TB-Profiler result

Run: ERR9787009
Summary

Run ID: ERR9787009

Sample name:

Date: 02-04-2023 12:55:51

Number of reads: 1024081

Percentage reads mapped: 99.46

Strain: lineage6.1.1;lineage5.1.5

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
lineage5 West-Africa 1 AFRI_2;AFRI_3 RD711 0.73
lineage6 West-Africa 2 AFRI_1 RD702 0.29
lineage5.1.5 West-Africa 1 AFRI_2;AFRI_3 RD711 0.73
lineage6.1.1 West-Africa 2 AFRI_1 RD702 0.29
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 6446 p.Ala403Ser missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8493 p.Leu398Phe missense_variant 0.18
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9566 c.2265C>T synonymous_variant 0.72
fgd1 491668 p.Lys296Glu missense_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 760855 p.Thr350Ile missense_variant 0.42
rpoB 760969 p.Ser388Leu missense_variant 0.31
rpoB 761723 p.Glu639Asp missense_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766231 c.2862T>C synonymous_variant 0.21
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775753 c.2727delC frameshift_variant 0.84
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1302948 c.18T>G synonymous_variant 0.78
Rv1258c 1406685 p.Val219Ala missense_variant 0.45
embR 1416633 p.Leu239Val missense_variant 0.35
atpE 1461251 c.207G>T synonymous_variant 0.3
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1673338 c.-864G>A upstream_gene_variant 0.57
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101921 c.1122G>A synonymous_variant 0.69
ndh 2103112 c.-70G>T upstream_gene_variant 0.72
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155503 c.609C>T synonymous_variant 0.23
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222364 p.Tyr267* stop_gained 1.0
Rv1979c 2223095 p.Ile24Val missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290062 c.-821G>A upstream_gene_variant 0.66
kasA 2518132 c.18C>T synonymous_variant 1.0
ald 3086728 c.-92C>T upstream_gene_variant 0.47
ald 3086788 c.-32T>C upstream_gene_variant 0.47
ald 3087084 c.266delA frameshift_variant 1.0
ald 3087184 c.368_373delCCGACG disruptive_inframe_deletion 0.76
ald 3087603 p.Ala262Pro missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474786 c.780C>T synonymous_variant 0.18
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612143 p.Arg325His missense_variant 0.19
Rv3236c 3613016 p.Pro34Gln missense_variant 0.24
alr 3840932 c.489C>T synonymous_variant 0.75
ddn 3986987 c.144G>T synonymous_variant 0.82
ddn 3987180 p.Asp113Asn missense_variant 0.75
clpC1 4040824 c.-120C>T upstream_gene_variant 0.8
embC 4239843 c.-20A>C upstream_gene_variant 0.61
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241843 p.Leu661Ile missense_variant 0.16
embA 4242643 c.-590C>T upstream_gene_variant 0.97
embA 4243570 p.Thr113Arg missense_variant 0.28
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244379 p.Pro383Ser missense_variant 0.35
embA 4244635 p.Val468Ala missense_variant 0.76
embA 4245147 p.Pro639Ser missense_variant 0.68
embA 4245924 p.Val898Phe missense_variant 0.66
embB 4246864 c.351C>T synonymous_variant 0.43
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4269351 c.-515C>T upstream_gene_variant 0.43
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269522 c.-686C>T upstream_gene_variant 0.43
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326465 p.Ile337Val missense_variant 0.31
ethR 4326928 c.-621G>A upstream_gene_variant 0.79
ethA 4327103 p.Gly124Asp missense_variant 0.78
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408034 p.Glu57Lys missense_variant 0.36