TB-Profiler result

Run: SRR4035721
Summary

Run ID: SRR4035721

Sample name:

Date: 04-04-2023 07:15:26

Number of reads: 742789

Percentage reads mapped: 99.45

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 0.99
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 2288992 c.249delC frameshift_variant 0.17 pyrazinamide, 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9455 c.2154T>G synonymous_variant 0.15
fgd1 491186 p.Ser135Trp missense_variant 0.17
fgd1 491409 c.627G>T synonymous_variant 0.22
fgd1 491453 p.Gly224Asp missense_variant 0.25
fgd1 491570 p.Asp263Val missense_variant 0.17
fgd1 491591 p.Lys270Met missense_variant 1.0
fgd1 491748 p.Glu322Asp missense_variant 0.2
fgd1 491774 p.Arg331Met missense_variant 0.13
mshA 575204 c.-144C>T upstream_gene_variant 0.2
mshA 575896 c.549G>T synonymous_variant 0.29
ccsA 620247 c.357G>A synonymous_variant 0.25
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760271 c.465C>A synonymous_variant 0.22
rpoB 761392 p.Glu529Gly missense_variant 0.15
rpoB 762145 p.Glu780Gly missense_variant 0.13
rpoC 763979 p.Glu204Lys missense_variant 0.12
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 765034 c.1665T>C synonymous_variant 0.1
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765545 p.Arg726Cys missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776184 p.Lys766Arg missense_variant 0.14
mmpL5 776774 c.1707C>T synonymous_variant 0.2
mmpL5 777319 p.Arg388Cys missense_variant 0.18
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpL5 777340 p.Lys381* stop_gained 0.15
mmpL5 777704 c.777G>T synonymous_variant 0.2
mmpR5 778007 c.-983G>A upstream_gene_variant 0.22
mmpR5 779424 p.Tyr145* stop_gained 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781401 c.-159T>A upstream_gene_variant 0.13
rpsL 781409 c.-151T>C upstream_gene_variant 0.13
rplC 800717 c.-92C>T upstream_gene_variant 0.25
rplC 800722 c.-86_-85delCA upstream_gene_variant 0.22
rplC 801201 c.393C>T synonymous_variant 0.12
fbiC 1303710 c.780G>A synonymous_variant 0.17
fbiC 1303765 p.Lys279* stop_gained 0.13
fbiC 1304772 c.1842C>T synonymous_variant 0.18
fbiC 1304795 p.Lys622Met missense_variant 0.2
fbiC 1305150 c.2220C>T synonymous_variant 0.18
embR 1416653 p.Lys232Met missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472308 n.463T>C non_coding_transcript_exon_variant 0.11
rrs 1472406 n.561G>A non_coding_transcript_exon_variant 0.17
rrs 1472832 n.987A>C non_coding_transcript_exon_variant 0.13
rrl 1473764 n.107G>T non_coding_transcript_exon_variant 0.22
rrl 1474285 n.628C>T non_coding_transcript_exon_variant 0.15
rrl 1475136 n.1479G>C non_coding_transcript_exon_variant 0.12
rrl 1475187 n.1530C>T non_coding_transcript_exon_variant 0.14
rrl 1476037 n.2380C>T non_coding_transcript_exon_variant 0.14
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.25
fabG1 1673322 c.-118C>G upstream_gene_variant 0.13
fabG1 1673698 p.Ser87Thr missense_variant 0.18
fabG1 1673921 p.Ile161Asn missense_variant 0.17
fabG1 1673956 p.Lys173Glu missense_variant 0.2
fabG1 1674143 p.Ala235Gly missense_variant 0.17
inhA 1674344 p.Gln48Arg missense_variant 0.17
inhA 1674351 c.150C>T synonymous_variant 0.15
rpsA 1834007 p.Arg156Gly missense_variant 0.2
rpsA 1834014 p.Val158Glu missense_variant 0.22
rpsA 1834620 p.Leu360Ser missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918364 p.Glu142Val missense_variant 0.17
ndh 2102648 p.Ala132Val missense_variant 0.33
ndh 2102720 p.Tyr108Cys missense_variant 0.15
katG 2153976 c.2136C>G synonymous_variant 0.18
katG 2154267 p.Asn615Lys missense_variant 0.12
PPE35 2167782 p.Ser944Tyr missense_variant 0.22
PPE35 2169511 p.Asn368Asp missense_variant 0.17
PPE35 2169852 p.Gly254Val missense_variant 0.22
PPE35 2170783 c.-171A>T upstream_gene_variant 0.17
PPE35 2170789 c.-177C>T upstream_gene_variant 0.17
Rv1979c 2221926 c.1239C>T synonymous_variant 0.2
Rv1979c 2222685 p.Lys160Asn missense_variant 0.29
Rv1979c 2222791 p.Lys125Met missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289366 c.-125C>T upstream_gene_variant 0.22
pncA 2289553 c.-312C>T upstream_gene_variant 0.15
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2519298 p.Arg395His missense_variant 0.13
eis 2714428 p.Pro302Arg missense_variant 0.12
eis 2715436 c.-104G>A upstream_gene_variant 0.17
eis 2715450 c.-118T>A upstream_gene_variant 0.18
folC 2746911 p.Thr230Ser missense_variant 0.2
folC 2747236 c.363G>A synonymous_variant 0.15
pepQ 2860050 c.369G>C synonymous_variant 0.14
ribD 2987338 c.501delC frameshift_variant 0.22
ribD 2987460 p.Leu208Ile missense_variant 0.15
ribD 2987474 p.Cys212* stop_gained 0.17
ribD 2987482 p.Ile215Thr missense_variant 0.2
Rv2752c 3065833 p.Arg120His missense_variant 0.17
Rv2752c 3066209 c.-18C>T upstream_gene_variant 0.12
Rv2752c 3067100 c.-909G>T upstream_gene_variant 0.15
Rv2752c 3067110 c.-919A>T upstream_gene_variant 0.15
thyA 3073809 c.663C>T synonymous_variant 0.18
thyA 3074519 c.-48C>A upstream_gene_variant 0.3
ald 3086636 c.-184A>G upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339275 p.Val53Asp missense_variant 0.13
fprA 3473963 c.-44G>T upstream_gene_variant 0.22
fprA 3473985 c.-22G>A upstream_gene_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474053 p.Phe16Ser missense_variant 0.12
fprA 3474796 p.His264Tyr missense_variant 0.13
fprA 3474834 c.828C>T synonymous_variant 0.18
fprA 3474847 p.Lys281* stop_gained 0.18
fprA 3474975 c.969C>G synonymous_variant 0.2
fprA 3475098 c.1092G>A synonymous_variant 0.14
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
Rv3236c 3613119 c.-3C>T upstream_gene_variant 0.17
fbiB 3640836 c.-699G>A upstream_gene_variant 0.15
fbiA 3641303 p.Gly254Asp missense_variant 0.22
fbiB 3641733 p.Pro67Thr missense_variant 0.13
alr 3840836 c.585G>A synonymous_variant 0.12
alr 3841504 c.-84C>G upstream_gene_variant 0.17
rpoA 3878171 p.Pro113Ser missense_variant 0.17
rpoA 3878384 p.Leu42Met missense_variant 0.14
rpoA 3878447 p.Phe21Leu missense_variant 0.1
clpC1 4038377 c.2328C>A synonymous_variant 0.2
clpC1 4040457 p.Arg83His missense_variant 0.22
panD 4044428 c.-147G>A upstream_gene_variant 0.22
embC 4240779 p.His306Leu missense_variant 0.2
embC 4242178 c.2316G>C synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244193 p.Gly321Cys missense_variant 0.12
embA 4244248 p.Val339Ala missense_variant 0.12
embB 4245606 c.-908C>T upstream_gene_variant 0.14
embB 4246838 p.Ala109Thr missense_variant 0.22
embB 4247286 p.Pro258Leu missense_variant 0.15
embB 4249707 p.Arg1065His missense_variant 0.17
aftB 4267354 p.Gly495Ser missense_variant 0.13
aftB 4268014 p.Pro275Ser missense_variant 0.17
aftB 4268236 c.601T>C synonymous_variant 0.2
ubiA 4268932 p.Phe301Ser missense_variant 0.2
ethA 4326033 p.Ala481Thr missense_variant 0.18
ethA 4326041 p.Leu478Pro missense_variant 0.2
ethA 4327333 p.Leu47Phe missense_variant 0.14
ethA 4327340 p.Trp45Ser missense_variant 0.13
ethA 4328210 c.-737C>A upstream_gene_variant 0.12
ethA 4328410 c.-937G>T upstream_gene_variant 0.15
whiB6 4338206 p.Val106Met missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407714 p.Lys163Asn missense_variant 0.17
gid 4407971 p.Pro78Thr missense_variant 0.12
gid 4407980 p.Pro75Ser missense_variant 0.13