TB-Profiler result

Run: SRR4035737
Summary

Run ID: SRR4035737

Sample name:

Date: 04-04-2023 07:16:01

Number of reads: 1205636

Percentage reads mapped: 99.41

Strain: lineage4.1.2

Drug-resistance: HR-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
lineage4.1 Euro-American T;X;H None 0.99
lineage4.1.2 Euro-American T;H None 0.99
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
fabG1 1673429 c.-11A>T upstream_gene_variant 0.12 isoniazid
katG 2154979 p.Leu378Pro missense_variant 0.17 isoniazid
pncA 2289009 p.Gly78Asp missense_variant 0.14 pyrazinamide
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 8061 p.Arg254Cys missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9628 p.Ala776Val missense_variant 0.13
gyrA 9688 p.Arg796Leu missense_variant 0.14
fgd1 491591 p.Lys270Met missense_variant 0.97
mshA 575313 c.-35C>T upstream_gene_variant 0.14
mshA 575538 p.Asp64Gly missense_variant 0.17
mshA 575915 p.Asp190Asn missense_variant 0.14
ccsA 619724 c.-167C>G upstream_gene_variant 0.12
ccsA 620450 p.Leu187Gln missense_variant 0.14
ccsA 620479 p.Leu197Val missense_variant 0.11
ccsA 620600 p.Phe237Ser missense_variant 0.12
rpoB 760115 c.309C>T synonymous_variant 0.95
rpoB 761520 p.Tyr572His missense_variant 0.25
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765257 p.Arg630Trp missense_variant 0.15
rpoC 765842 p.Thr825Ala missense_variant 0.11
rpoC 765900 p.Leu844Pro missense_variant 0.18
rpoC 766275 p.Ala969Gly missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776583 c.1897delC frameshift_variant 0.13
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpL5 777389 p.Phe364Leu missense_variant 0.13
mmpL5 777683 c.798C>T synonymous_variant 0.13
mmpL5 777873 c.607delA frameshift_variant 0.14
mmpL5 777994 c.486dupC frameshift_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781416 c.-144C>A upstream_gene_variant 0.14
rplC 801222 c.414T>C synonymous_variant 0.13
fbiC 1304308 p.Thr460Ala missense_variant 0.15
Rv1258c 1406191 p.Ala384Pro missense_variant 0.11
Rv1258c 1406299 p.Val348Ile missense_variant 0.15
Rv1258c 1406987 c.354G>C synonymous_variant 0.2
embR 1416701 p.Tyr216Cys missense_variant 0.14
embR 1417257 p.Gly31Ser missense_variant 0.13
embR 1417263 p.Pro29Ser missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471782 n.-64C>G upstream_gene_variant 0.11
rrs 1472787 n.942A>G non_coding_transcript_exon_variant 0.1
rrl 1474542 n.889dupG non_coding_transcript_exon_variant 0.13
rrl 1476127 n.2470C>G non_coding_transcript_exon_variant 0.12
fabG1 1673340 c.-100G>C upstream_gene_variant 0.15
fabG1 1673791 c.355delG frameshift_variant 0.17
inhA 1673901 c.-301A>G upstream_gene_variant 0.14
fabG1 1673909 p.Lys157Arg missense_variant 0.14
inhA 1674012 c.-190C>T upstream_gene_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918642 p.Gly235Ser missense_variant 0.15
tlyA 1918722 c.783C>T synonymous_variant 0.14
ndh 2102219 p.Val275Ala missense_variant 0.14
ndh 2102816 p.Leu76Gln missense_variant 0.14
katG 2154156 c.1956A>G synonymous_variant 0.11
katG 2154953 p.Asp387Asn missense_variant 0.18
katG 2154969 c.1143C>T synonymous_variant 0.15
katG 2155667 p.Trp149Arg missense_variant 0.17
PPE35 2169352 p.Ala421Thr missense_variant 0.13
PPE35 2169445 p.Gly390Cys missense_variant 0.17
PPE35 2169899 c.714G>T synonymous_variant 0.15
Rv1979c 2221903 p.Ala421Val missense_variant 0.14
Rv1979c 2222531 p.Glu212* stop_gained 0.13
Rv1979c 2222559 c.606G>A synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289034 p.Pro70Ser missense_variant 0.13
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518436 p.Phe108Leu missense_variant 0.15
eis 2714161 c.1171delG frameshift_variant 0.15
eis 2714397 c.936C>T synonymous_variant 0.15
eis 2714984 p.Ala117Thr missense_variant 0.22
eis 2715527 c.-195T>C upstream_gene_variant 0.14
folC 2746848 p.Arg251Gly missense_variant 0.15
folC 2746883 p.Pro239Gln missense_variant 0.2
folC 2746942 c.657C>T synonymous_variant 0.12
pepQ 2860346 p.Ser25Gly missense_variant 0.18
ribD 2986750 c.-89G>A upstream_gene_variant 0.15
ribD 2986778 c.-61G>C upstream_gene_variant 0.12
ribD 2986785 c.-54T>C upstream_gene_variant 0.1
ribD 2987099 c.261C>G synonymous_variant 0.18
Rv2752c 3064991 p.Arg401Trp missense_variant 0.17
thyX 3067463 c.483C>T synonymous_variant 0.17
thyX 3068066 c.-121T>A upstream_gene_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087763 p.Asn315Ser missense_variant 0.13
fbiD 3339103 c.-15T>C upstream_gene_variant 0.12
fbiD 3339354 c.237A>T synonymous_variant 0.15
Rv3083 3448408 c.-96T>C upstream_gene_variant 0.2
Rv3083 3448417 c.-87C>T upstream_gene_variant 0.2
Rv3083 3448672 p.Ser57Pro missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568532 c.148C>A synonymous_variant 0.22
whiB7 3568542 c.138C>T synonymous_variant 0.22
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
Rv3236c 3612009 p.Ala370Ser missense_variant 0.15
Rv3236c 3612057 p.Leu354Val missense_variant 0.15
Rv3236c 3612134 p.Thr328Ile missense_variant 0.13
fbiA 3640803 p.His87Gln missense_variant 0.13
alr 3841562 c.-142A>G upstream_gene_variant 0.14
clpC1 4038309 p.Val799Ala missense_variant 0.14
clpC1 4038790 c.1915C>T synonymous_variant 0.18
clpC1 4040021 c.684A>G synonymous_variant 0.12
clpC1 4040441 c.264C>A synonymous_variant 0.15
panD 4043971 p.Arg104Gln missense_variant 0.29
panD 4044054 c.228G>A synonymous_variant 0.14
embC 4239981 p.Gly40Asp missense_variant 0.15
embC 4239987 p.Val42Glu missense_variant 0.15
embC 4240411 c.549G>C synonymous_variant 0.16
embC 4240620 p.Thr253Ser missense_variant 0.11
embC 4241049 p.Leu396Pro missense_variant 0.11
embC 4241230 c.1368A>G synonymous_variant 0.11
embC 4241458 c.1596C>G synonymous_variant 0.17
embC 4241463 c.1602delC frameshift_variant 0.15
embC 4242102 p.Lys747Met missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4242942 p.His1027Arg missense_variant 0.1
embA 4243162 c.-71C>T upstream_gene_variant 0.13
embA 4243514 c.282G>C synonymous_variant 0.15
embA 4243614 c.383delG frameshift_variant 0.17
embA 4244045 c.813G>A synonymous_variant 0.18
embA 4244180 c.948G>T synonymous_variant 0.22
embA 4244356 p.Phe375Ser missense_variant 0.12
embA 4244790 p.Ala520Thr missense_variant 0.18
embA 4244840 c.1608G>A synonymous_variant 0.18
embB 4246346 c.-168C>G upstream_gene_variant 0.14
embB 4246608 p.Ile32Asn missense_variant 0.13
embB 4246774 c.261G>C synonymous_variant 0.13
embB 4246934 p.Thr141Ala missense_variant 0.15
embB 4246941 p.Pro143Leu missense_variant 0.17
embB 4246999 c.486C>T synonymous_variant 0.15
embB 4248374 p.Trp621Arg missense_variant 0.11
aftB 4267183 c.1653delC frameshift_variant 0.2
aftB 4267517 c.1320A>C synonymous_variant 0.15
aftB 4267539 p.Pro433Leu missense_variant 0.22
aftB 4267635 p.Arg401Leu missense_variant 0.14
aftB 4267770 p.Leu356Ser missense_variant 0.14
aftB 4267826 c.1011G>A synonymous_variant 0.13
aftB 4268752 p.Asp29Tyr missense_variant 0.22
ubiA 4269214 p.Arg207Pro missense_variant 0.12
ubiA 4269322 p.Pro171Gln missense_variant 0.13
ubiA 4269984 c.-151G>T upstream_gene_variant 0.14
ethR 4327150 c.-399A>G upstream_gene_variant 0.12
ethA 4328334 c.-861C>T upstream_gene_variant 0.14
ethA 4328416 c.-943G>A upstream_gene_variant 0.18
whiB6 4338355 p.Cys56Tyr missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0