TB-Profiler result

Run: SRR4033448
Summary

Run ID: SRR4033448

Sample name:

Date: 04-04-2023 06:06:18

Number of reads: 650689

Percentage reads mapped: 99.58

Strain: lineage4.3

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
lineage4.3 Euro-American (LAM) mainly-LAM None 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 7566 p.Asp89Asn missense_variant 0.29 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
katG 2154963 c.1147_1148delTC frameshift_variant 0.22 isoniazid
katG 2155060 p.Trp351* stop_gained 0.22 isoniazid
pncA 2289105 p.Ala46Val missense_variant 0.14 pyrazinamide
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 5520 p.Pro94Leu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7513 p.Ala71Val missense_variant 0.22
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7587 p.Leu96Met missense_variant 0.25
gyrA 7654 p.Ser118* stop_gained 0.5
gyrA 7844 c.543C>A synonymous_variant 0.18
gyrA 8402 c.1101C>T synonymous_variant 0.67
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9388 c.2088_2089insGC frameshift_variant 0.2
gyrA 9482 c.2181G>A synonymous_variant 0.18
fgd1 490909 p.Pro43Ala missense_variant 0.25
fgd1 490920 p.His46Gln missense_variant 0.25
ccsA 620636 p.Ile249Asn missense_variant 0.12
rpoB 759655 c.-152C>G upstream_gene_variant 0.2
rpoB 761045 c.1239C>T synonymous_variant 0.17
rpoB 761305 p.Val500Asp missense_variant 0.29
rpoB 762511 p.Ala902Val missense_variant 0.29
rpoC 762545 c.-825C>T upstream_gene_variant 0.29
rpoC 763484 p.Leu39Ile missense_variant 0.4
rpoC 764228 p.Gln287* stop_gained 0.2
rpoC 764509 c.1140G>A synonymous_variant 0.67
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765461 p.Asn698Tyr missense_variant 0.29
rpoC 766138 c.2769G>A synonymous_variant 0.2
rpoC 766404 p.Met1012Thr missense_variant 0.29
rpoC 766430 p.Gly1021Arg missense_variant 0.25
rpoC 767288 p.Leu1307Met missense_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775640 c.2841C>T synonymous_variant 0.25
mmpL5 775658 p.Gln941His missense_variant 0.25
mmpL5 776682 p.Leu600Gln missense_variant 0.33
mmpL5 776991 p.Ile497Thr missense_variant 0.29
mmpL5 777529 p.Ala318Thr missense_variant 0.15
mmpL5 777817 p.Val222Ile missense_variant 0.4
mmpL5 778423 p.Ala20Thr missense_variant 0.12
mmpS5 778549 p.Asp119Glu missense_variant 0.29
mmpS5 778739 p.Val56Glu missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781586 c.27C>G synonymous_variant 0.22
rplC 800688 c.-121C>T upstream_gene_variant 0.25
fbiC 1303171 p.Arg81Trp missense_variant 0.33
fbiC 1303907 p.Gly326Asp missense_variant 0.17
fbiC 1304255 p.Ala442Val missense_variant 0.22
fbiC 1304340 p.Phe470Leu missense_variant 0.2
Rv1258c 1406085 p.Gln419Leu missense_variant 0.33
Rv1258c 1406256 p.Leu362* stop_gained 0.25
Rv1258c 1406538 p.Ala268Gly missense_variant 0.25
Rv1258c 1406579 p.His254Gln missense_variant 0.18
Rv1258c 1406586 p.Thr252Ile missense_variant 0.2
Rv1258c 1406599 p.Pro248Ala missense_variant 0.25
Rv1258c 1406858 c.483T>C synonymous_variant 0.29
Rv1258c 1407338 c.3G>A start_lost 0.33
Rv1258c 1407345 c.-5T>C upstream_gene_variant 0.29
Rv1258c 1407446 c.-106G>C upstream_gene_variant 0.22
embR 1416401 p.Asn316Ser missense_variant 0.25
embR 1417376 c.-30delC upstream_gene_variant 0.2
embR 1417395 c.-48G>A upstream_gene_variant 0.18
embR 1417513 c.-166A>G upstream_gene_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrs 1473182 n.1337T>C non_coding_transcript_exon_variant 0.4
rrl 1474477 n.820C>T non_coding_transcript_exon_variant 0.67
rrl 1475116 n.1459G>A non_coding_transcript_exon_variant 0.5
rrl 1475608 n.1951T>A non_coding_transcript_exon_variant 0.67
rpsA 1833515 c.-27C>A upstream_gene_variant 0.17
rpsA 1833551 p.Pro4Ser missense_variant 0.17
rpsA 1833595 c.54T>C synonymous_variant 0.29
rpsA 1833768 p.Pro76His missense_variant 0.25
rpsA 1833996 p.Leu152Pro missense_variant 0.29
rpsA 1834388 p.Pro283Ser missense_variant 0.17
rpsA 1834637 p.Asn366Tyr missense_variant 0.2
tlyA 1917825 c.-115G>A upstream_gene_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918273 p.Asp112Tyr missense_variant 0.25
tlyA 1918423 p.Thr162Ala missense_variant 0.25
ndh 2102048 p.Val332Ala missense_variant 0.22
ndh 2102707 c.336C>T synonymous_variant 0.22
katG 2154002 p.Leu704Met missense_variant 0.33
katG 2154161 p.Glu651Lys missense_variant 0.18
katG 2154253 p.Ser620Thr missense_variant 0.25
katG 2154258 c.1854G>A synonymous_variant 0.29
katG 2155310 p.Gly268Ser missense_variant 0.29
katG 2156321 c.-210A>G upstream_gene_variant 0.4
katG 2156523 c.-412G>A upstream_gene_variant 0.22
PPE35 2168585 c.2028T>A synonymous_variant 0.22
PPE35 2168724 p.Ile630Thr missense_variant 0.29
Rv1979c 2222269 p.Thr299Asn missense_variant 0.5
Rv1979c 2222475 c.690C>T synonymous_variant 0.29
Rv1979c 2222717 p.Ala150Thr missense_variant 0.22
Rv1979c 2222803 p.Ala121Val missense_variant 0.15
Rv1979c 2223205 c.-41A>T upstream_gene_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289185 c.57G>A synonymous_variant 0.13
pncA 2289699 c.-458T>C upstream_gene_variant 0.22
eis 2715207 c.124_125delAC frameshift_variant 0.18
eis 2715223 p.Arg37Gln missense_variant 0.17
ahpC 2725931 c.-262T>C upstream_gene_variant 0.17
ahpC 2725940 c.-253A>T upstream_gene_variant 0.18
ahpC 2725950 c.-243G>T upstream_gene_variant 0.17
ahpC 2725970 c.-223G>C upstream_gene_variant 0.17
ahpC 2725975 c.-218G>A upstream_gene_variant 0.14
folC 2746142 p.Pro486Gln missense_variant 0.25
folC 2746164 p.Arg479Trp missense_variant 0.33
folC 2747345 c.253delC frameshift_variant 0.33
pepQ 2859363 c.1056T>C synonymous_variant 0.22
pepQ 2859588 p.Ala277Val missense_variant 0.2
pepQ 2859653 p.Ala256Thr missense_variant 0.25
pepQ 2859829 p.Gly197Val missense_variant 0.17
pepQ 2859997 p.Ala141Val missense_variant 0.33
pepQ 2860330 p.Val30Ala missense_variant 0.33
ribD 2987164 p.Arg109Gln missense_variant 0.25
ribD 2987504 c.666C>T synonymous_variant 0.2
Rv2752c 3066139 p.Val18Ala missense_variant 0.2
Rv2752c 3067027 c.-836C>T upstream_gene_variant 0.25
thyX 3067716 p.Ser77Ile missense_variant 0.2
thyX 3068142 c.-197G>C upstream_gene_variant 0.33
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074096 c.376C>A synonymous_variant 0.18
ald 3086662 c.-158T>C upstream_gene_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087430 p.Leu204His missense_variant 0.4
ald 3087534 p.Val239Ile missense_variant 0.5
fbiD 3339159 c.42C>A synonymous_variant 0.33
fbiD 3339458 p.Gln114Leu missense_variant 0.29
Rv3083 3448510 p.Gln3Glu missense_variant 0.18
Rv3083 3449394 c.891G>A synonymous_variant 0.14
Rv3083 3449598 c.1095C>T synonymous_variant 0.17
Rv3083 3449930 c.1431dupC frameshift_variant 0.22
fprA 3473853 c.-154C>T upstream_gene_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474233 c.229delC frameshift_variant 0.29
fprA 3474891 c.885C>A synonymous_variant 0.29
Rv3236c 3612205 c.912C>T synonymous_variant 0.13
fbiA 3641191 p.Val217Leu missense_variant 0.29
fbiB 3641586 p.Ile18Phe missense_variant 0.17
fbiB 3641867 c.335delA frameshift_variant 0.17
fbiB 3642820 p.Ala429Val missense_variant 0.5
alr 3840278 p.Asp381Glu missense_variant 0.2
alr 3840592 p.Val277Met missense_variant 0.15
alr 3840604 p.Pro273Ser missense_variant 0.15
alr 3841214 c.207C>G synonymous_variant 0.4
alr 3841376 c.45A>G synonymous_variant 0.33
rpoA 3877692 c.815_816insA frameshift_variant 0.18
rpoA 3877800 c.708G>A synonymous_variant 0.4
ddn 3986721 c.-123G>A upstream_gene_variant 0.29
ddn 3986772 c.-72T>C upstream_gene_variant 0.33
ddn 3986875 p.Ser11Leu missense_variant 0.2
ddn 3986976 p.Pro45Ser missense_variant 0.22
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038507 p.Leu733Pro missense_variant 0.33
clpC1 4038819 p.Lys629Met missense_variant 0.2
clpC1 4038941 c.1764G>C synonymous_variant 0.29
clpC1 4039675 p.Pro344Ser missense_variant 0.29
clpC1 4040110 p.Arg199Gly missense_variant 0.25
clpC1 4040184 p.Phe174Ser missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243540 p.Ala103Val missense_variant 0.22
embA 4244589 c.1357C>T synonymous_variant 0.33
embA 4244658 p.Leu476Met missense_variant 0.29
embA 4244716 p.Trp495Ser missense_variant 0.33
embA 4245071 c.1839G>A synonymous_variant 0.13
embB 4246268 c.-246G>A upstream_gene_variant 0.33
embA 4246480 p.Gly1083Asp missense_variant 0.29
embB 4247789 p.Ser426Cys missense_variant 0.22
embB 4248089 p.Tyr526Asn missense_variant 0.2
embB 4248144 p.Leu544Trp missense_variant 0.17
embB 4248569 c.2056C>T synonymous_variant 0.18
embB 4248585 p.Arg691Leu missense_variant 0.17
embB 4249310 p.Arg933Cys missense_variant 0.29
embB 4249323 p.Ala937Val missense_variant 0.29
embB 4249391 p.Trp960Arg missense_variant 0.22
embB 4249716 p.Asp1068Val missense_variant 0.14
embB 4249729 p.Asp1072Glu missense_variant 0.12
aftB 4267223 p.Ile538Met missense_variant 0.25
aftB 4267238 c.1599C>T synonymous_variant 0.2
aftB 4267643 c.1194C>T synonymous_variant 0.25
aftB 4267671 p.Ala389Glu missense_variant 0.25
aftB 4267700 p.Trp379* stop_gained 0.2
aftB 4267711 p.Ser376Cys missense_variant 0.2
aftB 4267798 c.1039C>T synonymous_variant 0.29
ubiA 4269339 c.494delG frameshift_variant 0.22
ubiA 4269912 c.-79T>A upstream_gene_variant 0.15
ubiA 4269921 c.-88C>T upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4408230 c.-28C>T upstream_gene_variant 0.29