TB-Profiler result

Run: SRR4035594
Summary

Run ID: SRR4035594

Sample name:

Date: 04-04-2023 07:12:04

Number of reads: 632804

Percentage reads mapped: 96.5

Strain: lineage4.3.4.2.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 1.0
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 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
embB 4247580 p.Ala356Val missense_variant 0.14 ethambutol
embB 4247698 p.Trp395Cys missense_variant 0.29 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
gyrB 5514 p.Gly92Asp missense_variant 0.22
gyrB 6140 p.Val301Leu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8169 c.869delA frameshift_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9567 p.Asp756Asn missense_variant 0.13
mshA 575595 p.Gly83Asp missense_variant 0.33
mshA 576350 p.Asp335Asn missense_variant 0.18
rpoB 760080 p.Asp92Tyr missense_variant 0.14
rpoB 760525 p.Glu240Gly missense_variant 0.17
rpoB 760838 p.Glu344Asp missense_variant 0.13
rpoB 761364 p.Asp520Asn missense_variant 0.38
rpoB 763267 p.Ala1154Val missense_variant 0.12
rpoC 764950 p.Leu527Phe missense_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777776 p.Met235Ile missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781515 c.-45_-44insC upstream_gene_variant 0.13
fbiC 1303325 p.Ala132Asp missense_variant 0.12
fbiC 1304061 c.1131G>C synonymous_variant 0.2
fbiC 1305380 p.Ser817* stop_gained 0.33
Rv1258c 1406768 c.573G>A synonymous_variant 0.29
Rv1258c 1407388 c.-48T>C upstream_gene_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472545 n.702delG non_coding_transcript_exon_variant 0.14
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.1
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.12
rrl 1473684 n.27G>T non_coding_transcript_exon_variant 0.12
rrl 1473954 n.301delG non_coding_transcript_exon_variant 0.29
rrl 1474152 n.495G>T non_coding_transcript_exon_variant 0.5
rrl 1474431 n.774G>A non_coding_transcript_exon_variant 0.17
rrl 1474534 n.879delA non_coding_transcript_exon_variant 0.2
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.33
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.13
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.13
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.13
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.11
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.14
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.15
rrl 1476609 n.2952G>A non_coding_transcript_exon_variant 0.14
inhA 1674952 p.Pro251Ala missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918387 p.Leu150Met missense_variant 0.12
ndh 2102273 p.Ile257Thr missense_variant 0.14
ndh 2103096 c.-54G>T upstream_gene_variant 0.12
katG 2155010 p.Phe368Leu missense_variant 0.29
katG 2155752 c.360C>T synonymous_variant 0.25
PPE35 2168462 c.2151C>A synonymous_variant 0.25
Rv1979c 2221814 p.Leu451Met missense_variant 0.17
Rv1979c 2221821 c.1344G>T synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289041 c.201G>T synonymous_variant 0.22
pncA 2289941 c.-700C>T upstream_gene_variant 0.33
eis 2714345 p.Ala330Thr missense_variant 0.22
ahpC 2726338 p.Val49Gly missense_variant 0.43
folC 2747554 c.45C>T synonymous_variant 0.17
ribD 2987456 c.618C>T synonymous_variant 0.25
Rv2752c 3064647 c.1544delT frameshift_variant 0.33
Rv2752c 3064907 p.Val429Leu missense_variant 0.13
Rv2752c 3067104 c.-913C>T upstream_gene_variant 0.14
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449009 p.Trp169* stop_gained 0.18
Rv3083 3449486 p.Gly328Asp missense_variant 0.18
whiB7 3568797 c.-119delC upstream_gene_variant 0.15
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612228 p.Leu297Met missense_variant 0.17
fbiB 3641669 c.135C>T synonymous_variant 0.15
alr 3840500 c.920delT frameshift_variant 0.29
alr 3840702 p.Thr240Asn missense_variant 0.17
alr 3840719 c.702A>G synonymous_variant 1.0
alr 3840823 p.Ala200Ser missense_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4240103 p.Asp81Tyr missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244436 p.Leu402Ile missense_variant 0.2
embA 4245464 c.2232C>T synonymous_variant 0.25
embB 4249171 c.2658C>T synonymous_variant 0.25
aftB 4267311 p.Gly509Val missense_variant 0.2
aftB 4268709 p.Ala43Asp missense_variant 0.25
ubiA 4269959 c.-126C>A upstream_gene_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0