TB-Profiler result

Run: SRR19303775
Summary

Run ID: SRR19303775

Sample name:

Date: 03-04-2023 21:06:12

Number of reads: 1103329

Percentage reads mapped: 41.56

Strain: lineage3

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
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 0.12 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 7650 p.Gly117Ser missense_variant 0.12
gyrA 8649 p.Arg450Gly missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9367 p.Ala689Gly missense_variant 1.0
fgd1 490756 c.-27T>G upstream_gene_variant 0.21
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.18
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764521 c.1152T>C synonymous_variant 0.21
rpoC 764536 c.1167G>C synonymous_variant 0.26
rpoC 764537 p.Pro390Val missense_variant 0.28
rpoC 764540 p.Val391Ile missense_variant 0.32
rpoC 764548 c.1179G>C synonymous_variant 0.3
rpoC 764549 p.Pro394Ala missense_variant 0.3
rpoC 764552 p.Gly395Asn missense_variant 0.32
rpoC 764557 p.Asn396Lys missense_variant 0.3
rpoC 764566 c.1197C>G synonymous_variant 0.29
rpoC 764575 c.1206T>C synonymous_variant 0.29
rpoC 764576 p.Ser403Ala missense_variant 0.29
rpoC 764581 c.1212T>C synonymous_variant 0.28
rpoC 764582 p.Leu405Met missense_variant 0.31
rpoC 764605 c.1236G>C synonymous_variant 0.41
rpoC 764611 c.1242G>C synonymous_variant 0.37
rpoC 764620 c.1251G>C synonymous_variant 0.33
rpoC 764621 c.1252_1254delCTCinsTTG synonymous_variant 0.33
rpoC 764632 c.1263T>C synonymous_variant 0.33
rpoC 764641 c.1272C>T synonymous_variant 0.3
rpoC 764650 c.1281G>T synonymous_variant 0.24
rpoC 764671 c.1302G>C synonymous_variant 0.19
rpoC 764672 p.Gln435Glu missense_variant 0.19
rpoC 764677 c.1308C>G synonymous_variant 0.19
rpoC 764686 c.1317C>T synonymous_variant 0.19
rpoC 764689 c.1320G>A synonymous_variant 0.19
rpoC 764695 c.1326T>C synonymous_variant 0.19
rpoC 764701 c.1332C>G synonymous_variant 0.19
rpoC 764705 p.Leu446Lys missense_variant 0.19
rpoC 764716 c.1347G>C synonymous_variant 0.17
rpoC 764719 c.1350G>A synonymous_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777484 p.Gln333Glu missense_variant 0.97
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.12
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.1
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.1
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.16
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 1472172 n.327T>C non_coding_transcript_exon_variant 0.17
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.14
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.14
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.1
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.15
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.11
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.11
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.16
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.12
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.1
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.14
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.21
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.21
rrs 1472803 n.958T>C non_coding_transcript_exon_variant 0.13
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.12
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.1
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.15
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.15
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.11
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.13
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.12
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.14
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.1
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.11
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.12
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.12
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.12
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.14
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.12
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.17
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.12
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.12
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.12
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.14
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.14
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.11
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.13
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.13
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.13
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.2
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.12
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.14
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.13
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.12
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.17
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.2
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.12
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.13
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.12
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.16
rrl 1474883 n.1226T>C non_coding_transcript_exon_variant 0.16
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.1
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.11
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.1
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.1
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.1
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.17
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.14
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.13
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.19
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.2
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.23
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.11
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.11
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.12
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.12
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.12
rrl 1475978 n.2321C>T non_coding_transcript_exon_variant 0.12
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.11
rrl 1475993 n.2336C>T non_coding_transcript_exon_variant 0.12
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.35
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.13
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.33
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.35
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.48
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.36
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.15
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.42
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.5
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.38
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.4
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.36
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.39
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.18
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.25
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.21
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.18
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.31
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.18
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.28
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918064 p.Pro42Arg missense_variant 0.21
tlyA 1918066 p.Ala43Pro missense_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 0.98
pepQ 2860159 p.Ala87Gly missense_variant 0.21
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.75
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.23
fbiB 3642877 p.Lys448Arg missense_variant 1.0
ddn 3986682 c.-162A>G upstream_gene_variant 1.0
embC 4240409 p.Pro183Ala missense_variant 0.2
embC 4240422 p.Glu187Val missense_variant 0.33
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246529 p.Ser6Arg missense_variant 0.29
embB 4248319 c.1806A>C synonymous_variant 0.25
embB 4248324 p.Ala604Gly missense_variant 0.5
embB 4248328 c.1815G>C synonymous_variant 0.21
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0