TB-Profiler result

Run: SRR12830373
Summary

Run ID: SRR12830373

Sample name:

Date: 03-04-2023 06:58:33

Number of reads: 529662

Percentage reads mapped: 99.87

Strain: lineage4.3.4.2

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
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 5933 p.Ser232Thr missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.93
gyrA 7860 p.Thr187Ser missense_variant 0.14
gyrA 8435 c.1134C>A synonymous_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 0.97
ccsA 620123 p.Arg78Pro missense_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765594 p.Lys742Arg missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777690 p.Asn264Ser missense_variant 0.11
mmpR5 779413 p.Leu142Met missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303187 p.Tyr86Cys missense_variant 0.12
fbiC 1305494 c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT frameshift_variant&stop_lost&splice_region_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472049 n.204G>T non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102335 c.708G>A synonymous_variant 0.15
katG 2154718 p.Ser465Leu missense_variant 0.14
PPE35 2167973 c.2640A>G synonymous_variant 0.14
PPE35 2168420 c.2193C>T synonymous_variant 0.25
PPE35 2168796 p.Thr606Met missense_variant 0.17
PPE35 2169005 c.1608G>T synonymous_variant 0.14
PPE35 2169684 p.Gly310Val missense_variant 0.2
Rv1979c 2222288 p.Ala293Thr missense_variant 0.17
Rv1979c 2222879 p.Val96Ile missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715213 c.120G>T synonymous_variant 0.13
Rv2752c 3065293 p.Val300Ala missense_variant 1.0
Rv2752c 3066105 c.87C>T synonymous_variant 0.17
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339310 p.Asp65Asn missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474265 p.His87Asp missense_variant 0.1
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
rpoA 3878535 c.-28G>T upstream_gene_variant 0.15
rpoA 3878629 c.-122A>C upstream_gene_variant 0.25
ddn 3987122 p.Lys93Asn missense_variant 0.15
ddn 3987281 p.Ile146Met missense_variant 0.1
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4239763 c.-100C>T upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 0.97
embA 4244606 c.1374G>T synonymous_variant 0.12
embA 4245173 c.1941G>T synonymous_variant 0.12
embB 4247884 c.1371C>A synonymous_variant 1.0
ubiA 4269412 p.Gly141Val missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
fbiC 1305494 c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN frameshift_variant&stop_lost&splice_region_variant 1.0