TB-Profiler result

Run: ERR2512474
Summary

Run ID: ERR2512474

Sample name:

Date: 31-03-2023 19:03:23

Number of reads: 953697

Percentage reads mapped: 99.31

Strain: lineage1.1.2

Drug-resistance: HR-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 0.99
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
katG 2155740 c.371delG frameshift_variant 0.15 isoniazid, isoniazid
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 6112 p.Met291Ile missense_variant 1.0
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrA 7174 c.-128C>T upstream_gene_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 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9658 p.Thr786Ile missense_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576387 p.Ala347Val missense_variant 0.15
rpoB 760490 c.684C>T synonymous_variant 1.0
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 765171 p.Pro601Leu missense_variant 1.0
rpoC 765450 p.Ala694Val missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776395 p.Phe696Leu missense_variant 1.0
mmpL5 776694 p.Val596Ser missense_variant 0.19
mmpL5 776702 c.1779C>T synonymous_variant 0.21
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406519 c.821delG frameshift_variant 0.12
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473717 n.60G>A non_coding_transcript_exon_variant 0.2
rrl 1476133 n.2476G>A non_coding_transcript_exon_variant 0.15
fabG1 1673560 p.Lys41Leu missense_variant 0.13
rpsA 1834957 c.1416C>A synonymous_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154230 p.Val628Ile missense_variant 0.33
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155170 c.942C>A synonymous_variant 0.14
PPE35 2167745 p.Thr956Arg missense_variant 0.21
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169543 p.Gly357Val missense_variant 0.12
PPE35 2169547 p.His356Asn missense_variant 0.12
PPE35 2169548 c.1065A>C synonymous_variant 0.12
PPE35 2169551 c.1062C>G synonymous_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.6
PPE35 2170053 p.Thr187Ser missense_variant 0.55
PPE35 2170247 p.Ile122Met missense_variant 0.12
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518864 c.750G>C synonymous_variant 0.18
kasA 2518983 p.Ala290Glu missense_variant 0.17
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.29
folC 2746539 p.His354Asn missense_variant 0.11
folC 2747186 c.403_412delGACCAGCAGT frameshift_variant 0.2
folC 2747205 c.393_394insCCC conservative_inframe_insertion 0.14
pepQ 2860413 c.6A>G synonymous_variant 0.15
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
thyX 3067408 p.Glu180Lys missense_variant 0.22
thyA 3074144 p.Asp110Tyr missense_variant 0.13
thyA 3074361 c.111T>C synonymous_variant 0.12
thyA 3074514 c.-43T>C upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087071 c.252C>A synonymous_variant 0.12
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449016 c.513A>G synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475128 p.Asp374Glu missense_variant 0.17
fprA 3475159 p.Asn385Asp missense_variant 1.0
fbiB 3642107 c.573G>A synonymous_variant 0.17
alr 3841546 c.-126C>A upstream_gene_variant 0.25
ddn 3986978 c.135G>A synonymous_variant 0.12
clpC1 4040144 c.561G>C synonymous_variant 0.18
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241458 c.1596C>A synonymous_variant 0.12
embC 4241931 p.Thr690Ile missense_variant 0.14
embA 4242613 c.-620C>T upstream_gene_variant 0.12
embA 4242616 c.-617C>G upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245218 c.1986C>T synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247002 c.489G>T synonymous_variant 0.13
embB 4247101 c.588G>T synonymous_variant 0.15
embB 4247470 c.957T>C synonymous_variant 0.21
embB 4247472 p.Phe320Tyr missense_variant 0.23
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248335 p.Ala608Thr missense_variant 0.13
ubiA 4269031 p.Gly268Asp missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0