TB-Profiler result

Run: SRR6807688
Summary

Run ID: SRR6807688

Sample name:

Date: 04-04-2023 16:21:13

Number of reads: 1813907

Percentage reads mapped: 91.13

Strain: lineage4.2.1

Drug-resistance: Pre-XDR-TB

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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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 None 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
gyrA 7581 p.Asp94His missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.21 streptomycin
inhA 1674048 c.-154G>A upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289213 p.Gln10Pro missense_variant 0.98 pyrazinamide
eis 2715342 c.-10G>A upstream_gene_variant 1.0 kanamycin
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 1.0 ethambutol
ethA 4326014 c.-2503_1459del frameshift_variant&start_lost 1.0 ethionamide
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 491247 c.465C>T synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.34
ccsA 619969 p.Val27Ile missense_variant 1.0
rpoC 764888 p.Leu507Val missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304253 c.1323G>T synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.15
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.15
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.14
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.15
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.15
rrs 1472545 n.700A>T 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 1472579 n.734G>T non_coding_transcript_exon_variant 0.1
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.12
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.12
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.15
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.15
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.13
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.13
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.13
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.12
rrs 1472669 n.824_825insTGGA non_coding_transcript_exon_variant 0.13
rrs 1472678 n.833T>G non_coding_transcript_exon_variant 0.12
rrs 1472679 n.834T>C non_coding_transcript_exon_variant 0.12
rrs 1472682 n.839_843delGGGAT non_coding_transcript_exon_variant 0.13
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.12
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.15
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.13
rrs 1472700 n.855C>T non_coding_transcript_exon_variant 0.14
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.16
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.15
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.17
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.15
rrl 1475751 n.2094C>G non_coding_transcript_exon_variant 0.17
rrl 1475752 n.2095C>A non_coding_transcript_exon_variant 0.17
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.17
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.19
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.17
rrl 1475776 n.2119G>T non_coding_transcript_exon_variant 0.17
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.17
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.17
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.17
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.17
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.16
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.16
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.19
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.17
rrl 1476135 n.2478T>C non_coding_transcript_exon_variant 0.19
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.28
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.38
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.28
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.34
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.34
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.34
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.31
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.31
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.31
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.31
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.31
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.31
rrl 1476214 n.2557G>A non_coding_transcript_exon_variant 0.31
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.31
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.41
rrl 1476229 n.2572C>G non_coding_transcript_exon_variant 0.41
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.44
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.47
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.44
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.26
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.26
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.26
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.26
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.26
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.26
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.27
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.29
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.29
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.3
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.46
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.52
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.54
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.54
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.54
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.56
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.54
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.54
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.52
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.56
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.57
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.57
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.55
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.46
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.36
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.31
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.28
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.27
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.27
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.27
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.26
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.26
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.26
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.26
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.27
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.19
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.18
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.17
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.17
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2986827 c.-12G>A upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.21
Rv3083 3448593 c.92_93dupCA frameshift_variant 0.9
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878641 c.-134C>G upstream_gene_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249594 c.3081G>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0