TB-Profiler result

Run: SRR3675538
Summary

Run ID: SRR3675538

Sample name:

Date: 04-04-2023 05:32:49

Number of reads: 674171

Percentage reads mapped: 97.76

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
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
mshA 576539 p.Trp398Arg missense_variant 0.2
rpoB 761156 c.1350G>C synonymous_variant 0.22
rpoC 764611 c.1242G>T synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777814 p.Tyr223His missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303259 p.Val110Ala missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472513 n.668T>C non_coding_transcript_exon_variant 0.12
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.15
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.13
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.12
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.2
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.18
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.18
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.14
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.17
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.17
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.16
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.15
rrs 1472687 n.842_843insC non_coding_transcript_exon_variant 0.11
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.18
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.13
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.14
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.14
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.13
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.13
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.17
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.14
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.14
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.17
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.13
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.12
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.14
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.13
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.13
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.12
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.11
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.11
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.11
rrl 1474779 n.1122G>A 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 0.18
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.15
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.14
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.11
rrl 1474883 n.1226T>C non_coding_transcript_exon_variant 0.1
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.14
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.11
rrl 1475756 n.2099T>C non_coding_transcript_exon_variant 0.11
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.11
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.19
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.18
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.14
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.13
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.11
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.13
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.1
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.1
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.11
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.1
rrl 1476214 n.2557G>C non_coding_transcript_exon_variant 0.11
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.12
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.23
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.23
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.22
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.25
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.25
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.12
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.15
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.15
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.15
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.12
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.12
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.18
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.18
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.15
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.16
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.12
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.19
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.17
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.13
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.15
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.15
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.12
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.2
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.16
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.17
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.2
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.27
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.17
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.1
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.15
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.12
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.12
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.12
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.12
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.13
rrl 1476544 n.2887T>C non_coding_transcript_exon_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.3
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.62
PPE35 2170053 p.Thr187Ser missense_variant 0.74
PPE35 2170157 p.Ala152Ser missense_variant 0.25
Rv1979c 2222381 p.Ser262Thr missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518348 c.234A>T synonymous_variant 0.17
ahpC 2725956 c.-237G>A upstream_gene_variant 0.14
ahpC 2726338 p.Val49Gly missense_variant 0.37
Rv3083 3448437 c.-67C>A upstream_gene_variant 0.2
clpC1 4039729 p.Asp326Asn missense_variant 0.86
clpC1 4040057 c.648C>T synonymous_variant 0.12
panD 4044155 p.Gln43* stop_gained 0.25
embC 4239744 c.-119C>A upstream_gene_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245703 p.Ser824* stop_gained 0.22
embB 4246544 p.Thr11Pro missense_variant 0.23
embB 4246548 p.Pro12Gln missense_variant 0.23
embB 4246555 c.42G>C synonymous_variant 0.17
embB 4246556 p.Ala15Pro missense_variant 0.17
embB 4246563 p.Leu17Trp missense_variant 0.15
embB 4246567 c.54G>T synonymous_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0