TB-Profiler result

Run: ERR4817377
Summary

Run ID: ERR4817377

Sample name:

Date: 01-04-2023 14:57:34

Number of reads: 475605

Percentage reads mapped: 99.5

Strain: lineage3

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
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 5322 p.Lys28Arg missense_variant 0.11
gyrB 5640 p.Arg134Leu missense_variant 0.11
gyrB 6804 p.Leu522Pro missense_variant 0.12
gyrA 6922 c.-380G>T upstream_gene_variant 0.2
gyrA 7010 c.-292C>T upstream_gene_variant 0.13
gyrB 7118 p.Asp627Tyr missense_variant 0.25
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7406 c.105G>A synonymous_variant 0.11
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7696 p.Ala132Val missense_variant 0.12
gyrA 8763 p.Asp488Tyr missense_variant 0.29
gyrA 8801 c.1500G>A synonymous_variant 0.18
gyrA 8873 c.1572A>G synonymous_variant 0.2
gyrA 9121 p.Arg607Leu missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
fgd1 491774 p.Arg331Met missense_variant 0.11
mshA 575950 c.607delG frameshift_variant 0.5
mshA 576463 c.1116G>A synonymous_variant 0.13
mshA 576517 c.1170G>A synonymous_variant 0.18
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763063 p.Lys1086Arg missense_variant 0.15
rpoC 765571 c.2202C>G synonymous_variant 0.2
rpoC 766126 c.2757G>A synonymous_variant 0.22
rpoC 766582 c.3213C>A synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776605 p.Arg626Ser missense_variant 0.11
mmpL5 777032 c.1449C>G synonymous_variant 0.12
mmpL5 777035 c.1446G>A synonymous_variant 0.12
mmpL5 777157 c.1324C>A synonymous_variant 0.15
mmpL5 777164 c.1317C>T synonymous_variant 0.15
mmpL5 777767 c.714C>T synonymous_variant 0.18
mmpL5 777811 p.Arg224Trp missense_variant 0.14
mmpR5 778349 c.-641G>T upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800640 c.-169A>G upstream_gene_variant 0.2
rplC 800856 c.48A>G synonymous_variant 0.25
rplC 800955 c.147C>A synonymous_variant 0.2
fbiC 1303817 p.Arg296His missense_variant 0.11
fbiC 1304113 p.Gln395Lys missense_variant 0.18
fbiC 1305232 p.Ala768Ser missense_variant 0.2
embR 1416408 p.His314Tyr missense_variant 0.12
embR 1417093 c.255C>A synonymous_variant 0.11
embR 1417528 c.-181C>A upstream_gene_variant 0.14
atpE 1461036 c.-9G>T upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673738 p.Met100Thr missense_variant 0.18
fabG1 1674020 p.Leu194Pro missense_variant 0.29
fabG1 1674152 p.Pro238Gln missense_variant 0.17
inhA 1674767 p.Val189Ala missense_variant 0.33
tlyA 1917828 c.-112G>T upstream_gene_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918034 p.Val32Gly missense_variant 0.5
ndh 2102077 c.966T>C synonymous_variant 0.25
ndh 2102631 p.Met138Val missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168260 c.2352delT frameshift_variant 0.33
PPE35 2169162 p.Ser484* stop_gained 0.17
Rv1979c 2222540 p.Gly209Cys missense_variant 0.14
Rv1979c 2222556 c.609C>T synonymous_variant 0.12
Rv1979c 2222982 c.183G>A synonymous_variant 0.12
Rv1979c 2223078 c.87C>T synonymous_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
pncA 2289786 c.-545G>T upstream_gene_variant 0.22
pncA 2289833 c.-592T>G upstream_gene_variant 0.29
pncA 2289887 c.-649_-647delCCG upstream_gene_variant 0.2
pncA 2290132 c.-891C>T upstream_gene_variant 0.12
ahpC 2726022 c.-171C>A upstream_gene_variant 0.12
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726257 p.Asp22Val missense_variant 0.25
ahpC 2726338 p.Val49Gly missense_variant 0.38
ahpC 2726583 p.Ala131Thr missense_variant 0.5
pepQ 2859372 c.1047G>A synonymous_variant 0.13
ribD 2986798 c.-41C>G upstream_gene_variant 0.12
ribD 2987096 c.258C>T synonymous_variant 0.15
ribD 2987127 p.Arg97Trp missense_variant 0.12
Rv2752c 3065586 p.Asp202Glu missense_variant 0.22
Rv2752c 3065995 p.His66Arg missense_variant 0.18
Rv2752c 3066157 p.Thr12Ile missense_variant 0.22
thyA 3074116 p.Leu119Pro missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3338993 c.-125C>T upstream_gene_variant 0.12
Rv3083 3449223 p.Tyr240* stop_gained 0.11
Rv3083 3449796 c.1293G>A synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475358 p.Leu451* stop_gained 0.22
whiB7 3568574 p.Leu36Val missense_variant 0.1
fbiB 3640674 c.-861C>T upstream_gene_variant 0.29
fbiB 3641573 p.Glu13Asp missense_variant 0.22
fbiB 3641850 p.Ala106Ser missense_variant 0.25
fbiB 3642370 p.Ala279Val missense_variant 0.11
fbiB 3642833 c.1299C>T synonymous_variant 0.17
alr 3841151 c.270C>A synonymous_variant 0.13
alr 3841473 c.-53G>A upstream_gene_variant 1.0
rpoA 3877850 p.Gly220Ser missense_variant 0.22
ddn 3987108 p.Tyr89Asp missense_variant 0.12
clpC1 4038588 p.Arg706Leu missense_variant 0.2
clpC1 4039597 p.His370Asn missense_variant 0.22
clpC1 4040724 c.-20G>T upstream_gene_variant 0.12
embC 4240133 p.Ala91Ser missense_variant 0.2
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242249 p.Ala796Val missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244780 c.1548C>A synonymous_variant 0.17
embA 4245313 p.Ala694Glu missense_variant 0.22
embB 4248563 p.Ala684Thr missense_variant 0.17
aftB 4267623 p.Ser405* stop_gained 0.22
aftB 4268418 p.Glu140Gly missense_variant 0.2
ubiA 4269032 p.Gly268Ser missense_variant 0.15
aftB 4269366 c.-530G>A upstream_gene_variant 0.15
ethA 4326011 p.Gly488Val missense_variant 0.11
ethA 4326548 p.Lys309Arg missense_variant 0.15
ethA 4326743 p.Leu244Pro missense_variant 0.17
ethR 4327042 c.-507G>A upstream_gene_variant 0.14
ethA 4327306 p.Asp56Glu missense_variant 0.18
ethR 4328047 p.Pro167Ser missense_variant 1.0
ethA 4328292 c.-819A>G upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408436 c.-234C>T upstream_gene_variant 0.2