TB-Profiler result

Run: SRR21677894
Summary

Run ID: SRR21677894

Sample name:

Date: 04-04-2023 02:49:42

Number of reads: 310233

Percentage reads mapped: 97.45

Strain: lineage4.1.1.3

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
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 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
ethA 4327282 c.191delT frameshift_variant 0.17 ethionamide
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 5500 c.261C>T synonymous_variant 0.2
gyrB 5558 p.Gly107Ser missense_variant 0.18
gyrB 6059 c.821delG frameshift_variant 0.18
gyrB 6070 p.Asp277Glu missense_variant 0.18
gyrB 6099 p.Val287Ala missense_variant 0.12
gyrA 7210 c.-92C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7552 p.Tyr84Cys missense_variant 0.4
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7598 p.Met99Ile missense_variant 0.5
gyrA 8023 p.Ala241Gly missense_variant 0.33
gyrA 8107 p.Leu269Pro missense_variant 0.25
gyrA 8309 p.Gln336His missense_variant 0.25
gyrA 9013 p.Thr571Ile missense_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9532 c.2233delC frameshift_variant 0.15
gyrA 9652 p.Ile784Thr missense_variant 0.25
fgd1 491732 p.Gln317Arg missense_variant 0.18
fgd1 491749 p.Leu323Ile missense_variant 0.22
mshA 575414 p.Gly23Cys missense_variant 0.14
mshA 575441 p.Gly32Arg missense_variant 0.13
mshA 575657 p.Ala104Pro missense_variant 0.15
ccsA 620034 c.144C>T synonymous_variant 0.2
ccsA 620655 p.Trp255* stop_gained 0.11
rpoB 760070 c.264T>C synonymous_variant 0.14
rpoB 760745 p.Lys313Asn missense_variant 0.12
rpoB 761154 p.Ser450Pro missense_variant 0.33
rpoB 762768 p.Pro988Thr missense_variant 0.17
rpoB 763197 p.Val1131Leu missense_variant 0.14
rpoC 763659 p.Leu97Pro missense_variant 0.4
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765451 c.2082C>T synonymous_variant 0.13
rpoC 765552 p.Gly728Asp missense_variant 0.12
rpoC 765618 p.Glu750Gly missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776146 p.Ala779Ser missense_variant 0.18
mmpL5 776906 c.1575G>A synonymous_variant 0.11
mmpL5 778171 p.Ala104Thr missense_variant 0.25
mmpL5 778411 p.Ile24Leu missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781435 c.-125G>C upstream_gene_variant 1.0
rpsL 781753 p.Ala65Glu missense_variant 0.29
fbiC 1303400 p.Gln157Leu missense_variant 0.17
fbiC 1303831 p.Thr301Pro missense_variant 0.13
fbiC 1304231 p.Pro434Arg missense_variant 0.15
Rv1258c 1406492 c.849C>T synonymous_variant 0.18
Rv1258c 1406607 p.Val245Glu missense_variant 0.15
Rv1258c 1407322 p.Gly7Ser missense_variant 0.22
atpE 1460855 c.-189delC upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472068 n.226delG non_coding_transcript_exon_variant 0.15
rrs 1472301 n.456C>A non_coding_transcript_exon_variant 0.11
rrs 1473124 n.1279A>G non_coding_transcript_exon_variant 0.15
rrs 1473279 n.1434G>A non_coding_transcript_exon_variant 0.18
rrl 1474868 n.1211T>C non_coding_transcript_exon_variant 0.14
rrl 1475231 n.1574C>T non_coding_transcript_exon_variant 0.11
rrl 1475238 n.1581A>C non_coding_transcript_exon_variant 0.12
rrl 1475673 n.2020_2021delAA non_coding_transcript_exon_variant 0.15
rrl 1475703 n.2046A>T non_coding_transcript_exon_variant 0.13
rrl 1476174 n.2520_2521delGC non_coding_transcript_exon_variant 0.17
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.17
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.17
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.17
rrl 1476324 n.2667G>A non_coding_transcript_exon_variant 0.18
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.25
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.29
rrl 1476339 n.2682G>A non_coding_transcript_exon_variant 0.29
rrl 1476356 n.2699C>T non_coding_transcript_exon_variant 0.17
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.15
rrl 1476366 n.2709A>C non_coding_transcript_exon_variant 0.15
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.15
rrl 1476374 n.2717T>G non_coding_transcript_exon_variant 0.15
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.17
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.17
rrl 1476384 n.2727G>A non_coding_transcript_exon_variant 0.17
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.15
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.15
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.14
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.13
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.13
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.17
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.17
inhA 1674114 c.-88T>A upstream_gene_variant 0.25
inhA 1674675 c.474C>T synonymous_variant 0.13
rpsA 1833650 p.Asp37Asn missense_variant 0.11
rpsA 1833839 p.Leu100Phe missense_variant 0.17
rpsA 1834211 p.Ala224Thr missense_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918097 p.Thr53Asn missense_variant 0.22
tlyA 1918527 c.588G>T synonymous_variant 0.12
tlyA 1918688 p.Ala250Glu missense_variant 0.2
ndh 2101767 p.Arg426Cys missense_variant 0.33
ndh 2102413 c.630G>T synonymous_variant 0.15
ndh 2102414 c.628delC frameshift_variant 0.15
katG 2154281 p.Leu611Ile missense_variant 0.33
katG 2155479 p.Ser211Arg missense_variant 0.14
katG 2156188 c.-77T>A upstream_gene_variant 0.2
katG 2156332 c.-221C>T upstream_gene_variant 0.14
katG 2156488 c.-377C>A upstream_gene_variant 0.17
PPE35 2168269 p.Gly782Arg missense_variant 0.17
PPE35 2168320 p.Thr765Ala missense_variant 0.12
PPE35 2168357 c.2256T>C synonymous_variant 0.14
PPE35 2168375 c.2238T>C synonymous_variant 0.12
PPE35 2168806 p.Gly603Ser missense_variant 0.25
PPE35 2169650 p.Leu321Phe missense_variant 0.13
PPE35 2169713 c.900C>T synonymous_variant 0.17
Rv1979c 2221870 p.Tyr432Cys missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288824 p.Arg140Cys missense_variant 0.17
pncA 2290065 c.-824G>A upstream_gene_variant 0.29
kasA 2517962 c.-153C>A upstream_gene_variant 0.25
kasA 2517976 c.-139C>T upstream_gene_variant 0.25
kasA 2518476 p.Arg121Met missense_variant 0.18
kasA 2519159 p.Ala349Thr missense_variant 0.33
kasA 2519197 c.1083G>T synonymous_variant 0.4
eis 2714341 p.Leu331Pro missense_variant 0.13
eis 2715164 p.Glu57* stop_gained 0.2
ahpC 2725966 c.-227C>T upstream_gene_variant 0.15
ahpC 2726115 c.-77delT upstream_gene_variant 0.17
ahpC 2726215 p.Asp8Gly missense_variant 0.15
ahpC 2726480 p.Trp96Cys missense_variant 0.33
folC 2746376 p.Ser408Leu missense_variant 0.29
folC 2746393 c.1206C>A synonymous_variant 0.4
folC 2746636 c.963C>T synonymous_variant 0.25
folC 2746699 p.His300Gln missense_variant 0.33
pepQ 2859363 c.1056T>C synonymous_variant 0.17
pepQ 2860488 c.-70C>A upstream_gene_variant 0.14
ribD 2986863 p.Ala9Ser missense_variant 0.12
Rv2752c 3064999 p.Gly398Glu missense_variant 0.14
Rv2752c 3065155 p.Glu346Gly missense_variant 0.11
Rv2752c 3065298 p.Asp298Glu missense_variant 0.15
thyX 3067351 p.Arg199Trp missense_variant 0.13
thyA 3073981 p.Tyr164Cys missense_variant 0.17
thyA 3074424 c.48G>A synonymous_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087130 p.Thr104Ile missense_variant 0.18
ald 3087369 p.Ala184Ser missense_variant 0.2
fbiD 3339194 p.Leu26Arg missense_variant 0.22
fbiD 3339326 p.Ala70Val missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474453 c.447G>A synonymous_variant 0.13
fprA 3475113 c.1107G>A synonymous_variant 0.15
whiB7 3568516 p.Ala55Val missense_variant 0.2
whiB7 3568687 c.-8A>G upstream_gene_variant 0.18
Rv3236c 3612564 p.Met185Leu missense_variant 0.17
fbiA 3640504 c.-39A>T upstream_gene_variant 0.2
fbiB 3641124 c.-411C>T upstream_gene_variant 0.12
fbiB 3642566 c.1032A>G synonymous_variant 0.15
fbiB 3642728 c.1194C>T synonymous_variant 0.18
alr 3840299 c.1122C>A synonymous_variant 0.18
alr 3841100 c.321A>C synonymous_variant 0.14
alr 3841111 p.Gly104Cys missense_variant 0.15
alr 3841347 p.Met25Thr missense_variant 0.29
alr 3841571 c.-151A>T upstream_gene_variant 0.15
rpoA 3877876 p.Ala211Val missense_variant 0.33
rpoA 3878541 c.-34C>T upstream_gene_variant 0.5
clpC1 4038548 p.Phe719Leu missense_variant 0.11
clpC1 4038805 p.Ile634Phe missense_variant 0.33
clpC1 4039388 c.1315_1316delAT frameshift_variant 0.17
clpC1 4039498 p.Ile403Val missense_variant 0.2
clpC1 4039971 p.Lys245Thr missense_variant 0.15
clpC1 4040475 p.His77Arg missense_variant 0.2
clpC1 4040722 c.-18G>T upstream_gene_variant 0.2
clpC1 4040866 c.-162T>A upstream_gene_variant 0.13
clpC1 4040901 c.-197C>T upstream_gene_variant 0.13
embC 4239928 c.66G>A synonymous_variant 0.12
embC 4241090 p.Trp410Arg missense_variant 0.13
embC 4241136 p.Val425Ala missense_variant 0.13
embC 4241295 p.Ala478Val missense_variant 0.14
embC 4241491 c.1629G>T synonymous_variant 0.33
embC 4241603 p.Phe581Ile missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243293 p.Gly21* stop_gained 0.12
embA 4244860 p.Gly543Glu missense_variant 1.0
embB 4248032 p.Arg507Trp missense_variant 0.17
embB 4248495 p.Pro661Leu missense_variant 0.12
embB 4249174 p.Ser887Arg missense_variant 0.12
embB 4249315 p.Phe934Leu missense_variant 0.29
embB 4249362 p.Ala950Asp missense_variant 0.29
embB 4249408 c.2895G>A synonymous_variant 1.0
embB 4249520 p.Ala1003Thr missense_variant 0.17
aftB 4266993 p.Leu615Pro missense_variant 0.18
aftB 4267741 p.Glu366* stop_gained 0.17
aftB 4268952 c.-116G>C upstream_gene_variant 0.14
ethA 4327521 c.-48G>T upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407798 c.405G>T synonymous_variant 1.0