TB-Profiler result

Run: ERR4831716
Summary

Run ID: ERR4831716

Sample name:

Date: 01-04-2023 21:04:50

Number of reads: 2071876

Percentage reads mapped: 94.23

Strain: lineage1.1.1.1

Drug-resistance: HR-TB

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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 0.97
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.96
lineage1.1.1 Indo-Oceanic EAI4;EAI5 RD239 0.96
lineage1.1.1.1 Indo-Oceanic EAI4;ZERO RD239 0.95
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
katG 2154671 c.1438_1440delGCG conservative_inframe_deletion 0.2 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 6039 p.Thr267Ser missense_variant 0.98
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 8291 c.990C>T synonymous_variant 0.88
gyrA 8452 p.Ala384Val missense_variant 0.95
gyrA 8730 p.Gly477Trp missense_variant 0.15
gyrA 9143 c.1842T>C synonymous_variant 0.96
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490972 p.Arg64Ser missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575250 c.-98G>T upstream_gene_variant 0.15
mshA 575619 p.Arg91Gln missense_variant 0.17
mshA 575734 c.387T>G synonymous_variant 0.11
mshA 575737 c.390T>C synonymous_variant 0.12
mshA 575891 p.Ala182Ser missense_variant 0.13
mshA 576765 p.Thr473Met missense_variant 0.2
ccsA 620551 p.Asp221Tyr missense_variant 0.18
ccsA 620753 p.Arg288Gln missense_variant 0.14
rpoB 761645 c.1839C>G synonymous_variant 0.11
rpoB 761747 c.1941G>C synonymous_variant 0.1
rpoB 762736 p.Ala977Asp missense_variant 0.14
rpoC 762752 c.-618G>A upstream_gene_variant 0.25
rpoC 762824 c.-546C>T upstream_gene_variant 0.15
rpoC 762923 c.-447C>G upstream_gene_variant 0.11
rpoC 762929 c.-441G>C upstream_gene_variant 0.1
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763040 c.-330C>G upstream_gene_variant 0.13
rpoC 763070 c.-300T>C upstream_gene_variant 0.32
rpoC 763082 c.-288C>T upstream_gene_variant 0.24
rpoC 763088 c.-282C>G upstream_gene_variant 0.31
rpoC 763094 c.-276G>C upstream_gene_variant 0.26
rpoC 763115 c.-255T>C upstream_gene_variant 0.24
rpoC 763127 c.-243G>C upstream_gene_variant 0.2
rpoC 763884 p.Ala172Val missense_variant 0.96
rpoC 763886 c.517C>A synonymous_variant 0.96
rpoC 763934 p.Ala189Ser missense_variant 0.17
rpoC 763969 c.600C>A synonymous_variant 0.25
rpoC 764011 c.642T>A synonymous_variant 0.14
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765478 c.2109T>G synonymous_variant 0.11
rpoC 766381 c.3012C>A synonymous_variant 0.18
rpoC 766521 p.Gly1051Asp missense_variant 0.17
rpoC 767056 c.3687C>A synonymous_variant 0.17
mmpL5 775620 p.Ser954Trp missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777581 p.Tyr300* stop_gained 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801449 p.Arg214Gln missense_variant 1.0
fbiC 1303090 p.Glu54* stop_gained 0.15
fbiC 1303911 c.981G>A synonymous_variant 0.2
fbiC 1303965 c.1035G>T synonymous_variant 0.15
fbiC 1304226 c.1296C>A synonymous_variant 0.14
Rv1258c 1406760 c.580_581insC frameshift_variant 0.19
Rv1258c 1406973 p.Ala123Asp missense_variant 0.17
Rv1258c 1407050 c.291C>A synonymous_variant 0.17
Rv1258c 1407090 p.Ala84Val missense_variant 0.2
Rv1258c 1407534 c.-194C>T upstream_gene_variant 0.17
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473829 n.172G>C non_coding_transcript_exon_variant 0.11
rrl 1473839 n.182G>A non_coding_transcript_exon_variant 0.15
rrl 1474284 n.627G>T non_coding_transcript_exon_variant 0.17
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.17
rrl 1474496 n.839C>G non_coding_transcript_exon_variant 0.13
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.12
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.12
rrl 1474507 n.850G>C non_coding_transcript_exon_variant 0.12
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 0.91
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.15
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.25
rrl 1475114 n.1457C>T non_coding_transcript_exon_variant 0.18
rrl 1475120 n.1463G>T non_coding_transcript_exon_variant 0.18
rrl 1475202 n.1545G>C non_coding_transcript_exon_variant 0.14
rrl 1475220 n.1563G>T non_coding_transcript_exon_variant 0.23
rrl 1476319 n.2662C>A non_coding_transcript_exon_variant 0.15
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.16
fabG1 1673627 p.Thr63Ile missense_variant 0.14
fabG1 1673701 p.Asn88Asp missense_variant 0.11
inhA 1674364 p.Pro55Thr missense_variant 0.18
rpsA 1833949 c.408T>C synonymous_variant 0.12
rpsA 1833961 c.420C>G synonymous_variant 0.14
rpsA 1834319 p.Val260Ile missense_variant 0.9
tlyA 1917966 c.27C>T synonymous_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918009 p.Ala24Thr missense_variant 0.25
tlyA 1918094 p.Leu52Pro missense_variant 0.13
ndh 2101677 p.Ala456Ser missense_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154997 p.Gly372Val missense_variant 0.15
katG 2155783 p.Ala110Asp missense_variant 0.15
katG 2155809 c.303G>T synonymous_variant 0.14
katG 2156389 c.-278G>C upstream_gene_variant 1.0
katG 2156460 c.-349C>A upstream_gene_variant 0.4
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 0.92
PPE35 2169264 p.Ser450Ile missense_variant 0.15
PPE35 2170076 c.537G>A synonymous_variant 0.25
PPE35 2170400 c.213G>A synonymous_variant 0.29
PPE35 2170410 p.Ala68Val missense_variant 0.29
Rv1979c 2222308 p.Asp286Gly missense_variant 0.97
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289167 c.75C>T synonymous_variant 0.15
kasA 2518132 c.18C>T synonymous_variant 0.93
kasA 2518147 c.33C>T synonymous_variant 0.27
kasA 2518729 c.615G>T synonymous_variant 0.17
kasA 2519099 p.Ala329Phe missense_variant 0.2
kasA 2519158 c.1044C>A synonymous_variant 0.15
kasA 2519204 p.Asp364Tyr missense_variant 0.18
eis 2714754 c.579G>A synonymous_variant 0.27
ahpC 2726051 c.-142G>A upstream_gene_variant 0.98
folC 2746350 p.Leu417Met missense_variant 0.2
folC 2746433 p.Gly389Asp missense_variant 0.17
folC 2746629 p.Asp324Tyr missense_variant 0.22
pepQ 2859621 c.798G>A synonymous_variant 0.18
ribD 2986664 c.-175A>G upstream_gene_variant 0.11
Rv2752c 3064632 c.1560C>T synonymous_variant 0.98
Rv2752c 3064719 c.1473T>C synonymous_variant 0.98
Rv2752c 3064826 p.Asp456Asn missense_variant 0.14
Rv2752c 3067191 c.-1000G>T upstream_gene_variant 0.19
thyX 3067278 p.Ala223Val missense_variant 0.14
thyX 3067534 p.Ala138Ser missense_variant 0.21
thyX 3067548 p.Thr133Ile missense_variant 0.17
thyX 3067567 p.Asp127Asn missense_variant 0.17
thyA 3074031 c.441T>C synonymous_variant 0.12
thyA 3074034 c.438T>C synonymous_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087880 p.Arg354Leu missense_variant 0.5
fbiD 3339641 p.Ala175Asp missense_variant 0.14
fbiD 3339643 p.Val176Ile missense_variant 0.14
Rv3083 3448714 p.Asp71His missense_variant 0.9
Rv3083 3449097 c.594C>G synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.91
fprA 3474960 c.954C>A synonymous_variant 0.18
fprA 3475032 c.1026C>A synonymous_variant 0.14
fprA 3475159 p.Asn385Asp missense_variant 0.93
fprA 3475270 p.His422Asn missense_variant 0.17
Rv3236c 3612211 c.906A>G synonymous_variant 0.18
Rv3236c 3612813 p.Thr102Ala missense_variant 0.1
fbiB 3641949 c.415C>A synonymous_variant 0.18
fbiB 3642251 p.Asp239Glu missense_variant 0.15
alr 3841013 c.408C>T synonymous_variant 0.17
alr 3841060 p.Gly121Trp missense_variant 0.17
alr 3841082 c.339G>T synonymous_variant 0.25
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4038162 p.Arg848Leu missense_variant 0.3
clpC1 4039793 c.912C>G synonymous_variant 0.12
clpC1 4039814 c.891C>G synonymous_variant 0.14
clpC1 4039817 c.888A>C synonymous_variant 0.1
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240475 p.Ala205Ser missense_variant 0.13
embC 4240637 p.His259Asn missense_variant 0.22
embC 4240671 p.Thr270Ile missense_variant 0.6
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241644 c.1782G>T synonymous_variant 0.24
embC 4241656 c.1794G>T synonymous_variant 0.14
embC 4242166 c.2304G>C synonymous_variant 0.14
embC 4242525 p.Ala888Asp missense_variant 0.2
embA 4242530 c.-703C>A upstream_gene_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244096 c.864C>T synonymous_variant 1.0
embA 4244220 p.Leu330Met missense_variant 0.22
embA 4244275 p.Gly348Val missense_variant 0.17
embA 4244281 p.Gly350Val missense_variant 0.25
embA 4244433 p.Ala401Thr missense_variant 0.25
embA 4244584 p.Gly451Glu missense_variant 0.17
embA 4244602 p.Ala457Glu missense_variant 0.33
embA 4244894 c.1662C>A synonymous_variant 0.17
embA 4245816 p.Arg862Ser missense_variant 0.2
embA 4245969 p.Pro913Ser missense_variant 0.91
embA 4246484 p.Trp1084Cys missense_variant 0.17
embB 4246580 p.Ala23Thr missense_variant 0.25
embB 4246618 c.105G>A synonymous_variant 0.25
embB 4246942 c.429G>A synonymous_variant 0.14
embB 4247091 p.Thr193Ile missense_variant 0.15
embB 4247116 c.603G>A synonymous_variant 0.18
embB 4247627 p.Arg372Ser missense_variant 0.43
embB 4247632 c.1119C>A synonymous_variant 0.29
embB 4247637 p.Pro375Leu missense_variant 0.22
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267852 p.Gln329Lys missense_variant 0.14
aftB 4267887 p.Gly317Val missense_variant 0.14
aftB 4267927 p.Ala304Thr missense_variant 0.22
aftB 4268614 p.Gly75Arg missense_variant 0.22
ubiA 4269387 p.Glu149Asp missense_variant 0.93
ubiA 4269593 p.Asp81Tyr missense_variant 0.17
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269745 p.Val30Ala missense_variant 0.12
ethR 4326913 c.-636C>T upstream_gene_variant 0.2
ethA 4326996 p.Pro160Thr missense_variant 0.2
whiB6 4338242 p.Gln94Glu 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 4407926 p.Pro93Ser missense_variant 1.0