TB-Profiler result

Run: SRR6045308
Summary

Run ID: SRR6045308

Sample name:

Date: 04-04-2023 11:56:38

Number of reads: 919125

Percentage reads mapped: 93.53

Strain: lineage3.1.2.2

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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.99
lineage3.1.2.2 East-African-Indian CAS RD750 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 1.0 streptomycin
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 9304 p.Gly668Asp missense_variant 1.0
gyrA 9611 c.2310C>T synonymous_variant 1.0
fgd1 491027 p.Asn82Thr missense_variant 0.27
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 619831 c.-60T>G upstream_gene_variant 0.33
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760446 p.Asp214Tyr missense_variant 0.12
rpoB 761933 c.2127G>T synonymous_variant 0.12
rpoB 762068 c.2262C>T synonymous_variant 0.14
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777374 p.Glu369Asp missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304573 p.Val548Ala missense_variant 0.11
Rv1258c 1407489 c.-149G>A upstream_gene_variant 0.13
Rv1258c 1407538 c.-198T>C upstream_gene_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472498 n.653C>A non_coding_transcript_exon_variant 0.4
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.67
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.67
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.67
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.75
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.75
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.75
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.75
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.75
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.75
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.75
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.75
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.75
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.5
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 1.0
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 1.0
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 1.0
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 1.0
rrs 1472673 n.828T>A non_coding_transcript_exon_variant 1.0
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 1.0
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 1.0
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 1.0
rrs 1472687 n.843dupT non_coding_transcript_exon_variant 1.0
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.75
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.75
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.75
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.75
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 1.0
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 1.0
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 1.0
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 1.0
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 1.0
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 1.0
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 1.0
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 1.0
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 1.0
rrl 1474275 n.618T>C non_coding_transcript_exon_variant 1.0
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.4
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.4
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.5
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.5
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.33
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.29
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.25
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.33
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.33
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.33
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.33
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.44
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.38
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.5
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.3
fabG1 1674127 p.Ser230Gly missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102204 p.Val280Ala missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167965 p.Ala883Gly missense_variant 0.14
PPE35 2167967 c.2646A>C synonymous_variant 0.13
PPE35 2168604 p.Pro670Leu missense_variant 1.0
PPE35 2169002 c.1611G>A synonymous_variant 0.13
PPE35 2170202 c.411A>G synonymous_variant 0.15
PPE35 2170205 c.408C>G synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2518106 c.-9C>G upstream_gene_variant 0.15
kasA 2518147 c.33C>T synonymous_variant 0.29
kasA 2519140 c.1026G>C synonymous_variant 0.17
kasA 2519143 c.1029G>C synonymous_variant 0.17
eis 2714795 p.Glu180Lys missense_variant 0.11
eis 2715057 c.276C>T synonymous_variant 0.17
eis 2715060 p.His91Met missense_variant 0.17
eis 2715065 p.Thr90Ala missense_variant 0.15
eis 2715469 c.-137T>C upstream_gene_variant 0.13
eis 2715473 c.-141A>G upstream_gene_variant 0.13
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.29
ahpC 2726341 p.Val50Gly missense_variant 0.21
folC 2746453 c.1146G>A synonymous_variant 0.14
ribD 2987250 p.Met138Leu missense_variant 0.15
Rv2752c 3067053 c.-862C>T upstream_gene_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087476 c.657C>T synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474144 p.Trp46Cys missense_variant 0.11
fprA 3474165 c.159C>G synonymous_variant 0.12
clpC1 4038268 p.Gly813Cys missense_variant 0.12
clpC1 4039508 c.1197G>C synonymous_variant 0.17
clpC1 4039645 p.His354Asp missense_variant 0.15
clpC1 4039654 p.Thr351Ser missense_variant 0.1
clpC1 4039829 p.Leu292Ile missense_variant 0.3
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242232 c.2370T>C synonymous_variant 0.36
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245495 p.Gly755Ser missense_variant 0.11
embB 4246787 p.Pro92Thr missense_variant 0.12
ethA 4326176 p.Glu433Ala missense_variant 1.0
ethR 4327631 p.Ala28Glu missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0