TB-Profiler result

Run: SRR1049960
Summary

Run ID: SRR1049960

Sample name:

Date: 02-04-2023 18:25:15

Number of reads: 6079427

Percentage reads mapped: 98.83

Strain: lineage6.3.1

Drug-resistance: Pre-XDR-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
lineage6 West-Africa 2 AFRI_1 RD702 0.97
lineage6.3 West-Africa 2 AFRI_1 RD702 0.96
lineage6.3.1 West-Africa 2 AFRI_1 RD702 0.96
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
gyrA 7570 p.Ala90Val missense_variant 0.96 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.94 rifampicin
katG 2155168 p.Ser315Ile missense_variant 0.98 isoniazid
embB 4247431 p.Met306Ile missense_variant 0.95 ethambutol
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 0.97
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 0.96
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9591 p.Gly764Arg missense_variant 0.96
fgd1 491668 p.Lys296Glu missense_variant 0.9
fgd1 491742 c.960T>C synonymous_variant 0.93
rpoB 760969 p.Ser388Leu missense_variant 0.96
rpoB 761723 p.Glu639Asp missense_variant 0.96
rpoC 763031 c.-339T>C upstream_gene_variant 0.94
rpoC 764918 p.Val517Leu missense_variant 0.5
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.94
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 0.97
atpE 1461251 c.207G>T synonymous_variant 0.98
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471736 n.-110T>C upstream_gene_variant 0.96
inhA 1674434 p.Val78Ala missense_variant 0.96
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102694 p.Val117Ile missense_variant 0.93
katG 2154724 p.Arg463Leu missense_variant 0.97
katG 2155503 c.609C>T synonymous_variant 0.96
katG 2156366 c.-255G>A upstream_gene_variant 0.96
PPE35 2167926 p.Leu896Ser missense_variant 0.96
Rv1979c 2222308 p.Asp286Gly missense_variant 0.96
Rv1979c 2222852 p.Ala105Thr missense_variant 0.97
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.96
ald 3086728 c.-92C>T upstream_gene_variant 0.95
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_variant 0.98
Rv3083 3449781 c.1278G>A synonymous_variant 0.96
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 0.97
rpoA 3877696 p.Thr271Ile missense_variant 0.96
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241843 p.Leu661Ile missense_variant 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 0.89
embA 4244379 p.Pro383Ser missense_variant 0.86
embB 4246864 c.351C>T synonymous_variant 0.89
embB 4247646 p.Glu378Ala missense_variant 0.91
aftB 4268477 c.360C>T synonymous_variant 0.94
aftB 4269351 c.-515C>T upstream_gene_variant 0.98
ubiA 4269387 p.Glu149Asp missense_variant 0.97
aftB 4269522 c.-686C>T upstream_gene_variant 0.95
aftB 4269606 c.-770T>C upstream_gene_variant 0.95
ethA 4326465 p.Ile337Val missense_variant 0.93
whiB6 4338478 p.Phe15Ser missense_variant 0.97
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.88