TB-Profiler result

Run: SRR5341317
Summary

Run ID: SRR5341317

Sample name:

Date: 04-04-2023 10:14:27

Number of reads: 3850008

Percentage reads mapped: 87.47

Strain: lineage3

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
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
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674481 p.Ser94Ala missense_variant 1.0 isoniazid, ethionamide
embA 4243222 c.-11C>A upstream_gene_variant 1.0 ethambutol
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
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.15
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.31
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.34
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.45
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.51
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.17
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.46
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.31
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.19
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.2
rrs 1472222 n.377G>A non_coding_transcript_exon_variant 0.16
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.15
rrs 1472229 n.384C>T non_coding_transcript_exon_variant 0.15
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.11
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.12
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.11
rrs 1472378 n.533G>T non_coding_transcript_exon_variant 0.15
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.15
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.15
rrs 1472396 n.551A>T non_coding_transcript_exon_variant 0.11
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.16
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.12
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.28
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.31
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.31
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.41
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.43
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.22
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.14
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.13
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.12
rrs 1472708 n.863T>A non_coding_transcript_exon_variant 0.17
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.28
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.33
rrs 1472733 n.888G>C non_coding_transcript_exon_variant 0.29
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.28
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.28
rrs 1472742 n.897C>G non_coding_transcript_exon_variant 0.28
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.48
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.47
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.39
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.34
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.11
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.18
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.23
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.24
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.23
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.1
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 0.13
rrl 1474269 n.612C>T non_coding_transcript_exon_variant 0.11
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.12
rrl 1474816 n.1159G>C non_coding_transcript_exon_variant 0.1
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.21
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.2
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.12
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.12
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.27
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.35
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.35
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.23
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.21
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.19
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.17
rrl 1475144 n.1487G>C non_coding_transcript_exon_variant 0.11
rrl 1475696 n.2039T>C non_coding_transcript_exon_variant 0.12
rrl 1475703 n.2046A>G non_coding_transcript_exon_variant 0.12
rrl 1475707 n.2050T>A non_coding_transcript_exon_variant 0.12
rrl 1475713 n.2056C>G non_coding_transcript_exon_variant 0.12
rrl 1475716 n.2059A>G non_coding_transcript_exon_variant 0.1
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.29
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.3
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.38
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.38
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.3
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.21
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.22
rrl 1476229 n.2572C>G non_coding_transcript_exon_variant 0.21
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.2
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.21
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.21
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.22
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.21
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.49
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.48
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.51
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 0.6
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.46
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.51
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.17
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.41
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.28
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.14
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.14
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.16
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.24
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.29
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.27
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.27
rrl 1476595 n.2938C>A non_coding_transcript_exon_variant 0.32
rrl 1476602 n.2945G>T non_coding_transcript_exon_variant 0.31
rrl 1476608 n.2951C>A non_coding_transcript_exon_variant 0.24
rrl 1476614 n.2957A>G non_coding_transcript_exon_variant 0.18
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.14
rrl 1476621 n.2964C>T non_coding_transcript_exon_variant 0.11
rrl 1476624 n.2967T>G non_coding_transcript_exon_variant 0.12
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.13
rrl 1476630 n.2973A>G non_coding_transcript_exon_variant 0.11
rrl 1476637 n.2980C>G non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.97
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.99
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 3642877 p.Lys448Arg missense_variant 1.0
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
gid 4407981 c.221delT frameshift_variant 0.99