TB-Profiler result

Run: SRR9940980
Summary

Run ID: SRR9940980

Sample name:

Date: 04-04-2023 23:03:28

Number of reads: 563724

Percentage reads mapped: 99.81

Strain: lineage4.9

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
lineage4.9 Euro-American (H37Rv-like) T1 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
gyrB 6004 c.767dupG frameshift_variant 0.25
gyrA 7547 c.246C>A synonymous_variant 0.15
gyrA 9659 c.2358C>T synonymous_variant 0.12
mshA 575570 p.Ser75Gly missense_variant 0.17
ccsA 620218 p.Met110Val missense_variant 0.2
ccsA 620756 p.Asp289Gly missense_variant 0.18
rpoB 759611 c.-196G>C upstream_gene_variant 0.25
rpoB 760984 p.Val393Glu missense_variant 0.22
rpoB 762266 c.2460T>C synonymous_variant 0.13
rpoC 763542 p.Trp58Leu missense_variant 0.11
rpoC 765537 p.Trp723Leu missense_variant 0.25
mmpL5 776451 p.Gly677Asp missense_variant 0.12
Rv1258c 1406735 c.606C>A synonymous_variant 0.11
Rv1258c 1407340 c.1A>G start_lost 0.14
Rv1258c 1407392 c.-52G>T upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673346 c.-94C>G upstream_gene_variant 0.19
fabG1 1673349 c.-91G>C upstream_gene_variant 0.19
fabG1 1673357 c.-83G>A upstream_gene_variant 0.3
fabG1 1673359 c.-81T>C upstream_gene_variant 0.3
fabG1 1673361 c.-79C>G upstream_gene_variant 0.29
fabG1 1673380 c.-60C>G upstream_gene_variant 0.48
fabG1 1673560 p.Lys41Leu missense_variant 0.13
inhA 1674721 p.Phe174Leu missense_variant 0.29
inhA 1674985 p.Gly262Ser missense_variant 0.15
inhA 1674988 p.Gly263Ser missense_variant 0.15
rpsA 1834134 p.Val198Ala missense_variant 0.1
tlyA 1918454 p.Ser172* stop_gained 0.13
ndh 2103008 p.Pro12His missense_variant 0.14
katG 2154135 c.1977G>C synonymous_variant 0.1
katG 2155921 p.Tyr64Cys missense_variant 0.12
PPE35 2168261 c.2352T>C synonymous_variant 0.12
PPE35 2168453 c.2160C>G synonymous_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.6
PPE35 2170053 p.Thr187Ser missense_variant 0.6
PPE35 2170598 c.15G>A synonymous_variant 1.0
pncA 2289702 c.-461T>G upstream_gene_variant 0.33
ahpC 2726184 c.-9_-8insG upstream_gene_variant 0.11
ahpC 2726338 p.Val49Gly missense_variant 0.33
ribD 2986825 c.-14C>T upstream_gene_variant 0.17
thyX 3067257 p.Phe230Cys missense_variant 0.29
thyX 3067647 p.Ser100Tyr missense_variant 0.12
ald 3086901 p.Arg28Ser missense_variant 0.29
Rv3083 3448492 c.-12C>A upstream_gene_variant 0.22
Rv3083 3449825 p.Ser441Tyr missense_variant 0.13
fprA 3473868 c.-139G>T upstream_gene_variant 0.11
fprA 3474338 p.Met111Thr missense_variant 0.11
fbiA 3641402 p.Cys287Ser missense_variant 0.1
fbiB 3642532 p.Arg333Leu missense_variant 0.29
alr 3841379 c.42G>T synonymous_variant 0.25
rpoA 3877588 p.Ser307Leu missense_variant 0.18
clpC1 4039835 p.His290Gln missense_variant 0.15
embC 4241724 p.Val621Glu missense_variant 0.11
embA 4243633 p.Gly134Val missense_variant 0.22
embA 4244956 p.Gly575Asp missense_variant 0.33
embB 4246544 p.Thr11Pro missense_variant 0.3
embB 4246834 p.Lys107Asn missense_variant 0.12
embB 4247428 c.915C>A synonymous_variant 0.18
embB 4248274 p.Phe587Leu missense_variant 0.1
gid 4408067 p.Asp46Tyr missense_variant 0.17