TB-Profiler result

Run: SRR6797440
Summary

Run ID: SRR6797440

Sample name:

Date: 04-04-2023 16:09:49

Number of reads: 530315

Percentage reads mapped: 99.09

Strain:

Drug-resistance: Other

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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
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
gyrB 6575 p.Arg446Cys missense_variant 0.29 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
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 5717 p.Gln160Lys missense_variant 0.12
gyrB 6175 p.Glu312Asp missense_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7968 p.Val223Ile missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491546 p.Thr255Ile missense_variant 0.33
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576035 p.Ala230Thr missense_variant 0.25
ccsA 620409 c.519C>A synonymous_variant 0.15
ccsA 620581 c.691C>A synonymous_variant 0.67
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 763309 p.Val1168Asp missense_variant 0.13
rpoC 765895 p.Glu842Asp missense_variant 0.12
rpoC 767208 p.Ala1280Asp missense_variant 0.22
rpoC 767253 p.Pro1295Gln missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777101 c.1380C>A synonymous_variant 0.17
mmpL5 779175 c.-695G>T upstream_gene_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781928 p.Lys123Asn missense_variant 0.2
fbiC 1303305 c.375C>A synonymous_variant 0.22
fbiC 1304644 p.Gly572Cys missense_variant 0.2
fbiC 1304970 c.2040G>T synonymous_variant 0.22
fbiC 1305477 c.2547C>A synonymous_variant 0.33
embR 1416228 p.His374Asn missense_variant 0.17
embR 1416522 p.Val276Met missense_variant 1.0
embR 1417315 c.33C>A synonymous_variant 0.29
embR 1417522 c.-175C>A upstream_gene_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>A non_coding_transcript_exon_variant 0.18
rrl 1474119 n.462T>C non_coding_transcript_exon_variant 0.15
rrl 1474317 n.660G>T non_coding_transcript_exon_variant 0.13
rrl 1476546 n.2889C>A non_coding_transcript_exon_variant 0.13
rrl 1476704 n.3053delC non_coding_transcript_exon_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.29
fabG1 1673437 c.-3G>T upstream_gene_variant 0.29
inhA 1673839 c.-363C>A upstream_gene_variant 0.17
rpsA 1833443 c.-99C>A upstream_gene_variant 0.18
rpsA 1833848 p.Ser103Pro missense_variant 0.13
rpsA 1833886 c.345C>A synonymous_variant 0.14
rpsA 1834534 c.993C>A synonymous_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102799 p.Val82Phe missense_variant 0.15
ndh 2103113 c.-71C>T upstream_gene_variant 0.2
katG 2154086 p.Gly676Trp missense_variant 0.25
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155437 p.Met225Ile missense_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168054 c.2559G>T synonymous_variant 0.25
Rv1979c 2222562 p.Ser201Arg missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288896 p.Leu116Met missense_variant 0.11
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
ahpC 2726527 p.Ser112Tyr missense_variant 0.17
ahpC 2726666 c.474C>A synonymous_variant 0.22
ribD 2986798 c.-41C>A upstream_gene_variant 0.18
ribD 2986889 c.51C>A synonymous_variant 0.17
Rv2752c 3064527 c.1665C>A synonymous_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087155 c.336C>A synonymous_variant 0.29
Rv3083 3449060 p.Gly186Val missense_variant 0.22
Rv3083 3449538 c.1035G>T synonymous_variant 0.22
Rv3083 3449563 p.Gly354Cys missense_variant 0.12
Rv3083 3449587 p.Gly362Cys missense_variant 0.15
Rv3083 3449791 p.Ala430Ser missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568582 p.Pro33Gln missense_variant 0.22
Rv3236c 3612217 c.900C>A synonymous_variant 0.33
fbiA 3640991 p.Cys150Phe missense_variant 0.15
alr 3840329 c.1092T>C synonymous_variant 0.25
alr 3841473 c.-53G>A upstream_gene_variant 1.0
clpC1 4038821 p.Glu628Asp missense_variant 0.22
clpC1 4038955 p.Glu584* stop_gained 0.14
clpC1 4039489 p.Ala406Ser missense_variant 0.29
clpC1 4040330 c.375C>A synonymous_variant 0.15
panD 4044130 p.Asn51Ile missense_variant 0.14
embC 4240932 p.Trp357Leu missense_variant 0.2
embC 4241113 c.1251G>T synonymous_variant 0.22
embC 4241175 p.Ser438Phe missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247425 c.912G>T synonymous_variant 0.33
embB 4248931 c.2418C>A synonymous_variant 0.2
aftB 4268427 p.Ser137Tyr missense_variant 0.33
aftB 4268874 c.-38T>A upstream_gene_variant 0.4
ethA 4326178 p.Met432Ile missense_variant 0.14
ethR 4327252 c.-297C>A upstream_gene_variant 0.25
ethA 4327268 p.Trp69Leu missense_variant 0.33
ethA 4327302 p.Asp58Tyr missense_variant 0.22
ethA 4327780 c.-307G>T upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0