TB-Profiler result

Run: ERR4797603
Summary

Run ID: ERR4797603

Sample name:

Date: 01-04-2023 07:46:28

Number of reads: 2486350

Percentage reads mapped: 99.37

Strain: lineage1.1.2

Drug-resistance: RR-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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 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 761113 p.Gln436Leu missense_variant 0.17 rifampicin
rpsL 781585 p.Arg9His missense_variant 0.12 streptomycin
tlyA 1918322 c.385delG frameshift_variant 0.17 capreomycin
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 5076 c.-164_-163insT upstream_gene_variant 1.0
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 8556 p.Ala419Ser missense_variant 0.17
gyrA 9036 p.Ala579Ser missense_variant 0.11
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575327 c.-21G>A upstream_gene_variant 0.14
mshA 576363 p.Leu339Ser missense_variant 0.14
rpoB 760363 p.Asp186Gly missense_variant 0.11
rpoB 760422 p.Leu206Ile missense_variant 0.11
rpoB 761231 c.1425C>T synonymous_variant 1.0
rpoB 763018 c.3213_3214delGG frameshift_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764163 p.Ile265Asn missense_variant 0.12
rpoC 765171 p.Pro601Leu missense_variant 0.95
rpoC 765358 p.Met663Ile missense_variant 1.0
rpoC 765603 p.Ile745Thr missense_variant 0.11
rpoC 765614 p.Tyr749His missense_variant 0.11
rpoC 765909 c.2542_2544delGAG conservative_inframe_deletion 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781561 c.2T>C start_lost 0.11
fbiC 1304650 p.Ala574Thr missense_variant 0.12
Rv1258c 1406246 c.1094delT frameshift_variant 0.13
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417200 c.147delC frameshift_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474352 n.695G>A non_coding_transcript_exon_variant 0.11
rrl 1475881 n.2224T>A non_coding_transcript_exon_variant 0.13
rpsA 1833518 c.-24C>T upstream_gene_variant 1.0
rpsA 1834404 p.Ala288Val missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917993 c.54A>T synonymous_variant 0.18
ndh 2101881 c.1160_1161delTC frameshift_variant 0.17
ndh 2102221 c.822G>A synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155736 p.Met126Val missense_variant 0.18
katG 2155871 c.238_240delATC conservative_inframe_deletion 0.18
PPE35 2167701 p.Ala971Val missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169049 p.Ile522Leu missense_variant 0.23
Rv1979c 2221992 c.1173C>A synonymous_variant 0.12
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289167 c.75C>G synonymous_variant 0.11
pncA 2290018 c.-777C>T upstream_gene_variant 1.0
pncA 2290226 c.-985T>C upstream_gene_variant 0.1
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519235 c.1122_1124delGAC disruptive_inframe_deletion 0.11
ahpC 2726041 c.-152A>G upstream_gene_variant 0.11
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065545 c.646delA frameshift_variant 0.14
thyA 3074459 p.Glu5Lys missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086878 c.61delG frameshift_variant 0.12
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473944 c.-63A>G upstream_gene_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474110 p.Ala35Val missense_variant 0.15
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fbiB 3641343 c.-192C>T upstream_gene_variant 0.12
rpoA 3878630 c.-123G>C upstream_gene_variant 0.36
clpC1 4038408 p.Pro766Arg missense_variant 0.12
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239821 c.-42C>T upstream_gene_variant 0.14
embC 4240646 p.Phe262Leu missense_variant 0.11
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241264 p.Gly468Ser missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242945 p.Asn1028Ser missense_variant 0.11
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 0.91
embA 4246326 p.Phe1032Leu missense_variant 0.12
embB 4246548 p.Pro12Gln missense_variant 0.11
embB 4246555 c.42G>C synonymous_variant 0.12
embB 4246556 p.Ala15Pro missense_variant 0.12
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4268486 p.Met117Ile missense_variant 0.14
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269453 c.-617A>G upstream_gene_variant 0.14
ubiA 4269493 p.Leu114Gln missense_variant 0.15
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269859 c.-26A>T upstream_gene_variant 0.12
ethA 4326128 p.Gln449Arg missense_variant 0.11
ethA 4326139 p.Glu445Asp missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407539 p.Gly222Trp missense_variant 0.12
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408144 p.Arg20Pro missense_variant 1.0