A synonymous_variant 0.29
embR 1416359 p.Ala330Asp missense_variant 0.13
embR 1416788 p.Ala187Asp missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673357 c.-83G>A upstream_gene_variant 0.12
fabG1 1673359 c.-81T>C upstream_gene_variant 0.12
fabG1 1673361 c.-79C>G upstream_gene_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.11
fabG1 1673560 p.Lys41His missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918606 p.Val223Ile missense_variant 0.11
katG 2153970 p.Asp714Glu missense_variant 0.18
katG 2155255 p.Pro286Arg missense_variant 0.13
katG 2155371 c.741C>T synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 1.0
PPE35 2170331 c.282G>T synonymous_variant 0.13
Rv1979c 2222804 p.Ala121Thr missense_variant 0.15
Rv1979c 2222834 p.Ser111Pro missense_variant 0.15
Rv1979c 2222926 p.Ala80Asp missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288714 c.528C>A synonymous_variant 0.12
pncA 2290159 c.-918A>C upstream_gene_variant 0.25
pncA 2290202 c.-961C>T upstream_gene_variant 0.12
thyX 3067387 p.Gly187Cys missense_variant 0.18
thyX 3067699 c.246delC frameshift_variant 0.12
thyX 3067923 p.Arg8Leu missense_variant 0.13
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087397 p.Thr193Ile missense_variant 0.11
Rv3083 3448752 c.250delT frameshift_variant 0.11
Rv3083 3449617 c.1116delC frameshift_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474817 p.Phe271Leu missense_variant 0.25
Rv3236c 3612024 p.Val365Phe missense_variant 0.13
Rv3236c 3612931 c.186G>T synonymous_variant 0.11
fbiB 3641736 p.Glu68Lys missense_variant 0.17
rpoA 3878347 p.Ile54Thr missense_variant 0.11
clpC1 4039421 c.1283delT frameshift_variant 0.15
embC 4240049 c.191delA frameshift_variant 0.13
embC 4242444 p.Pro861Leu missense_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244942 p.Trp570Cys missense_variant 0.25
embA 4245645 p.Ala805Pro missense_variant 0.13
embA 4246030 p.Pro933Gln missense_variant 0.11
embB 4246205 c.-309A>G upstream_gene_variant 0.2
embB 4249594 c.3081G>A synonymous_variant 1.0
aftB 4267604 c.1233C>A synonymous_variant 0.12
aftB 4267905 c.928_931dupGCCG frameshift_variant 0.29
ethR 4326778 c.-771G>A upstream_gene_variant 1.0
ethR 4326949 c.-600A>G upstream_gene_variant 0.12
ethA 4328376 c.-903G>C upstream_gene_variant 0.97
whiB6 4338595 c.-75delG upstream_gene_variant 1.0