TB-Profiler result

Run: ERR4797037
Summary

Run ID: ERR4797037

Sample name:

Date: 01-04-2023 07:18:54

Number of reads: 2837129

Percentage reads mapped: 91.36

Strain: lineage3.1.2

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
lineage3 East-African-Indian CAS RD750 0.99
lineage3.1 East-African-Indian Non-CAS1-Delhi 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
gyrA 7582 p.Asp94Gly missense_variant 0.98 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.94 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.94 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288920 p.Gly108Arg missense_variant 1.0 pyrazinamide
embA 4243217 c.-16C>T upstream_gene_variant 1.0 ethambutol
embB 4247431 p.Met306Ile missense_variant 0.98 ethambutol
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 7123 c.-179C>A 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
gyrA 9308 c.2007C>T synonymous_variant 0.12
gyrA 9317 c.2016G>T synonymous_variant 0.12
gyrA 9323 c.2022C>G synonymous_variant 0.12
gyrA 9335 c.2034G>C synonymous_variant 0.13
gyrA 9758 c.2457C>T synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.42
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760982 c.1176G>C synonymous_variant 0.14
rpoB 760985 c.1179G>C synonymous_variant 0.14
rpoB 760988 c.1182C>G synonymous_variant 0.13
rpoB 760991 c.1185G>C synonymous_variant 0.13
rpoB 761006 c.1200C>G synonymous_variant 0.13
rpoB 761015 c.1209G>C synonymous_variant 0.13
rpoB 761027 c.1221A>G synonymous_variant 0.12
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764140 c.771C>T synonymous_variant 0.13
rpoC 764266 c.897T>C synonymous_variant 0.12
rpoC 764338 c.969G>A synonymous_variant 0.16
rpoC 764353 c.984G>C synonymous_variant 0.22
rpoC 764365 c.996C>T synonymous_variant 0.17
rpoC 764380 c.1011G>C synonymous_variant 0.12
rpoC 764539 c.1170C>G synonymous_variant 0.13
rpoC 764554 c.1185C>T synonymous_variant 0.18
rpoC 764560 c.1191T>C synonymous_variant 0.17
rpoC 764566 c.1197C>G synonymous_variant 0.17
rpoC 764575 c.1206T>G synonymous_variant 0.17
rpoC 764581 c.1212T>C synonymous_variant 0.16
rpoC 764593 c.1224C>T synonymous_variant 0.13
rpoC 765982 c.2613C>G synonymous_variant 0.14
rpoC 765994 c.2625A>T synonymous_variant 0.13
rpoC 766774 c.3405T>C synonymous_variant 0.14
rpoC 766801 c.3432C>G synonymous_variant 0.14
rpoC 766804 c.3435A>G synonymous_variant 0.14
rpoC 766864 c.3495G>C synonymous_variant 0.12
rpoC 766876 c.3507C>T synonymous_variant 0.13
rpoC 766882 c.3513C>T synonymous_variant 0.13
rpoC 766894 c.3525T>C synonymous_variant 0.14
rpoC 766933 c.3564A>G synonymous_variant 0.18
rpoC 766945 c.3576A>G synonymous_variant 0.16
rpoC 766963 c.3594T>C synonymous_variant 0.23
rpoC 766972 c.3603G>C synonymous_variant 0.18
rpoC 766996 c.3627C>T synonymous_variant 0.18
rpoC 767009 c.3640_3642delTCGinsAGC synonymous_variant 0.18
rpoC 767014 c.3645G>C synonymous_variant 0.17
rpoC 767033 c.3664_3666delTCGinsAGT synonymous_variant 0.18
rpoC 767059 c.3690T>G synonymous_variant 0.18
rpoC 767062 c.3693C>A synonymous_variant 0.18
rpoC 767098 c.3729T>C synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304983 c.2053C>T synonymous_variant 0.14
fbiC 1304994 c.2064A>G synonymous_variant 0.14
fbiC 1304995 p.Leu689Met missense_variant 0.13
fbiC 1305006 c.2076A>G synonymous_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474970 n.1313G>A non_coding_transcript_exon_variant 0.12
rrl 1475006 n.1349A>T non_coding_transcript_exon_variant 0.13
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.13
rrl 1475369 n.1712G>T non_coding_transcript_exon_variant 0.14
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.14
rrl 1475436 n.1779C>T non_coding_transcript_exon_variant 0.16
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.12
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.16
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.12
inhA 1674102 c.-100C>A upstream_gene_variant 0.99
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918104 c.165G>A synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 0.99
PPE35 2170065 p.Ala183Gly missense_variant 0.36
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
pepQ 2860159 p.Ala87Gly missense_variant 0.2
thyA 3074247 p.His75Gln missense_variant 0.99
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.6
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474291 c.285G>A synonymous_variant 1.0
rpoA 3877949 p.Thr187Ala missense_variant 0.93
clpC1 4040675 c.30C>G synonymous_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248220 c.1707A>C synonymous_variant 0.14
embB 4248304 c.1791G>C synonymous_variant 0.13
embB 4248316 c.1803C>G synonymous_variant 0.14
embB 4248319 c.1806A>G synonymous_variant 0.14
ethA 4327298 p.Met59Arg missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0