TB-Profiler result

Run: SRR4035711
Summary

Run ID: SRR4035711

Sample name:

Date: 04-04-2023 07:15:06

Number of reads: 947431

Percentage reads mapped: 99.46

Strain: lineage4.1.2

Drug-resistance: Sensitive

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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
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 7495 p.Arg65Pro missense_variant 0.18
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7971 p.Lys224* stop_gained 0.14
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 8360 c.1059G>A synonymous_variant 0.13
gyrA 8707 p.Leu469Pro missense_variant 0.14
gyrA 8759 c.1458C>T synonymous_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9360 p.Asp687His missense_variant 0.15
gyrA 9474 p.Val725Met missense_variant 0.12
fgd1 491591 p.Lys270Met missense_variant 1.0
ccsA 620853 c.963G>C synonymous_variant 0.18
ccsA 620860 p.Gly324Arg missense_variant 0.23
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761214 p.His470Asp missense_variant 0.12
rpoB 761453 c.1647C>G synonymous_variant 0.18
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 764418 p.Arg350His missense_variant 0.23
rpoC 764834 p.Glu489Lys missense_variant 0.13
rpoC 764846 p.Glu493Lys missense_variant 0.17
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765682 c.2313C>T synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpL5 777723 p.His253Leu missense_variant 0.13
mmpR5 778475 c.-515G>A upstream_gene_variant 0.13
mmpL5 779112 c.-632G>A upstream_gene_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801015 p.Gln69His missense_variant 0.13
rplC 801031 p.Val75Ile missense_variant 0.12
fbiC 1302837 c.-94G>C upstream_gene_variant 0.11
fbiC 1303055 p.Asp42Gly missense_variant 0.11
fbiC 1303604 p.Thr225Ile missense_variant 0.12
Rv1258c 1406326 p.Arg339Gly missense_variant 0.18
Rv1258c 1406470 p.Met291Val missense_variant 0.15
Rv1258c 1406519 c.822A>G synonymous_variant 0.12
Rv1258c 1407466 c.-127delC upstream_gene_variant 0.18
embR 1417037 p.Ser104Asn missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472335 n.490A>T non_coding_transcript_exon_variant 0.12
rrs 1472687 n.842A>G non_coding_transcript_exon_variant 0.17
rrl 1473641 n.-17T>C upstream_gene_variant 0.13
rrl 1475457 n.1800G>C non_coding_transcript_exon_variant 0.13
fabG1 1673173 c.-267G>C upstream_gene_variant 0.11
inhA 1674380 p.Leu60Pro missense_variant 0.12
inhA 1674992 p.Ala264Gly missense_variant 0.15
rpsA 1833862 c.321G>A synonymous_variant 0.29
rpsA 1834874 p.Ala445Pro missense_variant 0.12
tlyA 1917963 c.24C>T synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918499 p.Val187Glu missense_variant 0.15
ndh 2101803 p.Leu414Met missense_variant 0.13
ndh 2102708 p.Tyr112Cys missense_variant 0.11
ndh 2102801 p.Asn81Thr missense_variant 0.17
ndh 2102808 p.Gln79* stop_gained 0.17
ndh 2102814 p.Arg77Gly missense_variant 0.17
ndh 2102828 p.Thr72Ile missense_variant 0.15
ndh 2103224 c.-183A>G upstream_gene_variant 0.14
katG 2153933 p.Ala727Ser missense_variant 0.25
katG 2154339 c.1773A>G synonymous_variant 0.15
katG 2154985 p.Thr376Met missense_variant 0.2
katG 2156523 c.-412G>A upstream_gene_variant 0.15
PPE35 2169014 c.1599G>A synonymous_variant 0.18
PPE35 2169545 p.His356Gln missense_variant 0.18
PPE35 2170069 p.Pro182Ser missense_variant 0.2
Rv1979c 2222826 c.338delT frameshift_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289373 c.-132A>G upstream_gene_variant 0.12
kasA 2517925 c.-189delG upstream_gene_variant 0.14
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2714722 p.Cys204Ser missense_variant 0.13
eis 2715034 p.Met100Lys missense_variant 0.14
ahpC 2725915 c.-278C>T upstream_gene_variant 0.15
folC 2747148 p.Lys151Glu missense_variant 0.11
pepQ 2859931 p.Leu163Arg missense_variant 0.13
pepQ 2860480 c.-62G>A upstream_gene_variant 0.13
Rv2752c 3065940 c.251delA frameshift_variant 0.12
Rv2752c 3067098 c.-907A>G upstream_gene_variant 0.12
thyX 3067542 p.Ala135Val missense_variant 0.25
thyX 3068128 c.-183C>T upstream_gene_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087690 p.His291Tyr missense_variant 0.18
ald 3087723 p.Pro302Ala missense_variant 0.15
Rv3083 3448838 p.Arg112Gln missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474400 p.Tyr132His missense_variant 0.1
fprA 3475230 c.1224C>T synonymous_variant 0.14
fprA 3475236 c.1230A>G synonymous_variant 0.12
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
Rv3236c 3611981 p.Ala379Gly missense_variant 0.15
Rv3236c 3611999 p.Thr373Ile missense_variant 0.15
Rv3236c 3612449 p.Leu223Arg missense_variant 0.13
Rv3236c 3612509 p.Gly203Asp missense_variant 0.18
Rv3236c 3612922 c.195T>C synonymous_variant 0.12
Rv3236c 3612933 p.Ala62Thr missense_variant 0.13
fbiA 3640430 c.-113A>T upstream_gene_variant 0.12
fbiB 3642601 p.Gly356Ala missense_variant 0.11
alr 3840554 c.867G>A synonymous_variant 0.12
alr 3841031 c.390C>A synonymous_variant 0.14
alr 3841115 c.306T>C synonymous_variant 0.2
rpoA 3877851 p.Phe219Leu missense_variant 0.14
rpoA 3878442 c.66G>A synonymous_variant 0.13
rpoA 3878641 c.-134C>G upstream_gene_variant 0.3
clpC1 4038624 p.Lys694Ile missense_variant 0.14
clpC1 4039318 p.Glu463Lys missense_variant 0.15
clpC1 4040085 p.Arg207His missense_variant 0.22
embC 4240777 c.915G>A synonymous_variant 0.14
embC 4241847 p.Thr662Ser missense_variant 0.12
embA 4242340 c.-893C>A upstream_gene_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243123 c.-110T>C upstream_gene_variant 0.17
embA 4243976 p.Phe248Leu missense_variant 0.14
embA 4243994 c.762C>T synonymous_variant 0.15
embA 4244201 p.Trp323* stop_gained 0.14
embA 4244226 p.Gly332* stop_gained 0.14
embA 4244262 c.1030C>T synonymous_variant 0.18
embA 4245357 p.Ala709Thr missense_variant 0.14
embB 4245761 c.-753C>T upstream_gene_variant 0.2
embA 4246236 p.Leu1002Val missense_variant 0.11
embB 4246655 p.Pro48Ser missense_variant 0.2
embB 4246864 c.351C>G synonymous_variant 0.13
embB 4247081 p.Thr190Ser missense_variant 0.15
embB 4247413 p.Asp300Glu missense_variant 0.12
embB 4249132 c.2619G>A synonymous_variant 0.17
embB 4249523 p.Asn1004Tyr missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407961 p.Ile81Thr missense_variant 0.11