TB-Profiler result

Run: SRR21675425
Summary

Run ID: SRR21675425

Sample name:

Date: 04-04-2023 02:34:36

Number of reads: 192855

Percentage reads mapped: 93.31

Strain: lineage4.8

Drug-resistance: HR-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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
katG 2154995 c.1116delG frameshift_variant 0.4 isoniazid
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 5310 c.73delG frameshift_variant 0.25
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8884 c.1585_1586dupAC frameshift_variant 0.25
mshA 575580 p.His78Pro missense_variant 0.5
mshA 576598 p.Met417Ile missense_variant 0.22
ccsA 619789 c.-102G>T upstream_gene_variant 0.25
ccsA 620198 p.Gln103Pro missense_variant 0.25
rpoB 760101 c.295T>C synonymous_variant 0.12
rpoC 763905 p.Ala179Val missense_variant 0.29
rpoC 764157 p.Lys263Arg missense_variant 1.0
rpoC 765487 p.Met706Ile missense_variant 0.18
rpoC 765585 p.Pro739Gln missense_variant 0.22
rpoC 766162 p.Asp931Glu missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776673 p.Val603Ala missense_variant 0.13
mmpL5 776790 p.Val564Ala missense_variant 0.25
mmpL5 777285 c.1195delG frameshift_variant 0.5
mmpL5 778207 c.273delG frameshift_variant 0.25
mmpS5 778818 p.Thr30Ala missense_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800757 c.-52G>A upstream_gene_variant 0.14
rplC 801418 p.Gly204Arg missense_variant 0.14
fbiC 1303251 c.321C>T synonymous_variant 0.33
Rv1258c 1406653 p.Met230Val missense_variant 0.2
Rv1258c 1407495 c.-155C>A upstream_gene_variant 0.13
atpE 1460902 c.-143A>T upstream_gene_variant 0.4
atpE 1460907 c.-138T>C upstream_gene_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471892 n.47G>A non_coding_transcript_exon_variant 0.25
rrs 1472790 n.945T>A non_coding_transcript_exon_variant 0.17
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.12
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.12
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 0.12
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.12
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.11
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.11
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.15
rrl 1474627 n.970G>A non_coding_transcript_exon_variant 0.15
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.15
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.15
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.15
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.15
rrl 1474662 n.1005C>A non_coding_transcript_exon_variant 0.2
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 0.2
rrl 1474688 n.1031G>T non_coding_transcript_exon_variant 0.29
rrl 1474710 n.1053T>G non_coding_transcript_exon_variant 0.29
rrl 1474711 n.1054_1055insAA non_coding_transcript_exon_variant 0.33
rrl 1474714 n.1058delT non_coding_transcript_exon_variant 0.33
rrl 1474717 n.1060A>G non_coding_transcript_exon_variant 0.33
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.33
rrl 1474736 n.1079C>T non_coding_transcript_exon_variant 0.33
rrl 1474765 n.1108A>G non_coding_transcript_exon_variant 0.22
rrl 1474941 n.1284G>T non_coding_transcript_exon_variant 0.17
rrl 1475835 n.2178T>C non_coding_transcript_exon_variant 0.25
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.17
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.17
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.17
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.17
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.17
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.17
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.17
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.2
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 0.2
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.2
rrl 1476131 n.2474C>A non_coding_transcript_exon_variant 0.22
rrl 1476292 n.2635G>A non_coding_transcript_exon_variant 0.14
rrl 1476587 n.2930C>A non_coding_transcript_exon_variant 0.22
fabG1 1673233 c.-207T>G upstream_gene_variant 1.0
fabG1 1673373 c.-67G>T upstream_gene_variant 0.11
inhA 1674241 p.Gly14Arg missense_variant 0.15
rpsA 1834756 c.1215G>A synonymous_variant 0.15
rpsA 1834935 p.Ala465Val missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918326 c.387G>A synonymous_variant 0.18
tlyA 1918511 p.Gln191Pro missense_variant 0.33
ndh 2101757 p.Leu429Arg missense_variant 0.5
ndh 2102694 p.Val117Ile missense_variant 0.15
katG 2154250 p.Ala621Val missense_variant 0.5
katG 2154357 c.1755C>G synonymous_variant 0.33
katG 2156217 c.-106G>T upstream_gene_variant 0.22
PPE35 2167665 p.Gln983Arg missense_variant 0.18
PPE35 2167682 c.2930dupT frameshift_variant 0.22
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2169974 c.639T>G synonymous_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.5
PPE35 2170053 p.Thr187Ser missense_variant 0.5
Rv1979c 2222928 c.236delA frameshift_variant 0.14
Rv1979c 2223009 c.156T>C synonymous_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289319 c.-78C>A upstream_gene_variant 0.25
kasA 2518478 c.366delT frameshift_variant 0.25
kasA 2518511 p.Gly133Cys missense_variant 0.25
kasA 2518905 p.Arg264Gln missense_variant 0.15
kasA 2519081 p.Ala323Thr missense_variant 0.22
eis 2714454 c.878delG frameshift_variant 0.29
ahpC 2726255 c.63T>C synonymous_variant 0.29
ahpC 2726303 c.113_115dupTCA disruptive_inframe_insertion 0.18
folC 2746587 c.1012C>A synonymous_variant 0.5
folC 2747226 p.Arg125Trp missense_variant 0.2
folC 2747530 c.68delA frameshift_variant 0.2
pepQ 2860352 p.Leu23Met missense_variant 0.33
ribD 2987267 c.429C>T synonymous_variant 0.33
Rv2752c 3064832 p.Ala454Thr missense_variant 0.14
Rv2752c 3065633 p.Gly187Cys missense_variant 0.18
Rv2752c 3065781 c.411C>G synonymous_variant 0.22
Rv2752c 3066131 p.Leu21Met missense_variant 0.33
Rv2752c 3066331 c.-140G>T upstream_gene_variant 0.18
Rv2752c 3067102 c.-911T>A upstream_gene_variant 0.33
thyX 3067296 p.Arg217Leu missense_variant 0.18
thyX 3067403 c.543C>A synonymous_variant 0.22
thyX 3067745 c.201C>A synonymous_variant 0.2
thyX 3067864 p.Asp28Tyr missense_variant 0.13
thyX 3067901 c.45C>T synonymous_variant 0.12
thyX 3068036 c.-92delC upstream_gene_variant 0.29
fprA 3474391 p.Val129Ile missense_variant 0.2
whiB7 3568840 c.-161A>G upstream_gene_variant 0.29
fbiA 3640355 c.-188C>A upstream_gene_variant 0.4
alr 3840538 p.Tyr295His missense_variant 0.33
alr 3841045 p.Ala126Ser missense_variant 0.12
rpoA 3878069 p.Val147Phe missense_variant 0.18
ddn 3986688 c.-156G>T upstream_gene_variant 0.25
clpC1 4038489 p.Ala739Asp missense_variant 0.17
clpC1 4039434 p.Phe424Ser missense_variant 0.5
clpC1 4039729 p.Asp326Asn missense_variant 1.0
clpC1 4039844 p.Asp287Glu missense_variant 0.22
clpC1 4039960 p.Thr249Ser missense_variant 0.5
clpC1 4039988 c.717C>G synonymous_variant 0.33
clpC1 4039991 c.714G>C synonymous_variant 0.33
clpC1 4039994 p.Glu237Asp missense_variant 0.33
clpC1 4040001 p.His235Arg missense_variant 0.33
clpC1 4040003 p.Val234Asp missense_variant 0.33
clpC1 4040009 c.696C>G synonymous_variant 0.33
clpC1 4040015 c.690G>C synonymous_variant 0.33
clpC1 4040021 c.684A>C synonymous_variant 0.33
clpC1 4040024 c.681A>G synonymous_variant 0.33
clpC1 4040033 c.672G>C synonymous_variant 0.33
clpC1 4040063 c.642G>C synonymous_variant 0.33
clpC1 4040069 c.636G>C synonymous_variant 0.29
clpC1 4040087 c.618G>C synonymous_variant 0.22
clpC1 4040090 c.615T>C synonymous_variant 0.2
clpC1 4040108 c.597G>C synonymous_variant 0.2
embC 4240544 p.Pro228Ser missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246235 c.-279G>A upstream_gene_variant 0.29
embB 4247209 c.696A>T synonymous_variant 0.22
embB 4248212 p.Ala567Thr missense_variant 0.33
embB 4248548 p.Ala679Thr missense_variant 0.22
embB 4248555 p.Gly681Val missense_variant 0.22
embB 4249138 c.2629_2631delGTG conservative_inframe_deletion 0.22
embB 4249427 c.2917_2923dupTCACTGC frameshift_variant 0.25
aftB 4267815 c.1021delG frameshift_variant 0.25
aftB 4268863 c.-27G>T upstream_gene_variant 0.5
ubiA 4269184 p.Tyr217Cys missense_variant 0.12
ubiA 4269253 p.Ala194Asp missense_variant 0.17
ubiA 4269473 p.Thr121Ala missense_variant 0.33
ubiA 4269796 c.37dupC frameshift_variant 0.18
ethA 4327469 p.Thr2Ile missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408058 c.144delT frameshift_variant 0.67
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0