TB-Profiler result

Run: SRR5266542
Summary

Run ID: SRR5266542

Sample name:

Date: 04-04-2023 10:01:01

Number of reads: 978340

Percentage reads mapped: 94.78

Strain: lineage2.2.1

Drug-resistance: Pre-XDR-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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
gyrA 7582 p.Asp94Ala missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.81 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288792 c.449dupG frameshift_variant 1.0 pyrazinamide, pyrazinamide
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol
ethA 4327363 c.110delA frameshift_variant 1.0 ethionamide, ethionamide
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 6346 c.-956C>T upstream_gene_variant 0.13
gyrA 6388 c.-914T>C upstream_gene_variant 0.12
gyrA 6670 c.-632G>C upstream_gene_variant 0.13
gyrA 6673 c.-629A>C upstream_gene_variant 0.13
gyrA 6676 c.-626T>G upstream_gene_variant 0.12
gyrA 6700 c.-602T>C upstream_gene_variant 0.12
gyrA 6703 c.-599G>C upstream_gene_variant 0.12
gyrA 6709 c.-593A>G upstream_gene_variant 0.12
gyrA 6712 c.-590G>C upstream_gene_variant 0.12
gyrA 6728 c.-574_-572delCTAinsTTG upstream_gene_variant 0.13
gyrA 6742 c.-560A>G upstream_gene_variant 0.12
gyrA 6745 c.-557T>G upstream_gene_variant 0.13
gyrA 6751 c.-551G>C upstream_gene_variant 0.12
gyrA 6760 c.-542G>C upstream_gene_variant 0.12
gyrA 6763 c.-539G>C upstream_gene_variant 0.12
gyrA 6775 c.-527G>C upstream_gene_variant 0.12
gyrA 6844 c.-458T>C upstream_gene_variant 0.12
gyrA 6877 c.-425G>T upstream_gene_variant 0.12
gyrA 6973 c.-329G>C upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491013 c.231C>G synonymous_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759627 c.-180A>G upstream_gene_variant 0.25
rpoB 760715 c.909C>G synonymous_variant 0.18
rpoB 760718 c.912C>T synonymous_variant 0.2
rpoB 760724 c.918T>C synonymous_variant 0.2
rpoB 760730 c.924T>C synonymous_variant 0.19
rpoB 760751 c.945G>C synonymous_variant 0.17
rpoB 760757 c.951T>C synonymous_variant 0.16
rpoB 760759 p.Val318Ala missense_variant 0.16
rpoB 760769 c.963C>G synonymous_variant 0.15
rpoB 760775 c.969G>C synonymous_variant 0.15
rpoB 760776 c.970_972delTCGinsAGC synonymous_variant 0.15
rpoB 760793 c.987A>G synonymous_variant 0.15
rpoB 760805 c.999G>C synonymous_variant 0.13
rpoB 760845 p.Thr347Pro missense_variant 0.12
rpoB 760859 c.1053T>C synonymous_variant 0.13
rpoB 760862 c.1056G>C synonymous_variant 0.12
rpoB 760869 p.Val355Ile missense_variant 0.16
rpoB 760886 c.1080A>G synonymous_variant 0.15
rpoB 760925 c.1119T>C synonymous_variant 0.12
rpoB 761015 c.1209G>C synonymous_variant 0.16
rpoB 761021 c.1215G>C synonymous_variant 0.15
rpoB 761027 c.1221A>G synonymous_variant 0.16
rpoB 761036 c.1230G>C synonymous_variant 0.16
rpoB 761037 c.1231T>C synonymous_variant 0.16
rpoB 761057 c.1251G>C synonymous_variant 0.2
rpoB 761102 c.1296A>G synonymous_variant 0.18
rpoB 761129 c.1323G>C synonymous_variant 0.23
rpoB 761132 c.1326G>T synonymous_variant 0.23
rpoB 761133 c.1327T>C synonymous_variant 0.23
rpoB 761150 c.1344A>C synonymous_variant 0.23
rpoB 761153 c.1347G>C synonymous_variant 0.2
rpoB 761165 c.1359G>C synonymous_variant 0.19
rpoB 761180 c.1374A>C synonymous_variant 0.19
rpoB 761189 c.1383T>C synonymous_variant 0.16
rpoB 761195 c.1389G>C synonymous_variant 0.15
rpoB 761207 c.1401C>T synonymous_variant 0.15
rpoB 761213 c.1407G>C synonymous_variant 0.16
rpoB 761219 c.1413G>C synonymous_variant 0.17
rpoC 762929 c.-441G>C upstream_gene_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 0.96
rpoC 763492 c.123G>A synonymous_variant 0.12
rpoC 763528 c.159G>A synonymous_variant 0.13
rpoC 763546 c.177A>G synonymous_variant 0.19
rpoC 763570 c.201G>C synonymous_variant 0.15
rpoC 763573 c.204G>C synonymous_variant 0.15
rpoC 763594 c.225C>T synonymous_variant 0.21
rpoC 763603 c.234C>T synonymous_variant 0.22
rpoC 763636 c.267T>C synonymous_variant 0.18
rpoC 763657 c.288G>A synonymous_variant 0.15
rpoC 763660 c.291T>G synonymous_variant 0.15
rpoC 763696 c.327T>C synonymous_variant 0.13
rpoC 763702 c.333C>G synonymous_variant 0.13
rpoC 764703 p.Lys445Arg missense_variant 1.0
rpoC 764752 c.1383G>C synonymous_variant 0.25
rpoC 764764 c.1395T>C synonymous_variant 0.23
rpoC 764809 c.1440C>T synonymous_variant 0.17
rpoC 764815 c.1446A>G synonymous_variant 0.19
rpoC 764827 c.1458G>C synonymous_variant 0.16
rpoC 764858 c.1489T>C synonymous_variant 0.14
rpoC 764872 c.1503A>G synonymous_variant 0.14
rpoC 765835 c.2466C>T synonymous_variant 0.15
rpoC 765850 c.2481G>C synonymous_variant 0.17
rpoC 765883 c.2514C>G synonymous_variant 0.15
rpoC 765886 c.2517C>G synonymous_variant 0.17
rpoC 765892 c.2523T>C synonymous_variant 0.17
rpoC 766774 c.3405T>C synonymous_variant 0.14
rpoC 766801 c.3432C>G synonymous_variant 0.17
rpoC 766804 c.3435A>G synonymous_variant 0.21
rpoC 766861 c.3492G>C synonymous_variant 0.18
rpoC 766864 c.3495G>C synonymous_variant 0.17
rpoC 766900 c.3531T>C synonymous_variant 0.14
rpoC 766933 c.3564A>G synonymous_variant 0.14
rpoC 766945 c.3576A>G synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781892 c.333A>G synonymous_variant 0.19
rpsL 781898 c.339A>T synonymous_variant 0.19
rpsL 781916 c.357T>C synonymous_variant 0.19
rpsL 781929 p.Gly124Ser missense_variant 0.22
rplC 800720 c.-89T>C upstream_gene_variant 0.13
rplC 800723 c.-86C>G upstream_gene_variant 0.14
rplC 800747 c.-62C>G upstream_gene_variant 0.16
rplC 800771 c.-38C>T upstream_gene_variant 0.15
rplC 800794 c.-15A>G upstream_gene_variant 0.13
rplC 800796 c.-13A>G upstream_gene_variant 0.13
rplC 800798 c.-10_-9delGG upstream_gene_variant 0.13
fbiC 1304983 c.2053C>T synonymous_variant 0.12
fbiC 1304995 p.Leu689Met missense_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473756 n.99G>A non_coding_transcript_exon_variant 0.15
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.15
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.15
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.12
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.12
rrl 1473986 n.329T>C non_coding_transcript_exon_variant 0.17
rrl 1473987 n.330G>A non_coding_transcript_exon_variant 0.17
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.17
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.2
rrl 1474009 n.352A>G non_coding_transcript_exon_variant 0.22
rrl 1474012 n.355C>T non_coding_transcript_exon_variant 0.18
rrl 1474093 n.436G>T non_coding_transcript_exon_variant 0.12
rrl 1474099 n.442G>A non_coding_transcript_exon_variant 0.12
rrl 1474103 n.446A>T non_coding_transcript_exon_variant 0.15
rrl 1474291 n.635_649delTTCCTCTCCGGAGGA non_coding_transcript_exon_variant 0.2
rrl 1474308 n.651G>T non_coding_transcript_exon_variant 0.15
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 0.15
rrl 1474356 n.699T>C non_coding_transcript_exon_variant 0.13
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.13
rrl 1474376 n.719T>C non_coding_transcript_exon_variant 0.17
rrl 1475249 n.1592T>C non_coding_transcript_exon_variant 0.18
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.22
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.29
rrl 1475267 n.1610G>A non_coding_transcript_exon_variant 0.29
rrl 1475275 n.1618C>T non_coding_transcript_exon_variant 0.29
rrl 1475276 n.1619T>C non_coding_transcript_exon_variant 0.29
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.25
rrl 1475313 n.1656G>A non_coding_transcript_exon_variant 0.15
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834639 c.1098T>C synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102409 c.633dupG frameshift_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168285 c.2328C>T synonymous_variant 0.12
PPE35 2169871 p.Gly248Arg missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517989 c.-126T>C upstream_gene_variant 0.12
kasA 2518146 p.Phe11Tyr missense_variant 0.12
kasA 2518162 c.48G>A synonymous_variant 0.11
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3877656 c.852T>G synonymous_variant 0.12
rpoA 3877668 c.840A>G synonymous_variant 0.13
rpoA 3877679 p.Ala277Ser missense_variant 0.14
rpoA 3877686 c.822A>G synonymous_variant 0.15
rpoA 3877692 c.816G>C synonymous_variant 0.18
rpoA 3877704 c.804G>C synonymous_variant 0.17
rpoA 3877743 c.765T>C synonymous_variant 0.12
rpoA 3878115 c.393G>A synonymous_variant 0.14
rpoA 3878118 c.390T>C synonymous_variant 0.15
rpoA 3878130 c.378C>G synonymous_variant 0.14
rpoA 3878141 p.Met123Leu missense_variant 0.19
rpoA 3878143 p.Gly122Asp missense_variant 0.18
rpoA 3878157 c.351C>G synonymous_variant 0.18
rpoA 3878163 c.345C>T synonymous_variant 0.17
rpoA 3878169 c.339G>C synonymous_variant 0.15
rpoA 3878172 c.336G>C synonymous_variant 0.13
rpoA 3878641 c.-135delG upstream_gene_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338371 p.Thr51Pro missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0