TB-Profiler result

Run: SRR6046743

Summary

Run ID: SRR6046743

Sample name:

Date: 04-04-2023 12:22:34

Number of reads: 1024341

Percentage reads mapped: 93.84

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 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 1.0 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9369 c.2068C>T synonymous_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575204 c.-144C>A upstream_gene_variant 0.14
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 759786 c.-21G>C upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoB 762541 p.Asn912Ser missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763418 p.Ala17Ser missense_variant 0.2
rpoC 763872 p.Gly168Ala missense_variant 0.12
rpoC 763876 p.Glu169Asp missense_variant 0.12
rpoC 763879 c.510A>G synonymous_variant 0.12
rpoC 764277 p.Gln303Leu missense_variant 1.0
rpoC 765927 p.Thr853Ser missense_variant 0.1
rpoC 766623 p.Arg1085Gln missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779315 p.Arg109Leu missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781927 p.Lys123Arg missense_variant 0.11
embR 1416624 p.Asp242Asn missense_variant 0.12
embR 1417081 p.Asp89Glu missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471896 n.51T>C non_coding_transcript_exon_variant 0.25
rrs 1471900 n.55C>T non_coding_transcript_exon_variant 0.25
rrs 1471911 n.66C>A non_coding_transcript_exon_variant 0.33
rrs 1471917 n.72G>C non_coding_transcript_exon_variant 0.33
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 1.0
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 1.0
rrs 1472130 n.285G>A non_coding_transcript_exon_variant 1.0
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 1.0
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 1.0
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 1.0
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 1.0
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 1.0
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 1.0
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 1.0
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 1.0
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 1.0
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 1.0
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 1.0
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 1.0
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.71
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.71
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.6
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 1.0
rrs 1472733 n.888G>C non_coding_transcript_exon_variant 1.0
rrs 1472734 n.889C>A non_coding_transcript_exon_variant 0.4
rrs 1472741 n.896G>T non_coding_transcript_exon_variant 0.4
rrs 1472742 n.897C>G non_coding_transcript_exon_variant 1.0
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 1.0
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 1.0
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.4
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 1.0
rrs 1473316 n.1471C>A non_coding_transcript_exon_variant 1.0
rrs 1473318 n.1473G>A non_coding_transcript_exon_variant 1.0
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 1.0
rrs 1473327 n.1482A>G non_coding_transcript_exon_variant 1.0
rrs 1473328 n.1483C>T non_coding_transcript_exon_variant 1.0
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 1.0
rrs 1473365 n.1520C>A non_coding_transcript_exon_variant 0.67
rrl 1474801 n.1144G>A non_coding_transcript_exon_variant 0.67
rrl 1474802 n.1145T>C non_coding_transcript_exon_variant 0.67
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 1.0
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 1.0
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 1.0
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 1.0
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.4
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.4
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.4
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.4
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.4
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.4
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.4
rrl 1476126 n.2469C>T non_coding_transcript_exon_variant 1.0
rrl 1476130 n.2473G>A non_coding_transcript_exon_variant 1.0
rrl 1476135 n.2478T>C non_coding_transcript_exon_variant 1.0
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 1.0
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 1.0
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 1.0
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 1.0
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 1.0
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 1.0
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 1.0
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 1.0
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 1.0
rpsA 1833781 c.240T>C synonymous_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101975 c.1068G>A synonymous_variant 0.12
ndh 2103225 c.-183A>C upstream_gene_variant 0.23
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155824 c.288C>T synonymous_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170226 c.386delA frameshift_variant 0.11
PPE35 2170312 p.Arg101Gly missense_variant 0.15
Rv1979c 2222315 p.Ala284Thr missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2518297 c.183C>A synonymous_variant 0.12
kasA 2518704 p.Gly197Val missense_variant 0.11
kasA 2519179 c.1065G>T synonymous_variant 0.13
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726341 p.Val50Gly missense_variant 0.24
folC 2747105 p.Asp165Gly missense_variant 0.1
pepQ 2860271 p.Arg50Cys missense_variant 0.12
ribD 2987386 p.Ala183Val missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339435 c.318G>A synonymous_variant 0.15
fbiD 3339708 c.591C>T synonymous_variant 0.14
Rv3083 3448725 c.222G>A synonymous_variant 0.12
Rv3083 3448755 p.Tyr84* stop_gained 0.12
Rv3083 3448853 p.Thr117Asn missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3613280 c.-164G>T upstream_gene_variant 0.11
fbiB 3641802 p.Asp90Asn missense_variant 1.0
alr 3840632 c.789A>T synonymous_variant 0.11
alr 3841473 c.-53G>A upstream_gene_variant 1.0
rpoA 3878100 c.408C>T synonymous_variant 0.12
ddn 3986958 p.Gly39Cys missense_variant 0.2
ddn 3987031 p.Pro63Gln missense_variant 0.15
clpC1 4039746 p.Ile320Thr missense_variant 0.11
clpC1 4040304 p.Val134Ala missense_variant 0.13
panD 4044267 p.Met5Ile missense_variant 0.15
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244516 c.1284G>C synonymous_variant 0.12
embA 4244732 c.1500G>A synonymous_variant 0.11
embA 4245371 p.Tyr713* stop_gained 0.12
embA 4245762 p.Gly844Arg missense_variant 0.12
embA 4245812 c.2584delC frameshift_variant 0.18
embB 4248476 p.Pro655Ser missense_variant 0.13
ethA 4326105 c.1369C>T synonymous_variant 0.12
ethA 4327560 c.-87G>T upstream_gene_variant 0.12
ethR 4327588 p.Gly14Ser missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408107 p.Glu32Asp missense_variant 1.0