TB-Profiler result

Run: SRR11972458
Summary

Run ID: SRR11972458

Sample name:

Date: 03-04-2023 05:43:03

Number of reads: 877494

Percentage reads mapped: 97.61

Strain: 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 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
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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9047 c.1746C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 0.96
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9443 c.2142G>A synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576000 p.Asp218Ala missense_variant 1.0
mshA 576551 p.Ile402Val missense_variant 0.2
rpoB 759615 c.-192A>C upstream_gene_variant 0.23
rpoB 760490 c.684C>T synonymous_variant 1.0
rpoB 760807 p.Ala334Val missense_variant 1.0
rpoB 761613 p.Ala603Ser missense_variant 0.22
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
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775871 c.2610C>T synonymous_variant 0.12
mmpL5 775874 c.2607C>A synonymous_variant 0.12
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776395 p.Phe696Leu missense_variant 1.0
mmpL5 778086 c.394delG frameshift_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304610 c.1680C>A synonymous_variant 0.12
embR 1416671 p.Gly226Asp missense_variant 0.15
embR 1416676 c.672G>C synonymous_variant 0.15
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.34
rpsA 1833503 c.-39G>C upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101855 p.Trp396Cys missense_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167865 c.2748G>C synonymous_variant 0.17
PPE35 2167868 c.2745A>C synonymous_variant 0.16
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.16
PPE35 2170053 p.Thr187Ser missense_variant 0.16
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518049 c.-66G>A upstream_gene_variant 0.12
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518238 p.Gly42Cys missense_variant 0.2
kasA 2519140 c.1026G>C synonymous_variant 0.19
kasA 2519143 c.1029G>C synonymous_variant 0.19
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ribD 2987058 c.220T>C synonymous_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065305 p.Ala296Val missense_variant 1.0
thyX 3067244 c.702C>A synonymous_variant 0.12
thyA 3074648 c.-177T>G upstream_gene_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087740 p.Lys307Asn missense_variant 0.17
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612022 c.1095C>T synonymous_variant 0.13
rpoA 3877947 c.561C>G synonymous_variant 0.2
rpoA 3877971 p.Asp179Glu missense_variant 0.18
rpoA 3877974 c.534G>T synonymous_variant 0.18
clpC1 4039484 c.1221T>G synonymous_variant 0.22
clpC1 4039994 p.Glu237Asp missense_variant 0.11
clpC1 4040001 p.His235Pro missense_variant 0.11
clpC1 4040057 c.648C>T synonymous_variant 0.12
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239720 c.-143G>C upstream_gene_variant 0.11
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240801 c.939C>T synonymous_variant 0.14
embC 4240803 p.Tyr314Phe missense_variant 0.14
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243691 p.Met153Ile missense_variant 0.29
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244718 p.Tyr496Asn missense_variant 0.17
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.21
embB 4246841 p.Asn110Tyr missense_variant 0.25
embB 4247512 c.999T>C synonymous_variant 0.13
embB 4247516 p.Asn335Asp missense_variant 0.13
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267878 p.Val320Ala missense_variant 0.25
aftB 4268739 p.Ile33Asn missense_variant 0.12
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