TB-Profiler result

Run: ERR4799889
Summary

Run ID: ERR4799889

Sample name:

Date: 01-04-2023 09:26:38

Number of reads: 3831847

Percentage reads mapped: 99.33

Strain: lineage1.2.2.2;lineage1.1.2

Drug-resistance: Sensitive

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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 0.96
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.57
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.59
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.39
lineage1.2.2.2 Indo-Oceanic NA RD239 0.4
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
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 5075 c.-165C>T upstream_gene_variant 0.47
gyrB 5076 c.-164_-163insT upstream_gene_variant 0.44
gyrB 6112 p.Met291Ile missense_variant 0.95
gyrB 6124 c.885C>T synonymous_variant 0.41
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.96
gyrA 9143 c.1842T>C synonymous_variant 0.94
gyrA 9304 p.Gly668Asp missense_variant 0.97
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.96
rpoC 763886 c.517C>A synonymous_variant 0.96
rpoC 765171 p.Pro601Leu missense_variant 0.47
rpoC 765358 p.Met663Ile missense_variant 0.65
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
Rv1258c 1406381 c.960G>T synonymous_variant 0.51
embR 1417019 p.Cys110Tyr missense_variant 0.97
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474136 n.479A>G non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.99
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 0.6
PPE35 2168742 p.Gly624Asp missense_variant 0.53
Rv1979c 2222308 p.Asp286Gly missense_variant 0.95
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290018 c.-777C>T upstream_gene_variant 0.54
kasA 2518132 c.18C>T synonymous_variant 0.94
ahpC 2726051 c.-142G>A upstream_gene_variant 0.92
Rv2752c 3064632 c.1560C>T synonymous_variant 0.59
Rv2752c 3064889 p.Lys435Glu missense_variant 0.43
Rv2752c 3065688 c.504C>A synonymous_variant 0.46
ald 3086744 c.-76A>G upstream_gene_variant 0.43
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.98
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.96
fprA 3475159 p.Asn385Asp missense_variant 0.96
Rv3236c 3613221 c.-105C>T upstream_gene_variant 0.39
alr 3841546 c.-126C>A upstream_gene_variant 0.16
clpC1 4040517 p.Val63Ala missense_variant 0.95
embC 4240671 p.Thr270Ile missense_variant 0.93
embC 4241042 p.Asn394Asp missense_variant 0.99
embC 4241594 p.Ala578Thr missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.53
embA 4245969 p.Pro913Ser missense_variant 0.93
embB 4247646 p.Glu378Ala missense_variant 0.96
embB 4249111 c.2598T>G synonymous_variant 0.34
embB 4249441 c.2928A>G synonymous_variant 0.39
aftB 4268727 p.Thr37Met missense_variant 0.37
ubiA 4269387 p.Glu149Asp missense_variant 0.91
aftB 4269606 c.-770T>C upstream_gene_variant 0.92
aftB 4269705 c.-869T>C upstream_gene_variant 0.32
ethA 4326439 p.Asn345Lys missense_variant 0.36
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.94
whiB6 4338635 c.-114A>C upstream_gene_variant 0.48
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.99
gid 4408144 p.Arg20Pro missense_variant 0.59