TB-Profiler result

Run: SRR3732620

Summary

Run ID: SRR3732620

Sample name:

Date: 04-04-2023 05:36:39

Number of reads: 1212155

Percentage reads mapped: 99.78

Strain: lineage4.3.4.2

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
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 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
ethA 4327294 p.Tyr60* stop_gained 0.25 ethionamide
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 5600 p.His121Asn missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8101 p.Thr267Asn missense_variant 0.12
gyrA 8239 p.Arg313Leu missense_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490607 c.-176G>A upstream_gene_variant 0.17
fgd1 491278 p.Pro166Ser missense_variant 0.25
fgd1 491424 c.642C>A synonymous_variant 0.15
mshA 575406 p.Arg20His missense_variant 0.2
mshA 576331 c.984G>T synonymous_variant 0.17
ccsA 620733 c.843G>T synonymous_variant 0.14
rpoB 760431 p.Asp209His missense_variant 0.14
rpoB 762474 p.Gly890Cys missense_variant 0.17
rpoB 762623 p.Lys939Asn missense_variant 0.17
rpoC 764269 c.900G>A synonymous_variant 0.13
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776339 p.His714Gln missense_variant 0.18
mmpL5 778044 p.Ala146Val missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781402 c.-158A>T upstream_gene_variant 0.2
rplC 800954 p.Ala49Asp missense_variant 0.25
rplC 801278 p.Pro157Gln missense_variant 0.13
fbiC 1303162 p.Pro78Thr missense_variant 0.13
fbiC 1303286 c.359_361delGCA disruptive_inframe_deletion 0.15
fbiC 1303929 c.999G>T synonymous_variant 0.15
Rv1258c 1406261 c.1080C>A synonymous_variant 0.15
embR 1417076 p.Arg91Leu missense_variant 0.33
embR 1417387 c.-40C>A upstream_gene_variant 0.12
rrs 1471979 n.134T>C non_coding_transcript_exon_variant 0.22
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 1.0
inhA 1673420 c.-782C>T upstream_gene_variant 0.13
rpsA 1833461 c.-81T>C upstream_gene_variant 0.17
rpsA 1833475 c.-67G>T upstream_gene_variant 0.18
rpsA 1834123 c.582C>A synonymous_variant 0.15
rpsA 1834160 p.Gln207Lys missense_variant 0.25
rpsA 1834225 c.684C>A synonymous_variant 0.17
rpsA 1834400 p.Phe287Leu missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101974 p.Ala357Thr missense_variant 0.25
ndh 2103030 p.Gln5Lys missense_variant 0.18
ndh 2103078 c.-36C>A upstream_gene_variant 0.15
katG 2153935 p.Ala726Asp missense_variant 0.17
katG 2154017 p.Gly699Arg missense_variant 0.15
katG 2155204 p.Ser303* stop_gained 0.17
katG 2155786 p.Ala109Asp missense_variant 0.22
katG 2155802 p.Arg104Trp missense_variant 0.22
PPE35 2167928 c.2685G>T synonymous_variant 0.25
PPE35 2169939 p.Gly225Ala missense_variant 0.29
PPE35 2169941 c.672C>T synonymous_variant 0.29
PPE35 2169944 c.669G>C synonymous_variant 0.29
PPE35 2169947 c.666T>C synonymous_variant 0.29
PPE35 2170102 p.Pro171Thr missense_variant 0.17
PPE35 2170394 c.219G>A synonymous_variant 0.4
Rv1979c 2221861 p.Arg435Leu missense_variant 0.2
Rv1979c 2222700 c.465C>A synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288816 c.426G>T synonymous_variant 0.15
kasA 2518077 c.-38G>T upstream_gene_variant 0.15
kasA 2519151 p.Ser346* stop_gained 0.22
kasA 2519271 p.Ala386Asp missense_variant 0.17
eis 2714622 c.711C>A synonymous_variant 0.12
eis 2715116 p.Gly73Cys missense_variant 0.14
eis 2715423 c.-91G>T upstream_gene_variant 0.17
ahpC 2726334 p.Arg48Trp missense_variant 0.2
folC 2746660 c.938delT frameshift_variant 0.67
pepQ 2859350 p.Gln357Lys missense_variant 0.2
pepQ 2860187 p.Ala78Ser missense_variant 0.12
ribD 2987278 p.Ala147Val missense_variant 0.12
Rv2752c 3064780 p.Gly471Val missense_variant 0.15
Rv2752c 3065328 p.Asp288Glu missense_variant 0.2
Rv2752c 3065889 c.303G>T synonymous_variant 0.15
Rv2752c 3067079 c.-888C>G upstream_gene_variant 0.11
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074144 p.Asp110Asn missense_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087001 p.Ala61Asp missense_variant 0.22
fbiD 3339546 c.429G>T synonymous_variant 0.12
Rv3083 3448358 c.-146G>A upstream_gene_variant 0.22
Rv3083 3448923 c.420C>G synonymous_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474013 p.Pro3Thr missense_variant 0.15
fprA 3474180 c.174C>A synonymous_variant 0.18
fprA 3475371 c.1365C>A synonymous_variant 0.2
whiB7 3568819 c.-140C>T upstream_gene_variant 0.14
whiB7 3568857 c.-178C>A upstream_gene_variant 0.25
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612100 c.1017C>A synonymous_variant 0.2
Rv3236c 3612754 c.363G>C synonymous_variant 0.5
fbiA 3640574 p.Gly11Val missense_variant 0.33
fbiA 3641318 p.Cys259Phe missense_variant 0.12
fbiB 3641608 p.Pro25Leu missense_variant 0.14
fbiB 3642187 p.Arg218Leu missense_variant 0.12
fbiB 3642528 p.Glu332* stop_gained 0.22
alr 3840257 c.1164C>T synonymous_variant 0.2
alr 3841287 p.Ile45Thr missense_variant 0.14
ddn 3986888 p.Asp15Glu missense_variant 0.15
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038747 c.1957delC frameshift_variant 0.2
clpC1 4038821 p.Glu628Asp missense_variant 0.22
clpC1 4039560 p.Ala382Asp missense_variant 0.29
clpC1 4039673 c.1032G>A synonymous_variant 0.14
clpC1 4040234 c.471C>A synonymous_variant 0.29
panD 4044060 c.222C>T synonymous_variant 0.15
panD 4044107 p.Ala59Ser missense_variant 0.17
embC 4240145 p.Ala95Ser missense_variant 0.12
embA 4242268 c.-965T>A upstream_gene_variant 0.25
embC 4242332 p.Gly824Trp missense_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243031 c.3173delG frameshift_variant 0.29
embA 4243954 p.Arg241Leu missense_variant 0.13
embA 4245098 c.1866C>T synonymous_variant 0.12
embA 4245436 p.Met735Thr missense_variant 0.15
embA 4245493 p.Pro754Gln missense_variant 0.29
embA 4245813 p.Pro861Thr missense_variant 0.22
embA 4246338 p.Leu1036Met missense_variant 0.11
embB 4248317 p.Val602Pro missense_variant 0.33
embB 4248320 p.Gly603Thr missense_variant 0.33
embB 4249614 p.Gly1034Asp missense_variant 0.2
aftB 4267240 c.1596dupG frameshift_variant 0.14
aftB 4267266 p.Ala524Asp missense_variant 0.12
aftB 4269267 c.-431C>T upstream_gene_variant 0.25
ubiA 4269631 p.Ala68Val missense_variant 0.4
ethA 4326623 p.Pro284Leu missense_variant 0.22
ethA 4327893 c.-420C>T upstream_gene_variant 0.13
ethR 4328032 p.Ala162Thr missense_variant 0.12
whiB6 4338403 p.Arg40Leu missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407979 p.Pro75Gln missense_variant 0.18
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4408468 c.-266G>T upstream_gene_variant 0.25