TB-Profiler result

Run: ERR909753
Summary

Run ID: ERR909753

Sample name:

Date: 02-04-2023 09:28:01

Number of reads: 542162

Percentage reads mapped: 15.37

Strain: lineage5.1.1

Drug-resistance: Other

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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 1.0
lineage5.1.1 West-Africa 1 AFRI_2;AFRI_3 RD711 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.25 streptomycin
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 5785 c.546C>T synonymous_variant 0.12
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 7929 p.Ala210Thr missense_variant 0.2
gyrA 8954 c.1653G>A synonymous_variant 0.14
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9566 c.2265C>T synonymous_variant 1.0
gyrA 9690 p.Gln797Lys missense_variant 0.15
gyrA 9780 p.Ala827Ser missense_variant 0.12
fgd1 490751 c.-32T>G upstream_gene_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 619710 c.-181G>T upstream_gene_variant 0.18
rpoB 760567 p.Ser254* stop_gained 0.18
rpoB 761557 p.Ala584Val missense_variant 0.33
rpoB 761828 c.2022C>T synonymous_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763280 c.-90C>T upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776474 p.Met669Ile missense_variant 0.2
mmpL5 776487 p.Gln665Arg missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800938 p.Arg44Ser missense_variant 0.15
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1303463 p.Ala178Glu missense_variant 0.25
Rv1258c 1407121 p.Val74Leu missense_variant 0.15
Rv1258c 1407273 p.Asp23Val missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.25
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.25
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.25
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.22
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.22
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.27
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.27
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.27
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.25
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.18
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.13
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.17
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.22
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.17
rrl 1474430 n.773C>T non_coding_transcript_exon_variant 0.4
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.22
rrl 1475107 n.1450G>T non_coding_transcript_exon_variant 0.5
rrl 1475892 n.2235A>G non_coding_transcript_exon_variant 0.14
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.15
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 0.15
rrl 1475902 n.2245T>C non_coding_transcript_exon_variant 0.15
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.15
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.17
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.2
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.22
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.22
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.2
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.25
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.23
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.18
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.33
rrl 1476559 n.2902G>A non_coding_transcript_exon_variant 0.18
inhA 1673338 c.-864G>A upstream_gene_variant 1.0
inhA 1674194 c.-8G>A upstream_gene_variant 0.22
inhA 1674821 p.Leu207Pro missense_variant 0.18
rpsA 1834507 c.966C>T synonymous_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101840 c.1203G>A synonymous_variant 1.0
ndh 2101921 c.1122G>A synonymous_variant 1.0
ndh 2102449 p.Lys198Asn missense_variant 0.22
ndh 2102746 c.297C>A synonymous_variant 0.29
ndh 2103112 c.-70G>T upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156203 c.-92C>T upstream_gene_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169995 c.618C>T synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289018 p.Gly75Val missense_variant 0.17
pncA 2290039 c.-798C>T upstream_gene_variant 0.15
pncA 2290062 c.-821G>A upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
pepQ 2859498 c.921C>T synonymous_variant 0.2
ald 3087084 c.266delA frameshift_variant 1.0
ald 3087184 c.368_373delCCGACG disruptive_inframe_deletion 1.0
Rv3083 3448825 p.Glu108Lys missense_variant 0.12
Rv3083 3449118 c.615G>A synonymous_variant 0.2
Rv3083 3449240 p.Arg246His missense_variant 0.15
Rv3083 3449644 p.Ala381Thr missense_variant 1.0
Rv3083 3449967 c.1464G>A synonymous_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474736 p.Val244Ile missense_variant 0.17
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612162 p.Ala319Thr missense_variant 0.25
Rv3236c 3612919 c.198C>A synonymous_variant 0.14
fbiB 3640734 c.-801C>G upstream_gene_variant 0.12
fbiB 3642249 p.Asp239Asn missense_variant 0.13
fbiB 3642642 p.His370Asn missense_variant 0.12
alr 3840932 c.489C>T synonymous_variant 1.0
rpoA 3878169 c.339G>A synonymous_variant 0.17
rpoA 3878493 c.15G>A synonymous_variant 1.0
ddn 3986987 c.144G>T synonymous_variant 1.0
ddn 3987180 p.Asp113Asn missense_variant 1.0
clpC1 4039189 p.Arg506Trp missense_variant 0.14
clpC1 4040824 c.-120C>T upstream_gene_variant 1.0
panD 4044446 c.-165C>T upstream_gene_variant 1.0
embC 4239843 c.-20A>C upstream_gene_variant 1.0
embC 4240354 c.492C>A synonymous_variant 0.25
embC 4240671 p.Thr270Ile missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242772 c.-461G>T upstream_gene_variant 0.4
embA 4243899 p.Ala223Thr missense_variant 0.13
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244635 p.Val468Ala missense_variant 1.0
embA 4245147 p.Pro639Ser missense_variant 1.0
embA 4245227 c.1995C>T synonymous_variant 0.18
embB 4245587 c.-927G>A upstream_gene_variant 0.15
embA 4245645 p.Ala805Thr missense_variant 0.17
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267474 p.Gly455Cys missense_variant 0.2
aftB 4267876 c.961C>T synonymous_variant 0.22
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethR 4326928 c.-621G>A upstream_gene_variant 1.0
ethA 4327103 p.Gly124Asp missense_variant 1.0
whiB6 4338243 c.279C>T synonymous_variant 0.17
whiB6 4338547 c.-26A>G upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0