TB-Profiler result

Run: SRR1049962
Summary

Run ID: SRR1049962

Sample name:

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

Number of reads: 1764371

Percentage reads mapped: 98.21

Strain: lineage6.3.1;lineage4.1.3

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 0.9
lineage6 West-Africa 2 AFRI_1 RD702 0.21
lineage4.1 Euro-American T;X;H None 0.85
lineage6.3 West-Africa 2 AFRI_1 RD702 0.13
lineage4.1.3 Euro-American T;X;H None 0.12
lineage6.3.1 West-Africa 2 AFRI_1 RD702 0.19
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 0.17
gyrB 6507 p.Ala423Val missense_variant 0.68
gyrA 6847 c.-455C>T upstream_gene_variant 0.77
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9557 c.2256G>C synonymous_variant 0.12
gyrA 9656 c.2355C>G synonymous_variant 0.69
fgd1 491668 p.Lys296Glu missense_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 0.24
rpoC 763031 c.-339T>C upstream_gene_variant 0.18
rpoC 765150 p.Gly594Glu missense_variant 0.88
rpoC 765187 c.1818C>T synonymous_variant 0.79
rpoC 766012 c.2643C>G synonymous_variant 0.65
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775841 c.2640G>A synonymous_variant 0.28
mmpL5 776100 p.Thr794Ile missense_variant 0.24
mmpL5 777986 c.495C>A synonymous_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781421 c.-139C>A upstream_gene_variant 0.8
fbiC 1302899 c.-32A>G upstream_gene_variant 0.15
Rv1258c 1406260 p.Pro361Ser missense_variant 0.81
atpE 1461251 c.207G>T synonymous_variant 0.16
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474739 n.1082G>A non_coding_transcript_exon_variant 0.56
fabG1 1673166 c.-274C>T upstream_gene_variant 0.77
inhA 1674102 c.-100C>A upstream_gene_variant 0.12
inhA 1674434 p.Val78Ala missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.27
katG 2156007 c.105C>T synonymous_variant 0.86
PPE35 2167926 p.Leu896Ser missense_variant 0.11
PPE35 2168448 p.Gln722Arg missense_variant 0.72
PPE35 2169715 p.Gly300Ser missense_variant 0.13
Rv1979c 2222308 p.Asp286Gly missense_variant 0.17
Rv1979c 2222852 p.Ala105Thr missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086728 c.-92C>T upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_variant 0.21
fbiD 3339309 c.192C>A synonymous_variant 0.12
Rv3083 3449781 c.1278G>A synonymous_variant 0.23
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 0.23
embC 4240671 p.Thr270Ile missense_variant 0.27
embC 4241843 p.Leu661Ile missense_variant 0.34
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.97
embA 4244220 c.988C>T synonymous_variant 0.27
embA 4244699 c.1467C>A synonymous_variant 0.12
embB 4247646 p.Glu378Ala missense_variant 0.24
aftB 4268477 c.360C>T synonymous_variant 0.21
aftB 4269351 c.-515C>T upstream_gene_variant 0.16
ubiA 4269387 p.Glu149Asp missense_variant 0.17
aftB 4269522 c.-686C>T upstream_gene_variant 0.14
aftB 4269606 c.-770T>C upstream_gene_variant 0.12
ethA 4326465 p.Ile337Val missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.14