TB-Profiler result

Run: ERR386958
Summary

Run ID: ERR386958

Sample name:

Date: 01-04-2023 03:36:19

Number of reads: 7124140

Percentage reads mapped: 99.43

Strain: lineage4.1.1;lineage1.2.1.1

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
lineage4 Euro-American LAM;T;S;X;H None 0.48
lineage1 Indo-Oceanic EAI RD239 0.48
lineage4.1 Euro-American T;X;H None 0.48
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.48
lineage1.2.1 Indo-Oceanic EAI2 RD239 0.54
lineage1.2.1.1 Indo-Oceanic NA RD239 0.47
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 0.5
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.48
gyrA 9143 c.1842T>C synonymous_variant 0.52
gyrA 9260 c.1959G>C synonymous_variant 0.47
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.5
rpoC 763031 c.-339T>C upstream_gene_variant 0.55
rpoC 763884 p.Ala172Val missense_variant 0.47
rpoC 763886 c.517C>A synonymous_variant 0.5
rpoC 765150 p.Gly594Glu missense_variant 0.57
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775746 p.Met912Thr missense_variant 0.51
mmpL5 776100 p.Thr794Ile missense_variant 0.51
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303858 p.Gly310* stop_gained 0.49
embR 1417019 p.Cys110Tyr missense_variant 0.44
atpE 1460853 c.-192T>G upstream_gene_variant 0.57
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.46
katG 2155144 p.Asn323Ser missense_variant 0.36
PPE35 2167926 p.Leu896Ser missense_variant 0.61
PPE35 2168533 p.Val694Leu missense_variant 0.46
Rv1979c 2222308 p.Asp286Gly missense_variant 0.5
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290129 c.-888C>A upstream_gene_variant 0.51
kasA 2518132 c.18C>T synonymous_variant 0.46
kasA 2519035 c.921C>T synonymous_variant 0.48
ahpC 2726051 c.-142G>A upstream_gene_variant 0.54
thyA 3073863 c.609T>C synonymous_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339417 c.300A>G synonymous_variant 0.53
Rv3083 3448714 p.Asp71His missense_variant 0.44
Rv3083 3448835 p.Ser111Ile missense_variant 0.51
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.5
fprA 3475159 p.Asn385Asp missense_variant 0.48
fbiB 3640557 c.-978T>C upstream_gene_variant 0.58
fbiB 3641412 c.-123G>A upstream_gene_variant 0.52
fbiA 3641447 p.Thr302Met missense_variant 0.48
rpoA 3877553 p.Glu319Lys missense_variant 0.61
rpoA 3878601 c.-95delG upstream_gene_variant 0.2
rpoA 3878613 c.-113_-107delCAACCCA upstream_gene_variant 0.14
clpC1 4040517 p.Val63Ala missense_variant 0.57
embC 4240671 p.Thr270Ile missense_variant 0.49
embC 4240897 c.1035C>G synonymous_variant 0.53
embC 4241042 p.Asn394Asp missense_variant 0.42
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.61
embA 4244420 c.1188G>C synonymous_variant 0.5
embA 4244610 p.Ala460Thr missense_variant 0.46
embA 4245969 p.Pro913Ser missense_variant 0.55
embB 4247646 p.Glu378Ala missense_variant 0.45
embB 4248515 p.Val668Ile missense_variant 0.52
embB 4249352 c.2839C>A synonymous_variant 0.51
embB 4249408 c.2895G>A synonymous_variant 0.49
ubiA 4269387 p.Glu149Asp missense_variant 0.53
aftB 4269606 c.-770T>C upstream_gene_variant 0.55
ethR 4327360 c.-189C>G upstream_gene_variant 0.49
whiB6 4338361 p.Arg54Gln missense_variant 0.56
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.55
gid 4407588 c.615A>G synonymous_variant 0.55
gid 4407781 p.Ala141Glu missense_variant 0.49
gid 4407873 c.330G>T synonymous_variant 0.49
gid 4407995 p.Ser70Arg missense_variant 0.54