TB-Profiler result

Run: SRR11349178

Summary

Run ID: SRR11349178

Sample name:

Date: 02-04-2023 20:54:18

Number of reads: 5817241

Percentage reads mapped: 96.92

Strain: lineage4.4.1.1.1

Drug-resistance: MDR-TB


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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 1.0
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans None 1.0
lineage4.4.1.1.1 Euro-American S;Orphans 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289142 p.Tyr34Asp missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
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
mshA 576108 p.Ala254Gly missense_variant 0.21
rpoC 766487 p.Pro1040Ser missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472509 n.664G>A non_coding_transcript_exon_variant 0.2
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.2
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.25
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.29
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.29
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.2
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.15
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.15
rrs 1472750 n.907_908delAA non_coding_transcript_exon_variant 0.33
rrs 1472841 n.996G>A non_coding_transcript_exon_variant 0.4
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.29
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.29
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.29
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.33
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.25
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.25
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.43
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.29
rrl 1474711 n.1054G>A non_coding_transcript_exon_variant 0.5
rrl 1474713 n.1056T>G non_coding_transcript_exon_variant 0.4
rrl 1474717 n.1060A>G non_coding_transcript_exon_variant 0.4
rrl 1474721 n.1064G>A non_coding_transcript_exon_variant 0.4
rrl 1474722 n.1065T>C non_coding_transcript_exon_variant 0.4
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.5
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.67
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 1.0
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.67
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.4
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.4
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.4
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.4
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.4
rrl 1474802 n.1145T>C non_coding_transcript_exon_variant 0.4
rrl 1475686 n.2029C>G non_coding_transcript_exon_variant 0.29
rrl 1475696 n.2039T>C non_coding_transcript_exon_variant 0.27
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.27
rrl 1475703 n.2046A>G non_coding_transcript_exon_variant 0.27
rrl 1475715 n.2058G>C non_coding_transcript_exon_variant 0.36
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.5
rrl 1475756 n.2099T>C non_coding_transcript_exon_variant 0.5
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 0.56
rrl 1475767 n.2110G>T non_coding_transcript_exon_variant 0.56
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.5
rrl 1476626 n.2969G>T non_coding_transcript_exon_variant 0.27
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2986827 c.-12G>A upstream_gene_variant 1.0
Rv2752c 3064993 p.Trp400* stop_gained 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339287 p.Arg57Leu missense_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0