TB-Profiler result

Run: SRR4035578
Summary

Run ID: SRR4035578

Sample name:

Date: 04-04-2023 07:11:26

Number of reads: 1212842

Percentage reads mapped: 99.68

Strain: lineage4.3.4.2.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
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
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 0.95
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777174 p.Arg436His missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801048 p.Tyr80* stop_gained 0.13
embR 1417179 c.167_168dupTC frameshift_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475025 n.1368A>G non_coding_transcript_exon_variant 0.12
rrl 1475132 n.1475T>C non_coding_transcript_exon_variant 0.18
fabG1 1673346 c.-94C>G upstream_gene_variant 0.16
fabG1 1673349 c.-91G>C upstream_gene_variant 0.17
fabG1 1673357 c.-83G>A upstream_gene_variant 0.18
fabG1 1673359 c.-81T>C upstream_gene_variant 0.18
fabG1 1673361 c.-79C>G upstream_gene_variant 0.19
fabG1 1673380 c.-60C>G upstream_gene_variant 0.13
rpsA 1833470 c.-72T>C upstream_gene_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102939 p.Arg35Gln missense_variant 0.12
katG 2153933 p.Ala727Ser missense_variant 0.38
PPE35 2169320 p.Leu431Phe missense_variant 0.36
Rv1979c 2222185 c.979delT frameshift_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726526 p.Ser112Thr missense_variant 0.18
Rv2752c 3065817 c.375C>T synonymous_variant 0.17
thyX 3067343 c.603C>T synonymous_variant 0.2
thyX 3067896 p.Phe17Ser missense_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449950 c.1447C>T synonymous_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568476 c.204T>C synonymous_variant 0.15
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
alr 3840719 c.702A>G synonymous_variant 1.0
rpoA 3878641 c.-134C>G upstream_gene_variant 0.67
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4242203 p.Leu781Met missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246642 c.129G>A synonymous_variant 0.17
embB 4247068 c.555T>C synonymous_variant 0.22
embB 4247441 p.Ala310Thr missense_variant 0.14
aftB 4267191 p.Gly549Asp missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0