TB-Profiler result

Run: SRR19428521
Summary

Run ID: SRR19428521

Sample name:

Date: 03-04-2023 21:38:59

Number of reads: 282301

Percentage reads mapped: 99.64

Strain: lineage2

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
lineage2 East-Asian Beijing RD105 0.08
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 761155 p.Ser450Leu missense_variant 0.21 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.47 isoniazid
embB 4247431 p.Met306Ile missense_variant 0.56 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 5807 c.569_570delTC frameshift_variant 0.11
gyrB 6112 p.Met291Ile missense_variant 0.2
gyrB 6124 c.885C>T synonymous_variant 0.29
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7548 p.Asn83Asp missense_variant 0.15
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7602 p.Gln101Lys missense_variant 0.11
gyrA 7860 p.Thr187Ser missense_variant 0.1
gyrA 8688 p.Ala463Ser missense_variant 0.15
gyrA 8864 c.1563C>A synonymous_variant 0.15
gyrA 9143 c.1842T>C synonymous_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.79
mshA 575907 p.Ala187Val missense_variant 0.3
ccsA 620625 p.Ile245Met missense_variant 0.25
rpoB 759746 c.-61C>T upstream_gene_variant 0.89
rpoB 760866 p.Gly354Cys missense_variant 0.22
rpoB 761248 p.Glu481Ala missense_variant 0.11
rpoC 762434 c.-936T>G upstream_gene_variant 0.6
rpoC 763031 c.-339T>C upstream_gene_variant 0.83
rpoC 765171 p.Pro601Leu missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.18
mmpS5 778941 c.-36A>G upstream_gene_variant 0.18
mmpS5 779615 c.-710C>G upstream_gene_variant 0.43
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801205 p.Arg133Cys missense_variant 0.2
fbiC 1303051 p.Val41Met missense_variant 0.12
fbiC 1303238 p.His103Leu missense_variant 0.22
fbiC 1303389 c.459G>A synonymous_variant 0.4
Rv1258c 1407084 p.Val86Ala missense_variant 0.13
Rv1258c 1407323 c.18C>T synonymous_variant 0.22
embR 1416233 p.Cys372Tyr missense_variant 0.18
embR 1416889 c.459G>T synonymous_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471860 n.15T>C non_coding_transcript_exon_variant 0.11
rrs 1472351 n.506G>A non_coding_transcript_exon_variant 0.12
rrl 1473584 n.-74G>T upstream_gene_variant 0.12
rrl 1474388 n.731A>G non_coding_transcript_exon_variant 0.17
fabG1 1673470 p.Pro11Thr missense_variant 0.15
inhA 1674590 p.Met130Thr missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918726 p.Ala263Thr missense_variant 0.18
ndh 2101875 p.Phe390Leu missense_variant 0.25
ndh 2102422 c.621C>T synonymous_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 0.95
katG 2156364 c.-253T>A upstream_gene_variant 0.12
katG 2156377 c.-266C>T upstream_gene_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 0.77
PPE35 2167983 p.Gly877Asp missense_variant 0.24
PPE35 2168159 c.2453delA frameshift_variant 0.13
PPE35 2168804 c.1809C>T synonymous_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.44
PPE35 2170053 p.Thr187Ser missense_variant 0.44
PPE35 2170461 p.Gly51Glu missense_variant 1.0
PPE35 2170499 c.114A>G synonymous_variant 0.17
Rv1979c 2221739 p.Asp476Asn missense_variant 0.15
Rv1979c 2222957 p.Arg70Gly missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.65
pncA 2289365 c.-125delC upstream_gene_variant 0.79
kasA 2518348 c.234A>T synonymous_variant 0.12
eis 2714526 c.805_806delAC frameshift_variant 0.17
eis 2715348 c.-18_-17delAT upstream_gene_variant 0.14
ahpC 2726105 c.-88G>A upstream_gene_variant 0.83
folC 2746294 c.1305C>T synonymous_variant 0.33
folC 2746988 p.Tyr204Cys missense_variant 0.14
pepQ 2859920 p.Arg167* stop_gained 0.15
ribD 2986818 c.-21C>T upstream_gene_variant 0.13
Rv2752c 3064632 c.1560C>T synonymous_variant 0.11
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.22
thyX 3067203 p.Thr248Ile missense_variant 0.17
thyA 3073732 p.Val247Ala missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086877 p.Pro20Ser missense_variant 0.12
fbiD 3339741 c.624G>A synonymous_variant 0.22
Rv3083 3449065 p.Thr188Pro missense_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475215 c.1209C>T synonymous_variant 0.2
fprA 3475317 c.1311C>T synonymous_variant 0.15
Rv3236c 3612813 p.Thr102Ala missense_variant 0.13
fbiA 3640961 p.Ala140Asp missense_variant 0.15
fbiA 3641191 p.Val217Met missense_variant 0.12
alr 3840224 c.1197C>A synonymous_variant 0.1
alr 3841410 p.Phe4Tyr missense_variant 0.1
clpC1 4038654 p.Gly684Val missense_variant 0.1
clpC1 4039552 p.Leu385Met missense_variant 0.12
embC 4240172 p.Val104Met missense_variant 0.37
embC 4240318 p.Cys152* stop_gained 0.13
embC 4241562 p.Arg567His missense_variant 0.89
embC 4242075 p.Arg738Gln missense_variant 0.78
embA 4242349 c.-884A>T upstream_gene_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243323 p.Val31Ile missense_variant 0.44
embA 4243460 c.228C>T synonymous_variant 0.42
embA 4243848 p.Val206Met missense_variant 0.29
embA 4246045 p.Val938Ala missense_variant 0.2
embB 4247161 c.648G>C synonymous_variant 0.38
embB 4248102 p.Leu530Gln missense_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 0.25
ubiA 4269387 p.Glu149Asp missense_variant 0.32
ethA 4326213 c.1261C>A synonymous_variant 0.25
ethA 4326398 p.Gln359Arg missense_variant 0.18
ethA 4326609 p.Trp289Arg missense_variant 0.12
ethA 4326953 p.Asp174Gly missense_variant 0.12
ethR 4328051 p.Ala168Val missense_variant 0.67
ethA 4328209 c.-736C>A upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.95
gid 4407911 p.Thr98Ala missense_variant 0.14
gid 4407927 p.Glu92Asp missense_variant 0.33