TB-Profiler result

Run: SRR5341319
Summary

Run ID: SRR5341319

Sample name:

Date: 04-04-2023 10:14:44

Number of reads: 2620950

Percentage reads mapped: 83.87

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 0.28 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
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760859 c.1053T>C synonymous_variant 0.14
rpoB 760862 c.1056G>C synonymous_variant 0.13
rpoB 760877 c.1071G>C synonymous_variant 0.11
rpoB 760886 c.1080A>G synonymous_variant 0.12
rpoB 760887 p.Thr361Ala missense_variant 0.12
rpoB 762140 c.2334G>C synonymous_variant 0.12
rpoB 762143 c.2337T>C synonymous_variant 0.11
rpoB 762167 c.2361T>C synonymous_variant 0.12
rpoB 762176 c.2370T>C synonymous_variant 0.12
rpoB 762185 c.2379G>C synonymous_variant 0.12
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763615 c.246G>C synonymous_variant 0.13
rpoC 763618 c.249C>T synonymous_variant 0.16
rpoC 763633 c.264T>C synonymous_variant 0.15
rpoC 763660 c.291T>G synonymous_variant 0.15
rpoC 763666 c.297G>A synonymous_variant 0.15
rpoC 763675 c.306C>G synonymous_variant 0.11
rpoC 763702 c.333C>G synonymous_variant 0.13
rpoC 763709 c.340C>T synonymous_variant 0.13
rpoC 763714 c.345G>C synonymous_variant 0.11
rpoC 764405 c.1036_1038delAGGinsCGC synonymous_variant 0.11
rpoC 764431 c.1062G>C synonymous_variant 0.14
rpoC 764434 c.1065A>G synonymous_variant 0.12
rpoC 764435 c.1066_1068delAGGinsCGA synonymous_variant 0.12
rpoC 764446 c.1077T>C synonymous_variant 0.12
rpoC 764449 c.1080G>C synonymous_variant 0.12
rpoC 764458 c.1089G>C synonymous_variant 0.12
rpoC 764461 c.1092A>G synonymous_variant 0.12
rpoC 764632 c.1263T>C synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775904 c.2577G>A synonymous_variant 0.11
mmpL5 775915 p.Ala856Ser missense_variant 0.12
mmpL5 775951 c.2530C>T synonymous_variant 0.13
mmpL5 776030 c.2451G>C synonymous_variant 0.11
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781760 c.201T>C synonymous_variant 0.11
Rv1258c 1406277 p.Leu355Pro missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471922 n.78delT non_coding_transcript_exon_variant 0.12
rrs 1471925 n.80T>C non_coding_transcript_exon_variant 0.12
rrs 1471931 n.87delA non_coding_transcript_exon_variant 0.13
rrs 1471934 n.89A>G non_coding_transcript_exon_variant 0.12
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.18
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.11
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.11
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.24
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.24
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.26
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.26
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.27
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.27
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.22
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.16
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.12
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.13
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.14
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.14
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.14
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.12
rrs 1473291 n.1446_1447insT non_coding_transcript_exon_variant 0.13
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.13
rrl 1474174 n.517A>G non_coding_transcript_exon_variant 0.11
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.11
rrl 1474183 n.526T>C non_coding_transcript_exon_variant 0.11
rrl 1474185 n.528G>A non_coding_transcript_exon_variant 0.11
rrl 1474186 n.529A>G non_coding_transcript_exon_variant 0.11
rrl 1474803 n.1146G>A non_coding_transcript_exon_variant 0.14
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.16
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.15
rrl 1475120 n.1463G>T non_coding_transcript_exon_variant 0.15
rrl 1475995 n.2338G>A non_coding_transcript_exon_variant 0.12
rrl 1476088 n.2431A>C non_coding_transcript_exon_variant 0.15
rrl 1476099 n.2442A>G non_coding_transcript_exon_variant 0.12
rrl 1476103 n.2446C>G non_coding_transcript_exon_variant 0.12
rrl 1476110 n.2453G>C non_coding_transcript_exon_variant 0.12
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.13
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.15
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.12
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.17
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.16
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.19
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.23
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.23
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.25
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.26
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.19
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.18
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.11
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.2
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.24
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.3
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.31
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.32
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.32
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.37
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.41
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.39
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.39
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.33
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.24
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.16
rrl 1476529 n.2872A>G non_coding_transcript_exon_variant 0.19
rrl 1476540 n.2883C>T non_coding_transcript_exon_variant 0.19
rpsA 1834451 c.910T>C synonymous_variant 0.12
rpsA 1834456 c.915T>G synonymous_variant 0.13
rpsA 1834468 c.927A>G synonymous_variant 0.13
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 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
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642618 p.Asp362Asn missense_variant 1.0
alr 3841473 c.-53G>A upstream_gene_variant 0.98
clpC1 4039670 c.1035G>C synonymous_variant 0.13
clpC1 4039682 c.1023C>G synonymous_variant 0.14
clpC1 4039694 c.1011G>C synonymous_variant 0.13
clpC1 4039724 c.981A>G synonymous_variant 0.16
clpC1 4039733 c.972G>C synonymous_variant 0.14
clpC1 4039742 c.963C>T synonymous_variant 0.15
clpC1 4039748 c.957G>C synonymous_variant 0.13
clpC1 4039751 c.954A>G synonymous_variant 0.14
clpC1 4039757 c.948A>G synonymous_variant 0.12
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0