TB-Profiler result

Run: SRR11972231
Summary

Run ID: SRR11972231

Sample name:

Date: 03-04-2023 05:32:43

Number of reads: 368124

Percentage reads mapped: 98.15

Strain: lineage3.1.2

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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 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 6173 p.Glu312Gln missense_variant 0.25
gyrB 6372 p.Thr378Ser missense_variant 1.0
gyrB 6546 p.Gly436Asp missense_variant 0.25
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7484 p.Asp61Glu missense_variant 0.29
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7588 p.Leu96Gln missense_variant 0.2
gyrA 8267 c.966G>A synonymous_variant 0.25
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9505 p.Thr735Ile missense_variant 0.29
gyrA 9567 p.Asp756Asn missense_variant 0.14
fgd1 490915 p.Arg45Cys missense_variant 0.25
fgd1 490952 p.Trp57Leu missense_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760761 p.Gly319Ser missense_variant 0.25
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763107 p.Val1101Ile missense_variant 0.12
rpoC 766509 p.Ala1047Gly missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 778606 c.-126C>T upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781416 c.-144C>T upstream_gene_variant 0.18
rplC 800959 p.Gln51* stop_gained 0.11
rplC 801085 p.Thr93Ser missense_variant 0.12
fbiC 1303928 p.Ala333Val missense_variant 1.0
Rv1258c 1406556 p.Trp262Leu missense_variant 0.12
embR 1417330 c.18A>C synonymous_variant 0.92
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673638 p.Ala67Thr missense_variant 0.5
inhA 1674591 p.Met130Ile missense_variant 0.33
tlyA 1917757 c.-183T>A upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918065 c.126G>A synonymous_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156377 c.-266C>T upstream_gene_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 1.0
PPE35 2168799 p.Phe605Cys missense_variant 0.14
PPE35 2169266 c.1347C>T synonymous_variant 0.15
PPE35 2169939 p.Gly225Ala missense_variant 0.12
PPE35 2169941 c.672C>T synonymous_variant 0.12
PPE35 2169944 c.669G>C synonymous_variant 0.11
PPE35 2169947 c.666T>C synonymous_variant 0.11
PPE35 2170031 c.582C>T synonymous_variant 0.14
Rv1979c 2222663 p.Val168Leu missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
Rv2752c 3065609 p.Gly195Arg missense_variant 0.12
Rv2752c 3066312 c.-121C>G upstream_gene_variant 0.11
thyX 3067728 p.Leu73Gln missense_variant 0.12
thyA 3073692 c.780A>G synonymous_variant 0.12
thyA 3074023 p.Phe150Cys missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473909 c.-98G>A upstream_gene_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474462 c.456T>C synonymous_variant 0.33
Rv3236c 3613214 c.-98C>T upstream_gene_variant 0.12
fbiA 3640539 c.-4C>T upstream_gene_variant 0.13
fbiB 3641820 p.Glu96Lys missense_variant 0.17
clpC1 4039661 c.1044T>C synonymous_variant 0.1
panD 4044002 p.Asp94Asn missense_variant 0.11
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242897 p.Leu1012Pro missense_variant 0.2
embA 4244584 p.Gly451Glu missense_variant 1.0
embB 4249278 c.2766delC frameshift_variant 0.22
aftB 4267209 p.Trp543* stop_gained 0.18
aftB 4268314 c.523T>C synonymous_variant 1.0
ethA 4328220 c.-747G>A upstream_gene_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407610 p.Pro198Leu missense_variant 0.33