TB-Profiler result

Run: SRR4035817
Summary

Run ID: SRR4035817

Sample name:

Date: 04-04-2023 07:18:55

Number of reads: 1023692

Percentage reads mapped: 99.42

Strain: lineage4.1.2

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
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
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 5278 c.39C>T synonymous_variant 0.17
gyrA 7060 c.-242T>A upstream_gene_variant 0.14
gyrA 7315 p.Thr5Met missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7429 p.Glu43Gly missense_variant 0.11
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 8483 c.1182G>A synonymous_variant 0.22
gyrA 8521 p.Leu407Pro missense_variant 0.33
gyrA 9262 p.Arg654Pro missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575388 p.Ala14Val missense_variant 0.2
ccsA 620214 c.324C>G synonymous_variant 0.17
ccsA 620677 p.Pro263Ser missense_variant 0.15
ccsA 620681 p.Lys264Arg missense_variant 0.13
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 762403 p.Tyr866Cys missense_variant 0.13
rpoB 762411 p.Gln869* stop_gained 0.18
rpoC 762416 c.-954A>G upstream_gene_variant 0.17
rpoB 762439 p.Lys878Arg missense_variant 0.12
rpoB 762784 p.Asp993Val missense_variant 0.15
rpoC 763772 p.Val135Leu missense_variant 0.15
rpoC 763982 p.Met205Val missense_variant 0.12
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765227 p.Met620Val missense_variant 0.15
rpoC 765558 p.Thr730Arg missense_variant 0.11
rpoC 765839 p.Val824Met missense_variant 0.12
rpoC 765854 c.2487_2488delTG frameshift_variant 0.13
rpoC 766176 p.Val936Ala missense_variant 0.1
mmpL5 775588 c.2893T>C stop_lost&splice_region_variant 0.15
mmpL5 775633 p.Gln950* stop_gained 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775945 p.Val846Ile missense_variant 0.14
mmpL5 776076 p.Ala802Val missense_variant 0.17
mmpL5 776101 p.Thr794Ala missense_variant 0.29
mmpL5 776669 p.Phe604Leu missense_variant 0.11
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpL5 777498 p.Arg328Pro missense_variant 0.14
mmpL5 778050 p.Gly144Asp missense_variant 0.13
mmpL5 778065 p.Ala139Val missense_variant 0.15
mmpR5 778319 c.-671T>C upstream_gene_variant 0.12
mmpR5 779192 p.Ser68Asn missense_variant 0.13
mmpR5 779212 p.Ile75Phe missense_variant 0.13
mmpS5 779559 c.-654G>A upstream_gene_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781690 p.Lys44Met missense_variant 0.15
rplC 800618 c.-191T>C upstream_gene_variant 0.17
rplC 800644 c.-165G>T upstream_gene_variant 0.14
rplC 801245 p.Arg146His missense_variant 0.14
rplC 801284 p.Arg159Gln missense_variant 0.18
fbiC 1303516 p.Met196Val missense_variant 0.12
fbiC 1303529 p.Glu200Gly missense_variant 0.13
fbiC 1303535 p.Ser202Leu missense_variant 0.14
fbiC 1303543 p.Lys205Glu missense_variant 0.13
fbiC 1303555 p.Pro209Ser missense_variant 0.14
fbiC 1303937 p.Asn336Ile missense_variant 0.14
Rv1258c 1406640 p.Thr234Ile missense_variant 0.17
Rv1258c 1407509 c.-169C>G upstream_gene_variant 0.17
embR 1416511 c.837G>A synonymous_variant 0.17
embR 1417190 p.Asp53Gly missense_variant 0.25
embR 1417223 p.Leu42* stop_gained 0.18
embR 1417281 p.Ile23Phe missense_variant 0.18
embR 1417451 c.-104G>A upstream_gene_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472050 n.205G>C non_coding_transcript_exon_variant 0.14
rrs 1473158 n.1313T>A non_coding_transcript_exon_variant 0.14
rrl 1474310 n.653T>A non_coding_transcript_exon_variant 0.15
rrl 1474327 n.670T>C non_coding_transcript_exon_variant 0.14
rrl 1474561 n.904G>A non_coding_transcript_exon_variant 0.12
rrl 1474973 n.1316T>C non_coding_transcript_exon_variant 0.11
rrl 1475941 n.2284G>T non_coding_transcript_exon_variant 0.13
fabG1 1673533 p.Ala32Thr missense_variant 0.15
fabG1 1673627 p.Thr63Ser missense_variant 0.12
fabG1 1673632 p.Ser65Gly missense_variant 0.12
fabG1 1674155 p.Val239Ala missense_variant 0.11
inhA 1674230 p.Ile10Asn missense_variant 0.15
inhA 1674462 c.261G>A synonymous_variant 0.17
inhA 1674670 p.Ala157Thr missense_variant 0.13
inhA 1674923 p.Thr241Met missense_variant 0.18
rpsA 1833877 c.336C>A synonymous_variant 0.12
rpsA 1834016 p.Arg159Cys missense_variant 0.17
rpsA 1834088 p.Val183Met missense_variant 0.15
tlyA 1917893 c.-47G>T upstream_gene_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918241 p.Leu101Pro missense_variant 0.22
ndh 2102051 p.Gly331Asp missense_variant 0.18
ndh 2102541 p.Ala168Pro missense_variant 0.15
ndh 2102543 p.Arg167Pro missense_variant 0.12
katG 2153992 p.Leu707His missense_variant 0.12
katG 2154791 p.Pro441Ala missense_variant 0.12
PPE35 2168034 p.Thr860Ile missense_variant 0.13
PPE35 2169665 c.948C>T synonymous_variant 0.14
PPE35 2170792 c.-180T>A upstream_gene_variant 0.12
Rv1979c 2222738 p.Gly143Cys missense_variant 0.14
Rv1979c 2222749 p.Leu139Pro missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288936 c.306G>A synonymous_variant 0.15
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2714333 p.Gly334Ser missense_variant 0.15
eis 2714617 p.Ser239Ile missense_variant 0.13
eis 2714752 p.Gln194Arg missense_variant 0.12
eis 2714894 p.Ala147Pro missense_variant 0.17
eis 2715434 c.-102G>C upstream_gene_variant 0.17
folC 2746428 c.1171C>T synonymous_variant 0.17
folC 2746523 c.1075delG frameshift_variant 0.33
folC 2746602 p.Val333Phe missense_variant 0.18
folC 2746748 p.Gly284Ala missense_variant 0.25
pepQ 2859470 p.Leu317Val missense_variant 0.12
pepQ 2859488 p.Thr311Ala missense_variant 0.12
pepQ 2859496 p.Ile308Asn missense_variant 0.17
ribD 2987307 p.Ala157Pro missense_variant 0.18
Rv2752c 3065531 p.Thr221Ser missense_variant 0.12
Rv2752c 3065650 p.Arg181Leu missense_variant 0.18
Rv2752c 3065949 c.243C>T synonymous_variant 0.22
Rv2752c 3066094 p.Val33Ala missense_variant 0.14
Rv2752c 3066297 c.-106G>C upstream_gene_variant 0.14
Rv2752c 3066372 c.-181G>A upstream_gene_variant 0.12
thyX 3067462 p.Leu162Met missense_variant 0.25
thyX 3067470 p.Asn159Ile missense_variant 0.25
thyX 3067508 c.438G>T synonymous_variant 0.25
thyX 3068012 c.-67G>A upstream_gene_variant 0.17
thyA 3074382 p.Phe30Leu missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3338942 c.-176G>A upstream_gene_variant 0.18
fbiD 3338952 c.-166C>T upstream_gene_variant 0.15
fbiD 3338968 c.-150A>G upstream_gene_variant 0.12
fbiD 3339363 p.Asp82Glu missense_variant 0.14
Rv3083 3448498 c.-6G>T upstream_gene_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474701 p.Gly232Asp missense_variant 0.12
fprA 3474854 p.Lys283Ile missense_variant 0.14
fprA 3474903 c.897C>T synonymous_variant 0.14
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
Rv3236c 3612030 p.Ala363Thr missense_variant 0.2
Rv3236c 3612084 p.Gly345Cys missense_variant 0.2
Rv3236c 3613170 c.-54G>A upstream_gene_variant 0.12
fbiA 3640474 c.-68delC upstream_gene_variant 0.15
fbiA 3640539 c.-4C>A upstream_gene_variant 0.18
fbiA 3640552 p.Thr4Ala missense_variant 0.18
fbiB 3640611 c.-924C>T upstream_gene_variant 0.13
fbiA 3640763 p.Asp74Gly missense_variant 0.12
fbiA 3640909 p.Tyr123His missense_variant 0.18
fbiB 3641295 c.-240G>C upstream_gene_variant 0.12
fbiB 3641890 p.Ala119Val missense_variant 0.15
fbiB 3642451 p.Arg306Leu missense_variant 0.17
fbiB 3642482 p.Lys316Asn missense_variant 0.1
rpoA 3878456 p.Arg18* stop_gained 0.17
rpoA 3878474 p.Asp12Asn missense_variant 0.2
clpC1 4040027 c.678C>T synonymous_variant 0.18
clpC1 4040271 p.Tyr145Cys missense_variant 0.12
clpC1 4040904 c.-200G>A upstream_gene_variant 0.2
embC 4239765 c.-98G>A upstream_gene_variant 0.15
embC 4239985 c.123T>C synonymous_variant 0.12
embC 4240014 p.Pro51Leu missense_variant 0.22
embC 4240626 p.Asp255Gly missense_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4242968 p.Thr1036Ala missense_variant 0.11
embA 4243449 p.Ser73Thr missense_variant 0.13
embA 4243504 p.Ser91Phe missense_variant 0.25
embA 4243601 c.369C>A synonymous_variant 0.14
embA 4243808 c.576C>T synonymous_variant 0.33
embA 4245675 p.Gly815Arg missense_variant 0.14
embB 4246705 c.192G>A synonymous_variant 0.2
embB 4249607 p.Thr1032Ala missense_variant 0.11
embB 4249644 p.Leu1044Gln missense_variant 0.14
embB 4249660 p.Met1049Ile missense_variant 0.17
aftB 4267949 c.888C>A synonymous_variant 0.17
aftB 4269725 c.-889C>T upstream_gene_variant 0.15
ubiA 4269769 p.Arg22His missense_variant 0.17
ethA 4326713 p.Gln254Arg missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408046 p.Ala53Ser missense_variant 0.18