TB-Profiler result

Run: SRR4035600
Summary

Run ID: SRR4035600

Sample name:

Date: 04-04-2023 07:12:24

Number of reads: 715028

Percentage reads mapped: 99.72

Strain: lineage4.3.4.2.1

Drug-resistance: RR-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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.99
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 1.0
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 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
rpoB 761116 p.Asn437Ile missense_variant 0.12 rifampicin
ethA 4326122 c.1351delT frameshift_variant 0.14 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
gyrB 6140 p.Val301Leu missense_variant 1.0
gyrB 6836 c.1599delC frameshift_variant 0.14
gyrB 6947 p.Lys570Glu missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576250 c.903G>A synonymous_variant 0.18
ccsA 619759 c.-132C>A upstream_gene_variant 0.2
rpoB 760571 c.765G>A synonymous_variant 0.18
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777395 c.1086C>T synonymous_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781793 c.234G>A synonymous_variant 0.18
rplC 800717 c.-92C>T upstream_gene_variant 0.12
fbiC 1304264 p.Gly445Asp missense_variant 0.17
embR 1416802 c.546C>A synonymous_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.18
rrl 1475823 n.2168delG non_coding_transcript_exon_variant 0.2
rrl 1476018 n.2361G>C non_coding_transcript_exon_variant 0.14
fabG1 1673249 c.-191C>T upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102709 c.333delC frameshift_variant 0.17
katG 2154206 p.Ala636Ser missense_variant 0.13
katG 2154358 p.Ala585Val missense_variant 0.29
PPE35 2168303 c.2310G>A synonymous_variant 0.12
PPE35 2169320 p.Leu431Phe missense_variant 0.26
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715052 p.Arg94His missense_variant 0.15
folC 2747505 p.His32Tyr missense_variant 0.33
Rv2752c 3064894 p.Ala433Val missense_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087136 p.Ala106Gly missense_variant 0.18
ald 3087285 p.Arg156Ser missense_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474011 p.Arg2His missense_variant 0.25
fprA 3475323 c.1321delC frameshift_variant 0.17
whiB7 3568660 p.Pro7His missense_variant 0.11
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
fbiA 3641168 p.Ile209Thr missense_variant 0.13
fbiB 3641797 p.Arg88His missense_variant 0.12
fbiB 3642547 p.Gly338Asp missense_variant 0.13
alr 3840719 c.702A>G synonymous_variant 1.0
alr 3841379 c.42G>A synonymous_variant 0.11
rpoA 3878382 c.126G>A synonymous_variant 0.18
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038373 p.Gln778Glu missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243108 c.-125C>A upstream_gene_variant 0.18
embA 4244049 p.Asp273Tyr missense_variant 0.11
embA 4245130 p.Pro633Leu missense_variant 0.14
embB 4247170 c.657G>A synonymous_variant 0.25
embB 4248296 p.His595Asn missense_variant 0.1
aftB 4268375 p.Met154Ile missense_variant 0.17
ethA 4327089 p.Leu129Ile missense_variant 0.2
ethA 4327896 c.-423C>T upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0