TB-Profiler result

Run: SRR4035835

Summary

Run ID: SRR4035835

Sample name:

Date: 04-04-2023 07:19:36

Number of reads: 1315466

Percentage reads mapped: 99.49

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 7585 p.Ser95Thr missense_variant 1.0
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490939 p.Phe53Leu missense_variant 0.11
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575406 p.Arg20His missense_variant 0.18
mshA 575633 p.Ala96Pro missense_variant 0.12
mshA 575652 p.Arg102Leu missense_variant 0.14
mshA 576497 p.Gly384Arg missense_variant 0.18
ccsA 619709 c.-182T>C upstream_gene_variant 0.12
ccsA 620025 c.135G>A synonymous_variant 0.14
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760836 c.1031delA frameshift_variant 0.11
rpoB 762985 p.Gln1060Arg missense_variant 0.11
rpoC 763871 p.Gly168Arg missense_variant 0.11
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 764832 p.Glu488Gly missense_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 0.94
rpoC 766379 p.Gly1004Ser missense_variant 0.17
rpoC 766631 p.Val1088Leu missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776357 c.2124C>T synonymous_variant 0.12
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpL5 777613 p.Gly290Arg missense_variant 0.22
mmpL5 777636 p.Ile282Thr missense_variant 0.2
mmpL5 777734 p.Phe249Leu missense_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304026 p.Asn366Asp missense_variant 0.1
fbiC 1304509 p.Ala527Thr missense_variant 0.15
Rv1258c 1406095 p.Gly416Arg missense_variant 0.1
Rv1258c 1407019 p.Val108Leu missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473587 n.-71A>G upstream_gene_variant 0.2
rrl 1473592 n.-66C>T upstream_gene_variant 0.18
rrl 1473681 n.24G>C non_coding_transcript_exon_variant 0.15
rrl 1473698 n.41G>A non_coding_transcript_exon_variant 0.2
rrl 1474624 n.967G>T non_coding_transcript_exon_variant 0.15
rrl 1474685 n.1028G>T non_coding_transcript_exon_variant 0.14
rrl 1474975 n.1318G>A non_coding_transcript_exon_variant 0.22
rrl 1476023 n.2366C>T non_coding_transcript_exon_variant 0.29
rrl 1476469 n.2812G>A non_coding_transcript_exon_variant 0.18
rrl 1476475 n.2818T>C non_coding_transcript_exon_variant 0.18
inhA 1674952 p.Pro251Ala missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154104 p.Pro670Ser missense_variant 0.12
katG 2155923 c.189C>T synonymous_variant 0.14
katG 2156212 c.-101G>C upstream_gene_variant 0.11
PPE35 2170130 c.483C>T synonymous_variant 0.2
PPE35 2170785 c.-173T>C upstream_gene_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290029 c.-788G>A upstream_gene_variant 0.13
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2519146 c.1032C>T synonymous_variant 0.2
eis 2714677 p.His219Arg missense_variant 0.11
ahpC 2725914 c.-279G>C upstream_gene_variant 0.11
ahpC 2726369 p.Phe59Leu missense_variant 0.17
folC 2747109 p.Ala164Ser missense_variant 0.13
pepQ 2859378 c.1041G>A synonymous_variant 0.12
pepQ 2860458 c.-40T>C upstream_gene_variant 0.22
pepQ 2860524 c.-106A>T upstream_gene_variant 0.12
pepQ 2860540 c.-122T>C upstream_gene_variant 0.12
Rv2752c 3065553 c.639A>T synonymous_variant 0.15
thyX 3067279 p.Ala223Thr missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087218 p.Met133Ile missense_variant 0.14
fbiD 3339299 p.Val61Ala missense_variant 0.12
fbiD 3339479 p.Gln121Arg missense_variant 0.11
fbiD 3339674 p.Arg186Leu missense_variant 0.12
Rv3083 3448314 c.-190C>T upstream_gene_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
Rv3236c 3613166 c.-50C>A upstream_gene_variant 0.29
alr 3841266 p.Leu52Pro missense_variant 0.11
clpC1 4038180 p.Gly842Ala missense_variant 0.11
clpC1 4039813 p.Ala298Thr missense_variant 0.13
clpC1 4040430 p.Leu92Ser missense_variant 0.11
panD 4044323 c.-43delC upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246525 c.12C>T synonymous_variant 0.22
embB 4246615 c.102G>A synonymous_variant 0.2
embB 4246635 p.Ser41* stop_gained 0.22
embB 4246705 c.192G>C synonymous_variant 0.14
embB 4249620 p.Leu1036Pro missense_variant 0.11
embB 4249656 p.Val1048Ala missense_variant 0.12
aftB 4267182 p.Gly552Ala missense_variant 0.12
aftB 4268388 p.Leu150Gln missense_variant 0.13
aftB 4268776 c.60delG frameshift_variant 0.12
aftB 4268795 c.42C>G synonymous_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0