TB-Profiler result

Run: SRR5535701
Summary

Run ID: SRR5535701

Sample name:

Date: 04-04-2023 10:38:26

Number of reads: 1280633

Percentage reads mapped: 99.24

Strain: lineage4.1.2.1

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
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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 5277 p.Gly13Val missense_variant 0.33
gyrB 5795 p.Asp186Tyr missense_variant 1.0
gyrB 6494 p.Ala419Ser missense_variant 0.22
gyrB 6599 p.Glu454Lys missense_variant 0.4
gyrA 7337 c.36C>G synonymous_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7850 c.549C>A synonymous_variant 0.18
gyrA 8646 p.Gln449Lys missense_variant 0.22
gyrA 8978 p.Phe559Leu missense_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9507 p.Ala736Thr missense_variant 0.33
gyrA 9612 p.Asp771Tyr missense_variant 0.14
fgd1 491075 p.Pro98Gln missense_variant 0.33
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575594 p.Gly83Cys missense_variant 0.12
mshA 575679 p.Asn111Ser missense_variant 0.89
ccsA 620340 c.450C>G synonymous_variant 0.18
ccsA 620486 p.Arg199Pro missense_variant 0.2
ccsA 620799 p.Met303Ile missense_variant 0.18
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760390 p.Ser195Ile missense_variant 0.21
rpoB 762979 p.Gly1058Asp missense_variant 0.18
rpoB 763290 p.Arg1162Ser missense_variant 0.29
rpoC 763921 c.552G>C synonymous_variant 0.22
rpoC 764246 p.Leu293Ile missense_variant 0.15
rpoC 765004 c.1635G>T synonymous_variant 0.14
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765253 c.1884C>T synonymous_variant 0.13
rpoC 766727 p.Glu1120* stop_gained 0.29
rpoC 766852 p.Met1161Ile missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775903 p.Glu860* stop_gained 0.14
mmpL5 775993 p.Glu830* stop_gained 0.18
mmpL5 776609 p.Met624Ile missense_variant 0.29
mmpL5 776988 p.Pro498Gln missense_variant 0.5
mmpL5 776990 c.1491C>A synonymous_variant 0.4
mmpL5 777569 c.912C>A synonymous_variant 0.12
mmpS5 778518 p.Gly130Ser missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800643 c.-166C>T upstream_gene_variant 0.17
rplC 800926 p.Arg40Cys missense_variant 0.33
rplC 801310 p.Gly168Trp missense_variant 0.14
fbiC 1302734 c.-197A>C upstream_gene_variant 0.29
fbiC 1303518 p.Met196Ile missense_variant 0.17
fbiC 1303558 p.Ser210Thr missense_variant 0.2
Rv1258c 1406218 p.Gly375* stop_gained 0.17
Rv1258c 1406875 p.Val156Phe missense_variant 0.2
Rv1258c 1407072 p.Pro90His missense_variant 0.14
Rv1258c 1407210 p.Ala44Asp missense_variant 0.22
embR 1416880 p.Phe156Leu missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472473 n.628G>T non_coding_transcript_exon_variant 0.29
fabG1 1673591 p.Ala51Glu missense_variant 0.18
inhA 1674615 p.Met138Ile missense_variant 0.2
rpsA 1834543 c.1002C>T synonymous_variant 0.33
rpsA 1834606 c.1065C>A synonymous_variant 0.33
rpsA 1834882 p.Asp447Glu missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102371 p.Met224Ile missense_variant 0.29
katG 2153901 c.2211C>T synonymous_variant 0.17
katG 2154045 p.Trp689Cys missense_variant 0.15
katG 2154984 c.1128G>T synonymous_variant 0.22
PPE35 2168883 p.Gly577Asp missense_variant 0.33
PPE35 2169896 c.717C>T synonymous_variant 0.5
Rv1979c 2222032 p.Ala378Val missense_variant 0.2
Rv1979c 2222497 p.Leu223Pro missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289187 p.Leu19Met missense_variant 0.14
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518593 p.Ala160Asp missense_variant 0.29
eis 2714567 p.Leu256Val missense_variant 0.17
ahpC 2726405 c.213C>A synonymous_variant 0.17
folC 2746683 p.Leu306Ile missense_variant 0.18
folC 2746853 p.Ser249* stop_gained 0.25
folC 2747030 p.Pro190Arg missense_variant 0.2
folC 2747789 c.-191G>T upstream_gene_variant 0.5
pepQ 2860103 p.Gly106Ser missense_variant 0.17
pepQ 2860279 p.Ala47Asp missense_variant 0.12
ribD 2987420 c.582C>T synonymous_variant 0.22
ribD 2987531 c.693C>A synonymous_variant 0.25
Rv2752c 3064673 p.Ala507Ser missense_variant 0.2
Rv2752c 3064782 c.1410G>T synonymous_variant 0.22
thyX 3067662 p.Arg95His missense_variant 0.17
thyA 3073805 p.Glu223* stop_gained 0.25
thyA 3074392 p.Arg27Leu missense_variant 0.29
thyA 3074411 p.Arg21Ser missense_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087257 c.438T>C synonymous_variant 0.11
ald 3087404 c.585G>T synonymous_variant 0.22
ald 3087447 p.Glu210* stop_gained 0.22
Rv3083 3448680 p.Met59Ile missense_variant 0.33
Rv3083 3449426 p.Thr308Lys missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612173 p.Arg315Leu missense_variant 0.17
Rv3236c 3612556 c.561G>C synonymous_variant 0.29
Rv3236c 3613078 c.39C>A synonymous_variant 0.2
fbiB 3642798 p.Gly422Cys missense_variant 0.14
alr 3841216 p.Gly69Arg missense_variant 0.12
alr 3841366 p.Gly19Ser missense_variant 0.13
rpoA 3878339 p.Asp57Tyr missense_variant 0.29
ddn 3987234 p.Pro131Thr missense_variant 0.2
clpC1 4038354 p.Gln784Arg missense_variant 0.17
clpC1 4038979 p.Ala576Ser missense_variant 0.4
embC 4240306 c.444C>A synonymous_variant 0.2
embC 4241083 c.1221G>T synonymous_variant 0.13
embC 4241619 p.Trp586Ser missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4242917 p.Glu1019* stop_gained 0.22
embA 4243265 c.33G>T synonymous_variant 0.29
embA 4245248 c.2016G>T synonymous_variant 0.29
embA 4245393 p.Ala721Ser missense_variant 0.33
embA 4245586 p.Pro785Leu missense_variant 0.25
embB 4245629 c.-885C>A upstream_gene_variant 0.14
embB 4246597 p.Trp28* stop_gained 0.17
aftB 4267333 p.Val502Ile missense_variant 0.4
aftB 4268222 c.615G>T synonymous_variant 0.13
aftB 4268653 p.Ala62Ser missense_variant 0.12
ubiA 4269487 p.Gly116Val missense_variant 0.18
ubiA 4269875 c.-42G>T upstream_gene_variant 0.18
whiB6 4338504 c.18G>A synonymous_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408012 p.Arg64Leu missense_variant 0.18