TB-Profiler result

Run: SRR1002698
Summary

Run ID: SRR1002698

Sample name:

Date: 02-04-2023 14:19:59

Number of reads: 440413

Percentage reads mapped: 97.87

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
gyrB 5949 p.Ala237Glu missense_variant 0.12
gyrB 6516 p.Leu426Ser missense_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7626 c.325C>T synonymous_variant 0.22
gyrA 7966 p.Arg222Leu missense_variant 0.14
gyrA 8802 p.Ala501Thr missense_variant 0.17
fgd1 491790 c.1008C>T synonymous_variant 0.18
rpoB 759750 c.-57G>A upstream_gene_variant 0.18
rpoB 759840 p.Ser12Gly missense_variant 0.15
rpoB 761636 c.1830G>A synonymous_variant 0.22
rpoC 763384 p.Asn5Lys missense_variant 0.13
rpoC 763570 c.201G>T synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776117 p.Phe788Leu missense_variant 0.15
mmpL5 777032 c.1449C>G synonymous_variant 0.14
mmpL5 777035 c.1446G>A synonymous_variant 0.14
mmpL5 777119 p.His454Gln missense_variant 0.21
mmpL5 777122 c.1359C>T synonymous_variant 0.21
mmpL5 777128 c.1353A>G synonymous_variant 0.24
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303635 p.Asp235Glu missense_variant 0.17
Rv1258c 1406447 c.894G>T synonymous_variant 0.12
Rv1258c 1406724 p.Gln206Arg missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475414 n.1757G>T non_coding_transcript_exon_variant 0.15
fabG1 1673346 c.-94C>G upstream_gene_variant 0.12
fabG1 1673349 c.-91G>C upstream_gene_variant 0.12
inhA 1673365 c.-837C>T upstream_gene_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.28
inhA 1674782 c.583dupC frameshift_variant 0.2
rpsA 1833774 p.Glu78Gly missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102868 p.Ala59Ser missense_variant 0.12
katG 2154400 p.Arg571His missense_variant 0.17
katG 2154538 p.Gln525Arg missense_variant 0.33
katG 2154795 p.Gln439His missense_variant 0.22
katG 2155414 p.Glu233Gly missense_variant 0.17
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.13
PPE35 2169272 c.1341C>G synonymous_variant 0.13
PPE35 2169278 c.1335T>C synonymous_variant 0.14
PPE35 2169281 c.1332T>G synonymous_variant 0.14
PPE35 2169287 c.1326T>C synonymous_variant 0.13
PPE35 2169302 p.Met437Ile missense_variant 0.15
PPE35 2169902 p.Leu237Phe missense_variant 0.3
PPE35 2169910 p.Asn235Tyr missense_variant 0.31
PPE35 2170147 p.Ser156Ala missense_variant 0.24
PPE35 2170157 p.Ala152Ser missense_variant 0.15
PPE35 2170238 c.375T>G synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288920 p.Gly108* stop_gained 0.22
pncA 2289649 c.-408G>T upstream_gene_variant 0.22
pncA 2289705 c.-464G>T upstream_gene_variant 0.2
pncA 2289709 c.-468G>T upstream_gene_variant 0.2
kasA 2518769 p.Arg219Ser missense_variant 0.67
kasA 2519140 c.1026G>C synonymous_variant 0.22
kasA 2519143 c.1029G>C synonymous_variant 0.22
kasA 2519153 p.Ile347Val missense_variant 0.2
eis 2714566 p.Leu256Pro missense_variant 0.25
eis 2714828 c.504delC frameshift_variant 0.25
eis 2715509 c.-177G>T upstream_gene_variant 0.4
ahpC 2726338 p.Val49Gly missense_variant 0.18
folC 2747296 c.303G>T synonymous_variant 0.18
pepQ 2859601 c.817delG frameshift_variant 0.18
pepQ 2860154 p.Glu89Gln missense_variant 0.2
ribD 2986921 c.88delC frameshift_variant 0.17
ribD 2987063 c.225T>C synonymous_variant 0.17
ribD 2987582 c.744C>T synonymous_variant 0.29
Rv2752c 3065286 c.906G>A synonymous_variant 0.17
thyX 3067942 p.Ala2Thr missense_variant 0.13
thyA 3073867 c.604delA frameshift_variant 0.13
fbiD 3339423 c.306G>T synonymous_variant 0.33
fprA 3474047 p.Ser14Trp missense_variant 0.15
fprA 3474637 p.Glu211* stop_gained 0.14
whiB7 3568455 c.225G>A synonymous_variant 0.12
Rv3236c 3612128 p.Leu330His missense_variant 0.29
Rv3236c 3612835 c.282T>G synonymous_variant 0.5
fbiB 3641819 c.285C>A synonymous_variant 0.13
clpC1 4038888 p.Glu606Gly missense_variant 0.13
clpC1 4039645 p.His354Asp missense_variant 0.17
clpC1 4039654 p.Thr351Ser missense_variant 0.19
clpC1 4039902 p.Arg268His missense_variant 0.12
clpC1 4040144 c.561G>C synonymous_variant 0.17
embC 4240444 c.582C>A synonymous_variant 0.25
embC 4240747 c.885C>A synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243829 c.597C>A synonymous_variant 0.33
embA 4245286 p.Leu685Ser missense_variant 0.13
embA 4245744 p.Pro838Ser missense_variant 0.4
embA 4246378 p.Asp1049Gly missense_variant 0.13
embB 4247512 c.999T>C synonymous_variant 0.12
embB 4247516 p.Asn335Asp missense_variant 0.12
embB 4248587 p.Gly692Cys missense_variant 0.22
embB 4249354 c.2841G>C synonymous_variant 1.0
embB 4249721 p.Leu1070Met missense_variant 0.33
aftB 4267769 p.Leu356Phe missense_variant 0.12
aftB 4268531 c.306C>A synonymous_variant 0.17
aftB 4268544 p.Leu98Pro missense_variant 0.17
aftB 4268867 c.-31G>T upstream_gene_variant 0.2
ethR 4327390 c.-159C>T upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338598 c.-77G>C upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0