TB-Profiler result

Run: SRR4034324

Summary

Run ID: SRR4034324

Sample name:

Date: 04-04-2023 06:43:05

Number of reads: 979574

Percentage reads mapped: 99.45

Strain: lineage4.1.2

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H 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
ethA 4327269 c.204delC frameshift_variant 0.12 ethionamide
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 7234 c.-68C>A upstream_gene_variant 0.12
gyrA 7342 p.Arg14Leu missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491429 p.Ala216Asp missense_variant 0.17
fgd1 491591 p.Lys270Met missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761261 c.1455G>T synonymous_variant 0.13
rpoB 762372 p.Pro856Thr missense_variant 0.12
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766811 p.Ser1148Thr missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775748 c.2733T>C synonymous_variant 0.12
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpL5 777851 c.630C>A synonymous_variant 0.15
mmpL5 778090 p.Gly131Trp missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800925 c.117C>A synonymous_variant 0.14
fbiC 1303961 p.Arg344Leu missense_variant 0.2
Rv1258c 1406132 c.1209G>T synonymous_variant 0.12
Rv1258c 1406954 c.387C>A synonymous_variant 0.18
embR 1416403 c.944delA frameshift_variant 0.2
embR 1416694 c.652_653delTC frameshift_variant 0.2
embR 1417169 c.177_178dupCT frameshift_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475282 n.1625T>C non_coding_transcript_exon_variant 0.18
fabG1 1673926 p.Met163Leu missense_variant 0.12
rpsA 1833732 p.Pro64His missense_variant 0.17
rpsA 1834166 p.Gly209Cys missense_variant 0.14
rpsA 1834681 p.Met380Ile missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101955 p.Gln363Arg missense_variant 0.16
ndh 2103022 c.21C>A synonymous_variant 0.14
ndh 2103046 c.-4G>T upstream_gene_variant 0.13
katG 2154417 c.1695G>T synonymous_variant 0.14
katG 2155638 p.Lys158Asn missense_variant 0.25
PPE35 2168220 p.Ala798Glu missense_variant 0.12
PPE35 2169261 p.Leu451Pro missense_variant 0.1
PPE35 2169311 c.1302G>T synonymous_variant 0.13
PPE35 2169929 c.683delG frameshift_variant 0.12
PPE35 2170269 p.Ser115Tyr missense_variant 0.12
Rv1979c 2222617 p.Trp183Leu missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
folC 2747213 p.Pro129Gln missense_variant 0.14
ribD 2987487 p.Pro217Thr missense_variant 0.22
Rv2752c 3064610 c.1582C>A synonymous_variant 0.12
Rv2752c 3066326 c.-135C>A upstream_gene_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449258 p.Arg252Leu missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474516 c.510C>A synonymous_variant 0.13
fprA 3474598 p.Gly198Trp missense_variant 0.15
fprA 3474788 p.Arg261Leu missense_variant 0.15
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
Rv3236c 3611979 p.Ala380Ser missense_variant 0.18
Rv3236c 3612372 p.Leu249Ile missense_variant 0.12
fbiB 3642313 p.Arg260Leu missense_variant 0.13
alr 3840546 p.Gly292Asp missense_variant 0.17
clpC1 4040447 c.257delA frameshift_variant 0.13
embC 4242019 p.Glu719Asp missense_variant 0.13
embC 4242057 p.Pro732Gln missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4243007 p.Leu1049Ile missense_variant 0.13
embA 4243078 c.-155C>A upstream_gene_variant 0.15
embA 4244281 p.Gly350Val missense_variant 0.14
embA 4244997 p.Ala589Thr missense_variant 0.19
embA 4246411 p.Tyr1060Cys missense_variant 0.14
embB 4246597 p.Trp28Cys missense_variant 0.29
embB 4247384 p.His291Asn missense_variant 0.17
embB 4247881 c.1368G>T synonymous_variant 0.18
embB 4249348 c.2835G>T synonymous_variant 0.17
ubiA 4269992 c.-159C>T upstream_gene_variant 0.12
whiB6 4338219 c.303C>A synonymous_variant 0.12
whiB6 4338307 p.Ala72Val missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407552 c.651G>T synonymous_variant 0.22
gid 4408315 c.-113C>T upstream_gene_variant 0.13