TB-Profiler result

Run: SRR6511597
Summary

Run ID: SRR6511597

Sample name:

Date: 04-04-2023 15:14:27

Number of reads: 358950

Percentage reads mapped: 99.57

Strain: lineage4.3.2

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
lineage4.3.2 Euro-American (LAM) LAM3 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
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 575739 p.Ala131Val missense_variant 0.25
mshA 576577 c.1233delG frameshift_variant 0.5
ccsA 619857 c.-34C>T upstream_gene_variant 0.33
rpoB 760606 p.Ala267Val missense_variant 0.18
rpoB 760731 p.Lys309Glu missense_variant 0.11
rpoB 761863 p.Ala686Val missense_variant 0.18
rpoB 762341 c.2535G>T synonymous_variant 0.29
rpoC 763676 p.His103Tyr missense_variant 0.18
rpoC 763799 p.Arg144Cys missense_variant 0.29
rpoC 764262 p.Val298Ala missense_variant 0.14
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766575 p.Asp1069Gly missense_variant 0.14
rpoC 766795 p.Tyr1142* stop_gained 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776157 p.Asp775Val missense_variant 0.11
mmpL5 776991 p.Ile497Thr missense_variant 0.14
mmpS5 778659 p.Gly83Ser missense_variant 0.22
mmpL5 779010 c.-530G>A upstream_gene_variant 0.2
mmpR5 779029 p.Pro14Thr missense_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303449 c.519C>T synonymous_variant 0.13
fbiC 1304242 p.Pro438Ser missense_variant 0.33
fbiC 1305017 p.Thr696Ile missense_variant 1.0
Rv1258c 1406555 p.Trp262Cys missense_variant 0.2
embR 1416642 p.Ala236Thr missense_variant 0.25
atpE 1461231 p.Ala63Thr missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471698 n.-148A>T upstream_gene_variant 0.22
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1473790 n.133C>T non_coding_transcript_exon_variant 0.18
inhA 1674607 p.Pro136Ser missense_variant 0.14
rpsA 1834264 c.723G>A synonymous_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918157 p.Ala73Val missense_variant 0.22
tlyA 1918727 p.Ala263Val missense_variant 0.33
ndh 2101904 p.Ala380Val missense_variant 0.22
ndh 2101910 p.Ala378Val missense_variant 0.29
ndh 2102225 p.Cys273Tyr missense_variant 0.2
katG 2153952 c.2160C>T synonymous_variant 0.15
katG 2155784 p.Ala110Thr missense_variant 0.67
PPE35 2168200 p.Ala805Ser missense_variant 0.18
PPE35 2168930 c.1683G>T synonymous_variant 0.2
PPE35 2169221 c.1392T>A synonymous_variant 0.67
PPE35 2169327 p.Asn429Ile missense_variant 0.18
PPE35 2169691 p.Gly308Ser missense_variant 0.25
Rv1979c 2222486 p.Val227Phe missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289032 c.210G>A synonymous_variant 0.12
folC 2746496 p.His368Arg missense_variant 0.33
folC 2747287 c.312G>A synonymous_variant 0.14
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339700 c.583C>T synonymous_variant 0.4
Rv3083 3449950 c.1447C>T synonymous_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612935 p.Gly61Asp missense_variant 0.5
fbiA 3640384 c.-159T>A upstream_gene_variant 0.13
fbiB 3642700 p.Ala389Val missense_variant 0.14
alr 3841589 c.-169C>T upstream_gene_variant 0.12
ddn 3986910 p.Arg23Trp missense_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038956 c.1748delG frameshift_variant 0.17
clpC1 4039239 p.Gly489Asp missense_variant 0.2
clpC1 4039498 p.Ile403Val missense_variant 0.22
panD 4044211 p.Gly24Asp missense_variant 0.15
panD 4044248 p.Arg12Cys missense_variant 0.15
embC 4239750 c.-113G>A upstream_gene_variant 0.2
embC 4240986 p.Arg375Gln missense_variant 0.5
embC 4241332 p.Asp490Glu missense_variant 0.29
embC 4242524 p.Ala888Thr missense_variant 0.4
embC 4242629 p.Ala923Thr missense_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243019 c.3159delG frameshift_variant 0.11
embB 4249302 p.Arg930His missense_variant 0.13
embB 4249547 p.Phe1012Leu missense_variant 0.17
aftB 4268521 p.Tyr106Asn missense_variant 0.11
aftB 4268830 p.Arg3Trp missense_variant 0.2
ubiA 4270017 c.-184G>T upstream_gene_variant 0.33
ethA 4327710 c.-237G>A upstream_gene_variant 0.13
whiB6 4338469 p.Asn18Thr missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0