TB-Profiler result

Run: SRR17658572
Summary

Run ID: SRR17658572

Sample name:

Date: 03-04-2023 18:04:13

Number of reads: 1773497

Percentage reads mapped: 98.19

Strain: lineage1.1.2

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 0.99
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.2 Indo-Oceanic EAI3;EAI5 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 6112 p.Met291Ile missense_variant 0.97
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrB 6911 p.Asn558His missense_variant 0.12
gyrA 6931 c.-371A>G upstream_gene_variant 0.12
gyrA 6949 c.-353A>G upstream_gene_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9047 c.1746C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9386 c.2085T>C synonymous_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576000 p.Asp218Ala missense_variant 1.0
rpoB 760490 c.684C>T synonymous_variant 1.0
rpoB 760835 p.His343Gln missense_variant 0.97
rpoB 761954 c.2148C>G synonymous_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763166 c.-204A>G upstream_gene_variant 0.13
rpoC 763169 c.-201A>G upstream_gene_variant 0.13
rpoC 763884 p.Ala172Val missense_variant 0.9
rpoC 763886 c.517C>A synonymous_variant 0.9
rpoC 763996 c.627T>C synonymous_variant 0.13
rpoC 764005 c.636G>C synonymous_variant 0.16
rpoC 764011 c.642T>C synonymous_variant 0.14
rpoC 764040 p.Ser224Thr missense_variant 0.13
rpoC 764044 c.675T>G synonymous_variant 0.14
rpoC 764059 c.690G>T synonymous_variant 0.13
rpoC 764083 c.714A>G synonymous_variant 0.14
rpoC 764098 c.729A>G synonymous_variant 0.15
rpoC 764101 c.732C>G synonymous_variant 0.15
rpoC 764140 c.771C>T synonymous_variant 0.14
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765826 c.2457T>C synonymous_variant 0.12
rpoC 765883 c.2514C>G synonymous_variant 0.14
rpoC 765886 c.2517C>G synonymous_variant 0.14
rpoC 765892 c.2523T>C synonymous_variant 0.13
rpoC 765934 c.2565C>T synonymous_variant 0.14
rpoC 767158 c.3789T>A synonymous_variant 0.12
rpoC 767206 c.3837C>G synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776395 p.Phe696Leu missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303512 c.582T>C synonymous_variant 0.13
fbiC 1303534 p.Ser202Ala missense_variant 0.15
fbiC 1303538 p.Arg203Leu missense_variant 0.15
fbiC 1303545 c.615A>G synonymous_variant 0.14
fbiC 1303575 c.645G>C synonymous_variant 0.14
fbiC 1303578 c.648G>A synonymous_variant 0.14
fbiC 1303584 c.654C>G synonymous_variant 0.14
fbiC 1303632 c.702T>G synonymous_variant 0.12
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.15
rrl 1473813 n.156C>T non_coding_transcript_exon_variant 0.13
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.14
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.19
rpsA 1834375 c.834G>A synonymous_variant 0.12
rpsA 1834396 c.855G>T synonymous_variant 0.12
rpsA 1834411 c.870T>C synonymous_variant 0.13
rpsA 1834423 c.882G>T synonymous_variant 0.13
rpsA 1834477 c.936C>T synonymous_variant 0.14
rpsA 1834489 c.948T>C synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289463 c.-222C>T upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 0.97
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
rpoA 3877587 c.921A>C synonymous_variant 0.14
rpoA 3877613 p.Ile299Val missense_variant 0.15
rpoA 3877617 c.891G>C synonymous_variant 0.14
rpoA 3877638 c.870T>G synonymous_variant 0.15
rpoA 3877656 c.852T>C synonymous_variant 0.15
rpoA 3877677 p.Ala277Ser missense_variant 0.14
rpoA 3877680 c.828G>C synonymous_variant 0.14
rpoA 3877685 c.823C>T synonymous_variant 0.14
rpoA 3877686 c.822A>G synonymous_variant 0.13
rpoA 3877692 c.816G>C synonymous_variant 0.13
rpoA 3877704 c.804G>T synonymous_variant 0.13
rpoA 3877743 c.765T>C synonymous_variant 0.12
clpC1 4038875 c.1830C>G synonymous_variant 0.13
clpC1 4038878 c.1827A>G synonymous_variant 0.14
clpC1 4038893 c.1812C>T synonymous_variant 0.14
clpC1 4038965 c.1740T>C synonymous_variant 0.11
clpC1 4040517 p.Val63Ala missense_variant 0.97
embC 4240165 c.303C>T synonymous_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_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