TB-Profiler result

Run: SRR12882720
Summary

Run ID: SRR12882720

Sample name:

Date: 03-04-2023 07:59:34

Number of reads: 745771

Percentage reads mapped: 99.4

Strain: lineage3.1.1

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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.9
lineage3.1.1 East-African-Indian CAS1-Kili RD750 0.99
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7669 p.Pro123Gln missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575527 c.180G>T synonymous_variant 0.18
mshA 576230 p.Ile295Val missense_variant 0.17
mshA 576342 p.Ser332Tyr missense_variant 0.22
mshA 576358 c.1011C>A synonymous_variant 0.25
mshA 576499 c.1152G>T synonymous_variant 0.13
ccsA 620159 p.Leu90Arg missense_variant 0.1
ccsA 620213 p.Gly108Val missense_variant 0.14
ccsA 620331 c.441C>A synonymous_variant 0.25
ccsA 620479 p.Leu197Ile missense_variant 0.29
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760249 c.446dupG frameshift_variant 0.14
rpoB 761785 p.Thr660Asn missense_variant 0.12
rpoC 762434 c.-936T>G upstream_gene_variant 0.9
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766901 p.Gly1178Cys missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777519 p.Thr321Lys missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800925 c.117C>A synonymous_variant 0.14
fbiC 1302865 c.-66G>T upstream_gene_variant 0.14
fbiC 1302885 c.-46G>T upstream_gene_variant 0.13
fbiC 1304386 p.Arg486Ser missense_variant 0.13
fbiC 1304999 p.Trp690Leu missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474091 n.434C>A non_coding_transcript_exon_variant 0.15
rrl 1474684 n.1027T>C non_coding_transcript_exon_variant 0.11
rrl 1474821 n.1164T>C non_coding_transcript_exon_variant 0.12
fabG1 1673409 c.-31C>A upstream_gene_variant 0.12
inhA 1673613 c.-589C>T upstream_gene_variant 0.2
rpsA 1834905 p.Pro455Gln missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918293 c.354G>A synonymous_variant 0.14
tlyA 1918318 c.379C>A synonymous_variant 0.15
tlyA 1918580 p.Arg214Gln missense_variant 0.14
tlyA 1918600 p.His221Tyr missense_variant 0.13
tlyA 1918684 c.745C>A synonymous_variant 0.18
ndh 2102067 p.Val326Leu missense_variant 0.14
ndh 2102191 c.852G>T synonymous_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155344 c.768C>A synonymous_variant 0.25
katG 2155351 p.Arg254Leu missense_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170154 c.459C>A synonymous_variant 0.13
PPE35 2170179 p.Ala145Asp missense_variant 0.12
PPE35 2170312 c.301C>A synonymous_variant 0.21
PPE35 2170461 p.Gly51Glu missense_variant 1.0
PPE35 2170516 p.Gly33Trp missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288815 p.Ala143Ser missense_variant 0.12
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.93
kasA 2518534 c.420G>A synonymous_variant 0.14
eis 2714804 p.Ala177Thr missense_variant 0.17
eis 2714967 p.Glu122Asp missense_variant 0.14
eis 2715166 p.Ser56Tyr missense_variant 0.18
eis 2715263 p.Phe24Leu missense_variant 0.11
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726459 c.268_269dupGA frameshift_variant 0.14
folC 2746466 c.1132dupG frameshift_variant 0.12
pepQ 2859453 c.966G>T synonymous_variant 0.14
Rv2752c 3064755 c.1437C>A synonymous_variant 0.14
Rv2752c 3065307 p.Met295Ile missense_variant 0.15
Rv2752c 3067073 c.-882G>A upstream_gene_variant 0.17
Rv2752c 3067120 c.-929C>A upstream_gene_variant 0.18
thyX 3067302 p.Cys215Phe missense_variant 0.15
thyX 3067418 c.528C>A synonymous_variant 0.33
thyX 3067577 p.Glu123Asp missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449529 c.1026C>T synonymous_variant 0.13
Rv3083 3449592 c.1089C>G synonymous_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612880 c.237G>T synonymous_variant 0.18
fbiA 3641018 p.Pro159Gln missense_variant 0.13
fbiB 3641714 c.180G>C synonymous_variant 0.2
fbiB 3641734 p.Pro67His missense_variant 0.2
fbiB 3641833 p.Gly100Val missense_variant 0.22
alr 3840604 p.Pro273Thr missense_variant 0.12
alr 3840611 c.810G>A synonymous_variant 0.12
ddn 3987264 p.Asp141Tyr missense_variant 0.15
embC 4240172 p.Val104Met missense_variant 1.0
embC 4240623 p.Ala254Asp missense_variant 0.15
embC 4240682 p.Asp274Tyr missense_variant 0.2
embC 4241076 p.Gly405Val missense_variant 0.13
embC 4241562 p.Arg567His missense_variant 1.0
embC 4241609 p.Pro583Thr missense_variant 0.15
embC 4241674 c.1812C>A synonymous_variant 0.18
embC 4241688 p.Thr609Met missense_variant 0.18
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242811 c.-422G>T upstream_gene_variant 0.13
embA 4244444 c.1212G>T synonymous_variant 0.14
embA 4244687 c.1455C>A synonymous_variant 0.18
embA 4244860 p.Gly543Val missense_variant 0.22
embA 4245461 c.2229C>A synonymous_variant 0.33
embB 4247225 p.Arg238Ser missense_variant 0.15
embB 4247228 p.Leu239Met missense_variant 0.15
embB 4248461 p.Ser650Pro missense_variant 0.14
embB 4249439 p.Glu976* stop_gained 0.14
embB 4249457 p.Gln982* stop_gained 0.14
aftB 4268492 c.345G>T synonymous_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407884 p.Asp107Tyr missense_variant 0.13