TB-Profiler result

Run: SRR4035799
Summary

Run ID: SRR4035799

Sample name:

Date: 04-04-2023 07:18:19

Number of reads: 873976

Percentage reads mapped: 99.47

Strain: lineage4.1.2

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H 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
pncA 2288730 p.Ala171Glu missense_variant 0.17 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 5351 p.Gly38Ser missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7870 p.Pro190Arg missense_variant 0.18
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491496 c.714C>T synonymous_variant 0.18
fgd1 491546 p.Thr255Ile missense_variant 0.17
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575219 c.-129T>A upstream_gene_variant 0.17
mshA 575506 c.159C>T synonymous_variant 0.15
mshA 576277 c.930C>T synonymous_variant 0.18
ccsA 619802 c.-89G>T upstream_gene_variant 0.17
ccsA 620020 p.Leu44Val missense_variant 0.1
ccsA 620390 p.Leu167Pro missense_variant 0.14
rpoB 759723 c.-84C>T upstream_gene_variant 0.14
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760601 c.795C>T synonymous_variant 0.15
rpoC 762677 c.-693G>A upstream_gene_variant 0.25
rpoC 763716 p.Tyr116Phe missense_variant 0.22
rpoC 764004 p.Ala212Val missense_variant 0.14
rpoC 764204 p.Asp279Asn missense_variant 0.13
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 764889 p.Leu507Ser missense_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765479 p.Tyr704His missense_variant 0.12
rpoC 765988 c.2620delA frameshift_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776277 p.Ile735Thr missense_variant 0.12
mmpL5 777050 c.1431G>A synonymous_variant 0.22
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpL5 777920 c.561C>A synonymous_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801083 p.Ala92Glu missense_variant 0.15
fbiC 1303326 c.396C>T synonymous_variant 0.13
fbiC 1304319 c.1389C>A synonymous_variant 0.15
fbiC 1304508 c.1578A>G synonymous_variant 0.17
Rv1258c 1406531 c.810C>T synonymous_variant 0.14
Rv1258c 1407482 c.-142G>A upstream_gene_variant 0.13
embR 1416945 p.Ser135Cys missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472545 n.702delG non_coding_transcript_exon_variant 0.18
rrs 1472739 n.896dupG non_coding_transcript_exon_variant 0.14
rrl 1473577 n.-81A>G upstream_gene_variant 0.12
rrl 1473810 n.153C>T non_coding_transcript_exon_variant 0.17
rrl 1474422 n.765C>T non_coding_transcript_exon_variant 0.2
rrl 1475651 n.1994C>A non_coding_transcript_exon_variant 0.18
inhA 1674326 p.Asp42Ala missense_variant 0.14
rpsA 1834481 p.Glu314Lys missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918072 p.Ala45Ser missense_variant 0.14
ndh 2102382 p.Leu221Met missense_variant 0.13
katG 2155548 c.564C>T synonymous_variant 0.2
katG 2155618 p.Ile165Thr missense_variant 0.12
katG 2155943 p.Pro57Ser missense_variant 0.17
katG 2156221 c.-110C>T upstream_gene_variant 0.15
PPE35 2167805 p.Tyr936* stop_gained 0.12
PPE35 2168056 p.Pro853Ser missense_variant 0.17
PPE35 2168213 c.2400G>C synonymous_variant 0.12
PPE35 2168628 p.Ile662Thr missense_variant 0.13
PPE35 2170627 c.-16delC upstream_gene_variant 0.14
Rv1979c 2222195 p.Pro324Thr missense_variant 0.2
Rv1979c 2222356 p.Thr270Ile missense_variant 0.22
Rv1979c 2223050 p.Val39Met missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288777 c.465G>A synonymous_variant 0.13
pncA 2290102 c.-861G>A upstream_gene_variant 0.14
kasA 2517948 c.-167C>T upstream_gene_variant 0.15
kasA 2517975 c.-140A>T upstream_gene_variant 0.12
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2519093 p.Arg327Cys missense_variant 0.13
eis 2715169 p.Gly55Asp missense_variant 0.17
pepQ 2859302 c.1117T>G stop_lost&splice_region_variant 0.25
pepQ 2859314 c.1105C>T synonymous_variant 0.25
pepQ 2859611 p.Leu270Met missense_variant 0.22
pepQ 2859813 p.Ile202Met missense_variant 0.12
pepQ 2860313 p.Phe36Leu missense_variant 0.11
pepQ 2860524 c.-106A>G upstream_gene_variant 0.17
ribD 2987377 p.Ser180Phe missense_variant 0.17
Rv2752c 3064606 p.Ile529Asn missense_variant 0.14
Rv2752c 3064788 c.1403delT frameshift_variant 0.2
thyA 3073987 p.Gln162Arg missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087750 p.Tyr311Asn missense_variant 0.14
ald 3087758 c.939G>A synonymous_variant 0.21
Rv3083 3448609 p.Glu36Lys missense_variant 0.12
Rv3083 3449121 p.His206Gln missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474854 p.Lys283Thr missense_variant 0.2
fprA 3475140 c.1134C>G synonymous_variant 0.12
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
Rv3236c 3612433 p.Ile228Met missense_variant 0.12
Rv3236c 3612807 p.Gly104Ser missense_variant 0.17
Rv3236c 3612929 p.Pro63His missense_variant 0.17
fbiA 3640753 p.Gly71Ser missense_variant 0.15
fbiA 3641510 p.Gly323Ala missense_variant 0.14
fbiB 3642010 p.Gly159Asp missense_variant 0.15
alr 3840299 c.1122C>A synonymous_variant 0.17
alr 3840673 p.Leu250Val missense_variant 0.25
alr 3840694 p.Arg243Cys missense_variant 0.25
alr 3840911 c.510A>T synonymous_variant 0.17
alr 3841240 p.Leu61Met missense_variant 0.2
alr 3841440 c.-20A>G upstream_gene_variant 0.17
clpC1 4039965 p.Leu247Pro missense_variant 0.12
clpC1 4040084 c.621C>T synonymous_variant 0.14
clpC1 4040893 c.-189G>T upstream_gene_variant 0.14
embC 4239778 c.-85C>A upstream_gene_variant 0.15
embC 4241138 p.Ala426Thr missense_variant 0.13
embC 4241184 p.Thr441Met missense_variant 0.13
embC 4241651 p.Ala597Pro missense_variant 0.1
embA 4242376 c.-857G>A upstream_gene_variant 0.14
embC 4242404 p.Thr848Ala missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4243146 c.3284A>G stop_lost&splice_region_variant 0.11
embA 4243722 p.Pro164Ser missense_variant 0.17
embA 4245255 p.Glu675* stop_gained 0.14
embA 4245918 p.Trp896Arg missense_variant 0.18
embB 4245935 c.-579G>A upstream_gene_variant 0.18
embB 4245947 c.-567C>T upstream_gene_variant 0.2
embB 4246748 p.Phe79Ile missense_variant 0.18
embB 4247476 c.963C>G synonymous_variant 0.11
embB 4247488 p.Ser325Arg missense_variant 0.12
embB 4248289 p.Trp592Cys missense_variant 0.13
embB 4248899 p.His796Asn missense_variant 0.14
embB 4249038 p.Val842Ala missense_variant 0.15
aftB 4268091 p.Lys249Met missense_variant 0.17
aftB 4268102 c.735C>T synonymous_variant 0.15
aftB 4268800 p.Val13Ile missense_variant 0.18
ubiA 4268930 p.Gly302Arg missense_variant 0.22
ubiA 4269029 p.Gly269Cys missense_variant 0.15
aftB 4269261 c.-425G>A upstream_gene_variant 0.13
ubiA 4269971 c.-138A>T upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407773 p.Lys144Glu missense_variant 0.11
gid 4408073 c.130C>T synonymous_variant 0.15
gid 4408086 c.117C>T synonymous_variant 0.17
gid 4408091 p.Pro38Ser missense_variant 0.18