TB-Profiler result

Run: SRR993002
Summary

Run ID: SRR993002

Sample name:

Date: 04-04-2023 23:00:01

Number of reads: 1739901

Percentage reads mapped: 98.46

Strain: lineage4

Drug-resistance: HR-TB

Download CSV Download TXT Download PDF Download JSON
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 1.0
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
katG 2155168 p.Ser315Thr missense_variant 0.62 isoniazid
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 5329 c.90C>T synonymous_variant 0.25
gyrA 6568 c.-734C>A upstream_gene_variant 0.15
gyrB 6900 p.Pro554Gln missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.86
gyrA 7965 p.Arg222Trp missense_variant 0.18
gyrA 8040 p.Gly247Ser missense_variant 0.38
gyrA 9304 p.Gly668Asp missense_variant 0.6
gyrA 9396 p.Gly699Cys missense_variant 0.22
gyrA 9796 p.Gly832Ala missense_variant 0.24
fgd1 491448 c.666C>T synonymous_variant 0.12
mshA 576564 p.Leu406Pro missense_variant 0.12
rpoB 761243 c.1437G>A synonymous_variant 0.2
rpoB 761818 p.Arg671Gln missense_variant 0.18
rpoB 762629 p.Asp941Glu missense_variant 0.2
rpoC 764995 c.1626C>G synonymous_variant 0.62
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777051 p.Gly477Ala missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800665 c.-144A>G upstream_gene_variant 0.13
fbiC 1303095 c.165G>A synonymous_variant 0.5
embR 1416187 c.1161C>A synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.11
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.11
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.62
rrl 1474233 n.576C>A non_coding_transcript_exon_variant 0.11
rrl 1474420 n.763C>T non_coding_transcript_exon_variant 0.12
rrl 1475223 n.1566G>A non_coding_transcript_exon_variant 0.31
fabG1 1673380 c.-60C>G upstream_gene_variant 0.14
rpsA 1833515 c.-27C>A upstream_gene_variant 0.11
rpsA 1834836 p.Met432Thr missense_variant 0.43
rpsA 1834929 p.Ser463* stop_gained 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918312 p.Asp125Asn missense_variant 0.11
ndh 2101874 p.Phe390Ser missense_variant 0.12
ndh 2103047 c.-5G>A upstream_gene_variant 0.11
katG 2154687 c.1425C>T synonymous_variant 0.14
katG 2156196 c.-85C>T upstream_gene_variant 0.83
katG 2156211 c.-100G>A upstream_gene_variant 0.17
PPE35 2169602 c.1011C>A synonymous_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289308 c.-67C>A upstream_gene_variant 0.11
pncA 2289960 c.-719C>A upstream_gene_variant 0.14
kasA 2518769 p.Arg219Ser missense_variant 0.17
kasA 2518826 p.Val238Met missense_variant 0.17
kasA 2518919 p.Gly269Ser missense_variant 0.6
kasA 2519261 p.Asp383Tyr missense_variant 0.14
ahpC 2726518 p.Pro109Gln missense_variant 0.18
ahpC 2726698 p.Gln169Arg missense_variant 0.12
folC 2746340 p.Ala420Val missense_variant 0.67
folC 2746608 p.Ala331Ser missense_variant 0.2
thyA 3073868 p.Thr202Ala missense_variant 0.6
thyA 3074578 c.-107C>T upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 0.73
ald 3087465 p.His216Asn missense_variant 0.13
fbiD 3338927 c.-191C>T upstream_gene_variant 0.1
fbiD 3339620 p.Ala168Val missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.67
fprA 3474133 p.Pro43Ser missense_variant 0.33
whiB7 3568649 p.Pro11Thr missense_variant 0.11
Rv3236c 3612068 p.Gly350Leu missense_variant 0.13
Rv3236c 3612640 p.Asp159Glu missense_variant 0.13
fbiA 3641525 p.Gly328Glu missense_variant 0.2
fbiB 3642215 c.681G>A synonymous_variant 0.15
fbiB 3642384 p.Leu284Ile missense_variant 0.11
rpoA 3877704 c.804G>C synonymous_variant 0.5
ddn 3987113 c.270C>A synonymous_variant 0.25
clpC1 4038287 c.2418C>T synonymous_variant 0.64
clpC1 4038968 c.1737G>A synonymous_variant 0.6
panD 4043901 c.381C>T synonymous_variant 0.14
embC 4240345 c.483C>T synonymous_variant 0.11
embC 4240752 p.Ile297Asn missense_variant 0.11
embC 4240822 c.960C>A synonymous_variant 0.12
embC 4242057 p.Pro732Gln missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243964 c.732G>T synonymous_variant 0.14
embA 4244559 p.Ile443Val missense_variant 0.29
embB 4246548 p.Pro12Gln missense_variant 0.18
embB 4246555 c.42G>C synonymous_variant 0.29
embB 4246556 p.Ala15Pro missense_variant 0.29
embB 4247695 c.1182G>C synonymous_variant 0.22
embB 4247699 p.Met396Leu missense_variant 0.22
ubiA 4269224 p.Ala204Ser missense_variant 0.25
whiB6 4338295 p.Trp76Leu missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4408171 p.Ile11Thr missense_variant 1.0