TB-Profiler result

Run: ERR6336806
Summary

Run ID: ERR6336806

Sample name:

Date: 02-04-2023 02:04:10

Number of reads: 630834

Percentage reads mapped: 99.09

Strain: lineage1.2.1.2.1

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.2.1 Indo-Oceanic EAI2 RD239 1.0
lineage1.2.1.2 Indo-Oceanic NA RD239 1.0
lineage1.2.1.2.1 Indo-Oceanic NA RD239 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 5148 c.-92C>T upstream_gene_variant 0.12
gyrB 5628 p.Ala130Glu missense_variant 0.13
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7801 p.Pro167His missense_variant 0.14
gyrA 8444 c.1144delC frameshift_variant 0.12
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9260 c.1959G>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9394 p.Ser698Trp missense_variant 0.25
fgd1 491645 p.Ser288Leu missense_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575368 c.21T>C synonymous_variant 1.0
mshA 575538 p.Asp64Gly missense_variant 0.14
mshA 576671 p.Arg442Trp missense_variant 0.25
ccsA 620833 p.Val315Ile missense_variant 0.22
rpoB 759626 c.-181C>T upstream_gene_variant 0.14
rpoB 759972 p.Glu56Lys missense_variant 0.22
rpoB 760370 c.564C>T synonymous_variant 0.22
rpoB 760373 c.567C>G synonymous_variant 0.22
rpoB 760406 c.600G>A synonymous_variant 0.17
rpoB 760641 p.Glu279Lys missense_variant 0.18
rpoB 761467 p.Leu554Pro missense_variant 0.13
rpoB 762976 p.Phe1057Tyr missense_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763531 c.162G>C synonymous_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 763942 c.573C>A synonymous_variant 0.33
rpoC 765874 c.2505G>A synonymous_variant 0.13
rpoC 766029 p.Arg887Leu missense_variant 0.16
rpoC 766032 p.Glu888Ala missense_variant 0.18
rpoC 766376 p.Ile1003Val missense_variant 0.5
rpoC 766739 p.Val1124Met missense_variant 0.2
rpoC 767050 p.Gln1227His missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775925 c.2556G>A synonymous_variant 0.17
mmpL5 776030 c.2451G>C synonymous_variant 0.12
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776647 p.Val612Ile missense_variant 0.12
mmpL5 777066 p.Ile472Thr missense_variant 0.12
mmpL5 777368 c.1113G>A synonymous_variant 0.12
mmpL5 777842 c.639C>T synonymous_variant 0.17
mmpL5 779031 c.-551G>A upstream_gene_variant 0.17
mmpR5 779247 c.262dupG frameshift_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781656 p.Val33Leu missense_variant 0.1
fbiC 1303045 c.115C>T synonymous_variant 0.13
fbiC 1303155 c.225G>A synonymous_variant 0.14
fbiC 1303498 p.His190Asn missense_variant 0.13
fbiC 1303661 p.Val244Gly missense_variant 0.12
fbiC 1303668 c.738C>T synonymous_variant 0.13
fbiC 1303812 c.882C>T synonymous_variant 1.0
fbiC 1304733 p.Met601Ile missense_variant 0.15
fbiC 1305196 p.Ala756Thr missense_variant 0.2
Rv1258c 1406312 c.1029T>C synonymous_variant 1.0
Rv1258c 1406641 p.Thr234Ala missense_variant 0.12
Rv1258c 1407095 c.245delC frameshift_variant 0.18
embR 1416856 c.492G>A synonymous_variant 0.29
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417400 c.-53C>G upstream_gene_variant 0.1
embR 1417506 c.-159T>C upstream_gene_variant 0.14
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472797 n.952A>G non_coding_transcript_exon_variant 0.17
rrl 1473916 n.259C>T non_coding_transcript_exon_variant 0.12
rrl 1474209 n.552G>A non_coding_transcript_exon_variant 0.17
rrl 1474893 n.1236G>A non_coding_transcript_exon_variant 0.14
rrl 1475021 n.1364G>A non_coding_transcript_exon_variant 0.15
rrl 1475880 n.2223C>T non_coding_transcript_exon_variant 0.18
rrl 1476621 n.2964C>T non_coding_transcript_exon_variant 0.13
fabG1 1674151 p.Pro238Thr missense_variant 0.18
inhA 1674162 c.-40C>T upstream_gene_variant 1.0
rpsA 1833851 p.Lys104Glu missense_variant 0.25
rpsA 1834538 p.Val333Met missense_variant 0.13
tlyA 1917838 c.-102G>A upstream_gene_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918520 p.Pro194Arg missense_variant 0.29
ndh 2102098 c.945G>A synonymous_variant 0.13
ndh 2102125 c.918G>A synonymous_variant 0.14
katG 2154351 c.1761G>A synonymous_variant 0.12
katG 2154556 p.Arg519His missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154748 p.Ile455Thr missense_variant 0.17
katG 2154867 c.1245G>A synonymous_variant 0.13
katG 2156166 c.-55T>G upstream_gene_variant 0.12
PPE35 2167693 p.Gly974Ser missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 0.14
PPE35 2169614 c.999C>T synonymous_variant 0.14
PPE35 2170662 c.-50G>A upstream_gene_variant 0.17
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222499 c.666G>C synonymous_variant 0.17
Rv1979c 2223159 c.5delT frameshift_variant 0.2
Rv1979c 2223186 c.-22C>A upstream_gene_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288707 p.Ser179Gly missense_variant 0.11
pncA 2289660 c.-419G>A upstream_gene_variant 0.12
pncA 2289727 c.-486G>A upstream_gene_variant 0.13
pncA 2289837 c.-596T>G upstream_gene_variant 0.22
pncA 2289925 c.-684T>A upstream_gene_variant 0.13
pncA 2290169 c.-928C>T upstream_gene_variant 0.15
kasA 2517971 c.-144G>C upstream_gene_variant 0.18
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518495 c.381C>T synonymous_variant 0.17
kasA 2519048 p.Gly312Ser missense_variant 1.0
eis 2714124 c.1209A>C stop_lost&splice_region_variant 0.15
eis 2714704 p.Gly210Val missense_variant 0.13
ahpC 2726041 c.-152A>G upstream_gene_variant 0.11
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746368 p.Ala411Ser missense_variant 0.15
folC 2746649 p.Ala317Val missense_variant 0.15
folC 2746840 c.759C>T synonymous_variant 0.12
Rv2752c 3065045 p.Phe383Leu missense_variant 0.12
Rv2752c 3065094 c.1098C>T synonymous_variant 0.17
Rv2752c 3065454 c.738G>A synonymous_variant 0.18
Rv2752c 3065872 p.Phe107Tyr missense_variant 0.22
Rv2752c 3066996 c.-805T>C upstream_gene_variant 0.13
thyX 3067365 p.His194Pro missense_variant 0.13
thyA 3073786 p.Lys229Arg missense_variant 0.12
thyA 3074594 c.-123C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087158 c.339G>A synonymous_variant 0.12
ald 3087632 c.813G>A synonymous_variant 0.18
ald 3087772 p.Met318Thr missense_variant 0.14
fbiD 3339417 c.300A>G synonymous_variant 1.0
fbiD 3339613 p.Ser166Thr missense_variant 0.25
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449218 p.Val239Ile missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474656 p.Asp217Val missense_variant 0.15
fprA 3474659 p.Leu218His missense_variant 0.15
fprA 3475133 p.Gln376Arg missense_variant 0.12
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568488 c.191delG frameshift_variant 1.0
Rv3236c 3612427 c.690G>A synonymous_variant 0.14
Rv3236c 3612905 p.Leu71Ser missense_variant 0.14
Rv3236c 3612915 c.202T>C synonymous_variant 0.14
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
fbiA 3640955 p.Pro138Arg missense_variant 0.14
fbiA 3641035 p.Lys165* stop_gained 0.15
fbiA 3641378 p.Arg279Gln missense_variant 0.12
fbiB 3641551 p.His6Arg missense_variant 0.11
fbiB 3641714 c.180G>A synonymous_variant 0.25
fbiB 3641974 p.Val147Ala missense_variant 0.15
fbiB 3642558 p.Tyr342Asn missense_variant 0.14
fbiB 3642752 c.1218C>T synonymous_variant 0.13
alr 3840554 c.867G>A synonymous_variant 0.14
alr 3841221 p.Ala67Val missense_variant 0.12
rpoA 3878239 p.Asp90Val missense_variant 0.29
clpC1 4038955 p.Glu584Gln missense_variant 0.22
clpC1 4039645 p.His354Asp missense_variant 0.25
clpC1 4040342 c.363C>A synonymous_variant 0.18
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241285 p.Pro475Ser missense_variant 0.14
embC 4241512 p.Met550Ile missense_variant 0.2
embC 4241668 c.1806G>A synonymous_variant 0.15
embC 4241688 c.1829delG frameshift_variant 0.15
embA 4242247 c.-986C>T upstream_gene_variant 0.15
embA 4242439 c.-794G>A upstream_gene_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243164 c.-69G>A upstream_gene_variant 0.15
embA 4243320 p.Ile30Val missense_variant 0.14
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4245463 c.2235delC frameshift_variant 0.14
embB 4245524 c.-990G>C upstream_gene_variant 0.18
embA 4245933 p.Pro901Ala missense_variant 0.11
embA 4245969 p.Pro913Ser missense_variant 1.0
embA 4246146 p.Gly972Arg missense_variant 0.12
embB 4246548 p.Pro12Gln missense_variant 0.42
embB 4246555 c.42G>C synonymous_variant 0.38
embB 4246556 p.Ala15Pro missense_variant 0.36
embB 4246563 p.Leu17Trp missense_variant 0.29
embB 4246567 c.54G>T synonymous_variant 0.38
embB 4246984 c.471C>T synonymous_variant 0.22
embB 4247360 p.Val283Met missense_variant 0.13
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248167 p.Thr552Ala missense_variant 0.12
embB 4249018 c.2505T>C synonymous_variant 0.17
aftB 4267637 c.1200C>T synonymous_variant 0.13
aftB 4268498 c.339T>C synonymous_variant 0.18
aftB 4269252 c.-416C>T upstream_gene_variant 0.14
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269864 c.-32delG upstream_gene_variant 1.0
ethA 4327394 p.Cys27Ser missense_variant 0.14
ethA 4327398 p.Arg26Gly missense_variant 0.14
ethA 4327719 c.-246C>A upstream_gene_variant 0.17
ethA 4328458 c.-985C>T upstream_gene_variant 0.13
whiB6 4338361 p.Arg54Gln missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408170 p.Ile11Met missense_variant 1.0