TB-Profiler result

Run: SRR7131221
Summary

Run ID: SRR7131221

Sample name:

Date: 04-04-2023 18:49:39

Number of reads: 1921709

Percentage reads mapped: 99.99

Strain: lineage4.6.2.2

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.2 Euro-American T;LAM RD726 1.0
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 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 1472644 n.799C>T non_coding_transcript_exon_variant 0.3 streptomycin
gid 4407851 c.351delG frameshift_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
mshA 576108 p.Ala254Gly missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778298 c.-692C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.11
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.11
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.11
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.15
rrs 1472282 n.437T>G non_coding_transcript_exon_variant 0.13
rrs 1472494 n.649A>G non_coding_transcript_exon_variant 0.25
rrs 1472496 n.651T>G non_coding_transcript_exon_variant 0.18
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.25
rrs 1472502 n.657G>T non_coding_transcript_exon_variant 0.17
rrs 1472507 n.662C>A non_coding_transcript_exon_variant 0.15
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.21
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.23
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.31
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.31
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.33
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.3
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.55
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.45
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.22
rrl 1474483 n.826C>T non_coding_transcript_exon_variant 0.2
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.3
rrl 1474495 n.838G>A non_coding_transcript_exon_variant 0.25
rrl 1474496 n.839C>G non_coding_transcript_exon_variant 0.29
rrl 1474497 n.840G>A non_coding_transcript_exon_variant 0.29
rrl 1474506 n.849C>T non_coding_transcript_exon_variant 0.29
rrl 1474508 n.851C>T non_coding_transcript_exon_variant 0.25
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.38
rrl 1474527 n.870T>C non_coding_transcript_exon_variant 0.25
rrl 1474528 n.871T>A non_coding_transcript_exon_variant 0.25
rrl 1474529 n.872A>G non_coding_transcript_exon_variant 0.29
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.38
rrl 1474540 n.883T>C non_coding_transcript_exon_variant 0.4
rrl 1474541 n.884G>T non_coding_transcript_exon_variant 0.33
rrl 1474542 n.885A>G non_coding_transcript_exon_variant 0.33
rrl 1474551 n.894G>A non_coding_transcript_exon_variant 0.25
rrl 1474734 n.1077G>A non_coding_transcript_exon_variant 0.5
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.5
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 1.0
rrl 1475672 n.2015C>T non_coding_transcript_exon_variant 0.5
rrl 1475673 n.2016T>C non_coding_transcript_exon_variant 0.5
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.5
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.4
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.25
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.25
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.29
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.33
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.29
rrl 1476253 n.2596A>G non_coding_transcript_exon_variant 0.29
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.29
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.33
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.33
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.25
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.25
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.25
rrl 1476297 n.2640C>A non_coding_transcript_exon_variant 0.22
rrl 1476299 n.2642C>G non_coding_transcript_exon_variant 0.22
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 0.22
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.22
rrl 1476308 n.2651G>C non_coding_transcript_exon_variant 0.22
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.25
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.25
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.29
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.25
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.18
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.36
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.29
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.28
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.37
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.35
rrl 1476513 n.2856G>T non_coding_transcript_exon_variant 0.11
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.11
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.17
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.11
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.12
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.17
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.12
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.18
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.17
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.17
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.11
rrl 1476701 n.3044A>G non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065258 p.Met312Val missense_variant 1.0
thyX 3067474 p.Pro158Ala missense_variant 1.0
fbiD 3339741 c.624G>T synonymous_variant 0.11
fbiD 3339744 c.627A>C synonymous_variant 0.11
Rv3083 3448567 p.His22Asp missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612571 c.546C>T synonymous_variant 1.0
embA 4242550 c.-683C>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246553 c.40C>A synonymous_variant 0.17
embB 4246584 p.Arg24Pro missense_variant 0.24
embB 4247028 p.Leu172Arg missense_variant 0.17
aftB 4267272 p.Lys522Arg missense_variant 1.0
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0