TB-Profiler result

Run: SRR7131297
Summary

Run ID: SRR7131297

Sample name:

Date: 04-04-2023 18:52:14

Number of reads: 2401661

Percentage reads mapped: 99.99

Strain: lineage1.2.1.2

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.2.1 Indo-Oceanic EAI2 RD239 1.0
lineage1.2.1.2 Indo-Oceanic NA RD239 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 0.13 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.16 kanamycin, capreomycin, aminoglycosides, amikacin
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 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9260 c.1959G>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575368 c.21T>C synonymous_variant 1.0
mshA 576482 p.Val379Leu missense_variant 0.25
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763531 c.162G>C synonymous_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
rrs 1471649 n.-197C>A upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.16
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.13
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.13
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.13
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.12
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.22
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.11
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.15
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.15
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.11
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.12
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.18
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.13
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.12
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.1
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.12
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.12
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.14
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.12
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.12
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.13
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.15
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.15
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.17
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.15
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.15
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.26
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.14
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.15
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.13
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.12
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.12
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.14
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.13
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.19
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.21
rrs 1473270 n.1425G>A non_coding_transcript_exon_variant 0.16
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.16
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.13
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.15
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.1
rrl 1474584 n.927C>T non_coding_transcript_exon_variant 0.12
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.1
rrl 1474732 n.1075A>G non_coding_transcript_exon_variant 0.88
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.12
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.13
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.12
rrl 1475751 n.2094C>T non_coding_transcript_exon_variant 0.12
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.11
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.12
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.14
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.16
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.2
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.2
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.19
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.15
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.16
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.15
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.13
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.13
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.12
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.12
rrl 1476001 n.2344T>C non_coding_transcript_exon_variant 0.11
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.17
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.14
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.13
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.12
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.14
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.14
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.13
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.15
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.19
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.22
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.13
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.18
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.22
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.11
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.23
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.23
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.11
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.17
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.29
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.3
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.19
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.27
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.2
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.14
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.12
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.12
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.11
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519048 p.Gly312Ser missense_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ald 3086693 c.-126delC upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339417 c.300A>G synonymous_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.12
Rv3083 3448379 c.-125G>A upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568488 c.191delG frameshift_variant 1.0
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 1.0
panD 4044312 c.-31G>A upstream_gene_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.17
embB 4247028 p.Leu172Arg missense_variant 0.16
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
whiB6 4338361 p.Arg54Gln missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0