TB-Profiler result

Run: SRR6896287
Summary

Run ID: SRR6896287

Sample name:

Date: 04-04-2023 18:01:19

Number of reads: 158084

Percentage reads mapped: 99.63

Strain:

Drug-resistance: Other

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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
lineage4.3.4 Euro-American (LAM) LAM 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
gyrB 6647 p.Gly470Cys missense_variant 0.22 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
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 6198 p.Phe320Tyr missense_variant 0.4
gyrB 6323 p.Val362Ile missense_variant 0.25
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 576192 p.Ile282Thr missense_variant 0.22
rpoB 759613 c.-194C>T upstream_gene_variant 0.4
rpoB 760433 p.Asp209Glu missense_variant 0.2
rpoB 761613 p.Ala603Thr missense_variant 0.2
rpoC 764980 c.1611C>T synonymous_variant 0.29
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766317 p.Met983Lys missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800882 c.76delG frameshift_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102918 p.Leu42Pro missense_variant 0.5
katG 2154034 p.Arg693His missense_variant 0.4
katG 2154764 p.Val450Ile missense_variant 0.22
PPE35 2168224 p.Pro797Thr missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747536 c.63G>C synonymous_variant 0.13
pepQ 2859902 p.Ser173Gly missense_variant 0.18
pepQ 2860181 p.Gly80Arg missense_variant 0.29
thyX 3067897 p.Phe17Leu missense_variant 0.33
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086680 c.-140C>A upstream_gene_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
fbiB 3641951 c.417G>A synonymous_variant 0.5
alr 3840719 c.702A>G synonymous_variant 1.0
rpoA 3877971 p.Asp179Glu missense_variant 0.33
ddn 3987063 p.Ile74Val missense_variant 0.29
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4240247 p.Asp129Tyr missense_variant 0.22
embC 4240310 p.Pro150Ser missense_variant 0.22
embC 4241074 c.1212G>T synonymous_variant 0.22
embC 4242248 c.2388delC frameshift_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248277 c.1767delC frameshift_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0