TB-Profiler result

Run: ERR4820702
Summary

Run ID: ERR4820702

Sample name:

Date: 01-04-2023 16:49:44

Number of reads: 622664

Percentage reads mapped: 99.21

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 0.99
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
gyrB 7045 c.1808delA frameshift_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7536 p.Glu79Lys missense_variant 0.12
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8059 p.Met253Lys missense_variant 0.11
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 8748 p.Leu483Val missense_variant 0.25
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9236 c.1935G>A synonymous_variant 0.22
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490646 c.-137G>A upstream_gene_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 760490 c.684C>T synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763780 c.412delT frameshift_variant 0.12
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 765825 p.Gly819Ala missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776279 c.2202C>T synonymous_variant 0.13
mmpL5 776395 p.Phe696Leu missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801194 p.Arg129Gln missense_variant 0.17
embR 1416351 p.Val333Phe missense_variant 0.18
embR 1416436 c.912A>G synonymous_variant 0.13
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417160 p.Trp63* stop_gained 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471664 n.-182C>T upstream_gene_variant 0.13
rrs 1471716 n.-130T>A upstream_gene_variant 0.12
rrs 1471720 n.-126G>T upstream_gene_variant 0.12
rrl 1473444 n.-214A>G upstream_gene_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101955 p.Gln363Ser missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167701 p.Ala971Gly missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289092 p.Phe50Leu missense_variant 0.14
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065625 c.567G>A synonymous_variant 0.15
thyX 3067554 p.Ile131Thr missense_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086837 c.18G>A synonymous_variant 0.22
fbiD 3339456 c.339G>A synonymous_variant 0.15
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449527 p.Ile342Val 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
rpoA 3878433 c.75G>A synonymous_variant 0.22
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 4242041 p.Met727Val missense_variant 1.0
embC 4242112 c.2250G>T synonymous_variant 0.13
embA 4242493 c.-740G>A upstream_gene_variant 0.14
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 4247646 p.Glu378Ala missense_variant 1.0
embB 4249101 p.Tyr863Cys missense_variant 0.11
ubiA 4269031 p.Gly268Asp missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269517 p.Ala106Val missense_variant 0.14
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4327044 p.Asp144Tyr missense_variant 0.12
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 4407706 p.Arg166Pro missense_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0