TB-Profiler result

Run: SRR5341221

Summary

Run ID: SRR5341221

Sample name:

Date: 04-04-2023 10:08:01

Number of reads: 772065

Percentage reads mapped: 99.3

Strain: lineage1.1.2

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.98
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 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
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 1.0
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrA 6736 c.-566C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620748 c.858T>G synonymous_variant 0.38
rpoB 760406 c.600G>A synonymous_variant 0.15
rpoB 760470 p.Arg222Ser missense_variant 0.13
rpoB 760524 p.Glu240* stop_gained 0.17
rpoB 761898 p.Asp698Asn missense_variant 0.22
rpoB 761990 c.2184G>T synonymous_variant 0.2
rpoB 762020 p.Glu738Asp missense_variant 0.18
rpoB 762035 c.2229G>T synonymous_variant 0.22
rpoB 762591 p.His929Asn missense_variant 0.25
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763278 p.Ile1158Val missense_variant 0.14
rpoC 763405 c.36C>A synonymous_variant 0.15
rpoC 763409 p.Leu14Ile missense_variant 0.14
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764412 p.Ile348Asn missense_variant 0.33
rpoC 764699 p.Pro444Ser missense_variant 0.17
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 766052 p.Arg895Ser missense_variant 0.22
rpoC 766201 c.2832G>T synonymous_variant 0.18
rpoC 766217 p.Asp950Tyr missense_variant 0.2
rpoC 767250 c.3884dupC frameshift_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777016 p.Gly489Cys missense_variant 0.14
mmpL5 777885 p.Ala199Ile missense_variant 0.14
mmpL5 777888 p.Gln198Leu missense_variant 0.14
mmpL5 777891 p.Gln197Leu missense_variant 0.15
mmpL5 777894 p.Gln196Leu missense_variant 0.15
mmpL5 777896 p.Asp195Gly missense_variant 0.15
mmpR5 778016 c.-974G>T upstream_gene_variant 0.15
mmpS5 778584 p.Asp108Tyr missense_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800861 p.Asp18Gly missense_variant 0.15
fbiC 1303095 c.165G>T synonymous_variant 0.25
fbiC 1303099 p.Asp57Tyr missense_variant 0.25
fbiC 1303110 c.180G>T synonymous_variant 0.22
fbiC 1303144 p.Ser72Pro missense_variant 0.13
fbiC 1303155 c.225G>A synonymous_variant 0.13
fbiC 1304344 p.Asp472Tyr missense_variant 0.15
fbiC 1304551 p.Gly541Cys missense_variant 0.67
fbiC 1304995 c.2065T>C synonymous_variant 0.14
fbiC 1305414 p.Lys828Asn missense_variant 0.12
Rv1258c 1406503 p.Val280Leu missense_variant 1.0
Rv1258c 1406817 p.Trp175Leu missense_variant 0.18
embR 1416837 p.Val171Ile missense_variant 0.17
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472789 n.944G>T non_coding_transcript_exon_variant 0.18
rrs 1472800 n.955C>A non_coding_transcript_exon_variant 0.2
rrs 1473250 n.1405C>A non_coding_transcript_exon_variant 0.2
rrl 1474093 n.436G>T non_coding_transcript_exon_variant 0.22
rrl 1474385 n.728C>A non_coding_transcript_exon_variant 0.17
rrl 1475316 n.1659G>T non_coding_transcript_exon_variant 0.22
rrl 1475767 n.2110G>T non_coding_transcript_exon_variant 0.22
rrl 1476070 n.2413A>T non_coding_transcript_exon_variant 0.18
rrl 1476103 n.2446C>A non_coding_transcript_exon_variant 0.17
rrl 1476492 n.2835G>T non_coding_transcript_exon_variant 0.27
rrl 1476526 n.2869G>T non_coding_transcript_exon_variant 0.22
rrl 1476563 n.2906G>T non_coding_transcript_exon_variant 0.29
inhA 1673685 c.-517C>A upstream_gene_variant 0.4
rpsA 1833707 p.Gly56Ser missense_variant 0.14
rpsA 1833886 c.345C>A synonymous_variant 0.22
rpsA 1834760 p.Phe407Ile missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2168589 p.Gln675Pro missense_variant 1.0
PPE35 2168803 p.Gly604* stop_gained 0.22
PPE35 2170035 p.Val193Ala missense_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.47
PPE35 2170053 p.Thr187Ser missense_variant 0.5
Rv1979c 2221948 p.Ala406Asp missense_variant 0.12
Rv1979c 2222115 p.Met350Ile missense_variant 0.18
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289476 c.-235G>T upstream_gene_variant 0.29
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518218 p.Gly35Asp missense_variant 1.0
eis 2714289 p.Glu348Asp missense_variant 0.18
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
pepQ 2859644 p.Ala259Ser missense_variant 0.29
pepQ 2859777 c.642C>T synonymous_variant 0.22
pepQ 2859794 p.Asp209Tyr missense_variant 0.15
pepQ 2859801 c.618G>A synonymous_variant 0.14
ribD 2987243 c.405G>T synonymous_variant 0.22
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
thyA 3074253 c.219C>T synonymous_variant 0.25
thyA 3074300 p.Glu58* stop_gained 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086919 p.Leu34Ile missense_variant 0.15
fbiD 3339454 p.Leu113Met missense_variant 0.29
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474825 c.819C>A synonymous_variant 0.18
fprA 3475086 c.1080C>A synonymous_variant 0.14
fprA 3475159 p.Asn385Asp missense_variant 1.0
fbiA 3641107 p.Gly189Cys missense_variant 0.17
fbiA 3641406 p.Trp288Cys missense_variant 0.17
fbiB 3642758 c.1224C>A synonymous_variant 0.29
alr 3840671 c.750G>T synonymous_variant 0.13
alr 3840783 c.637delC frameshift_variant 0.14
alr 3840820 p.Asp201Tyr missense_variant 0.15
alr 3840830 p.Met197Ile missense_variant 0.15
alr 3840848 c.573G>T synonymous_variant 0.17
alr 3840935 c.486G>T synonymous_variant 0.19
rpoA 3877557 c.951C>A synonymous_variant 0.2
rpoA 3877806 c.702C>A synonymous_variant 0.2
ddn 3986981 c.138C>A synonymous_variant 0.17
ddn 3986996 c.153C>A synonymous_variant 0.17
ddn 3987026 c.183C>A synonymous_variant 0.22
ddn 3987118 p.Leu92His missense_variant 0.17
clpC1 4038479 c.2226C>A synonymous_variant 0.18
clpC1 4038503 p.Met734Ile missense_variant 0.22
clpC1 4038506 c.2199G>T synonymous_variant 0.22
clpC1 4039551 p.Leu385Gln missense_variant 0.5
clpC1 4040145 p.Leu187Gln missense_variant 0.22
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239719 c.-144G>T upstream_gene_variant 0.17
embC 4239813 c.-50G>T upstream_gene_variant 0.15
embC 4239833 c.-30G>T upstream_gene_variant 0.15
embC 4240140 p.Gly93Val missense_variant 0.15
embC 4240618 c.756C>T synonymous_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242794 p.Ala978Ser missense_variant 0.13
embA 4243072 c.-161C>G upstream_gene_variant 0.18
embA 4243848 p.Val206Met missense_variant 1.0
embA 4243967 c.735G>T synonymous_variant 0.14
embA 4244603 c.1371G>T synonymous_variant 0.13
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.12
embB 4246548 p.Pro12Gln missense_variant 0.17
embB 4246555 c.42G>C synonymous_variant 0.22
embB 4246556 p.Ala15Pro missense_variant 0.21
embB 4246563 p.Leu17Trp missense_variant 0.11
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247965 c.1452C>A synonymous_variant 0.29
embB 4248274 p.Phe587Leu missense_variant 0.2
embB 4248301 p.Phe596Leu missense_variant 0.18
embB 4249653 c.3141delC frameshift_variant 0.67
embB 4249678 c.3165C>T synonymous_variant 0.67
embB 4249681 c.3168_3169insG frameshift_variant 0.67
aftB 4268617 p.Gly74Cys missense_variant 0.5
aftB 4268630 c.207G>T synonymous_variant 0.33
aftB 4268649 p.Trp63Leu missense_variant 0.29
aftB 4268798 c.39C>A synonymous_variant 0.2
aftB 4268825 c.12C>A synonymous_variant 0.29
ubiA 4269001 p.Ala278Glu missense_variant 0.18
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269540 c.-704C>T upstream_gene_variant 0.29
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269966 c.-133G>T upstream_gene_variant 0.2
whiB6 4338224 c.297delC frameshift_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0