TB-Profiler result

Run: SRR1140677
Summary

Run ID: SRR1140677

Sample name:

Date: 02-04-2023 20:57:28

Number of reads: 1266111

Percentage reads mapped: 49.52

Strain: lineage4.6.1

Drug-resistance: MDR-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
lineage4.6 Euro-American T;LAM None 0.99
lineage4.6.1 Euro-American (Uganda) T2 RD724 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288933 p.Tyr103* stop_gained 0.12 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
gid 4407851 c.351delG frameshift_variant 1.0 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 7539 p.Thr80Ala missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7709 c.408G>A synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490624 c.-159T>C upstream_gene_variant 0.11
mshA 575196 c.-152A>T upstream_gene_variant 0.13
mshA 575794 c.447C>T synonymous_variant 0.18
rpoC 764575 c.1206T>G synonymous_variant 0.17
rpoC 764581 c.1212T>C synonymous_variant 0.17
rpoC 764582 p.Leu405Met missense_variant 0.16
rpoC 764587 c.1218C>G synonymous_variant 0.16
rpoC 764593 c.1224C>T synonymous_variant 0.21
rpoC 764605 c.1236G>C synonymous_variant 0.24
rpoC 764611 c.1242G>T synonymous_variant 0.22
rpoC 764632 c.1263T>C synonymous_variant 0.19
rpoC 764641 c.1272C>T synonymous_variant 0.18
rpoC 764650 c.1281G>T synonymous_variant 0.21
rpoC 764663 p.Val432Thr missense_variant 0.15
rpoC 764672 p.Gln435Glu missense_variant 0.11
rpoC 766488 p.Pro1040Arg missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776030 c.2451G>A synonymous_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406411 c.930A>G synonymous_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471876 n.31G>A non_coding_transcript_exon_variant 0.15
rrs 1471892 n.47G>A non_coding_transcript_exon_variant 0.16
rrs 1471896 n.51T>C non_coding_transcript_exon_variant 0.15
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.3
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.43
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.41
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.3
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.3
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.28
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.19
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.23
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.23
rrs 1472264 n.419T>C non_coding_transcript_exon_variant 0.22
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.21
rrs 1472338 n.493A>C non_coding_transcript_exon_variant 0.13
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.22
rrs 1472349 n.504A>C non_coding_transcript_exon_variant 0.26
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.38
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.38
rrs 1472382 n.537G>T non_coding_transcript_exon_variant 0.32
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.27
rrs 1472427 n.582T>A non_coding_transcript_exon_variant 0.96
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.11
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.12
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.12
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.17
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.2
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 0.32
rrs 1472715 n.870C>A non_coding_transcript_exon_variant 0.3
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.33
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.68
rrs 1472770 n.925C>T non_coding_transcript_exon_variant 0.63
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.64
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.61
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.61
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.53
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.35
rrs 1472826 n.981G>C non_coding_transcript_exon_variant 0.27
rrs 1472887 n.1042G>C non_coding_transcript_exon_variant 0.2
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.21
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.2
rrs 1473223 n.1378G>A non_coding_transcript_exon_variant 0.3
rrs 1473352 n.1507C>G non_coding_transcript_exon_variant 0.22
rrs 1473353 n.1508C>G non_coding_transcript_exon_variant 0.21
rrs 1473358 n.1513G>C non_coding_transcript_exon_variant 0.21
rrs 1473359 n.1514G>C non_coding_transcript_exon_variant 0.2
rrl 1475295 n.1638C>G non_coding_transcript_exon_variant 0.15
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.27
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.27
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.5
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.54
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.26
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.26
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.11
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.54
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.65
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.65
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.7
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.62
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.72
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.66
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.59
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.67
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.6
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.56
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.51
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.46
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.45
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.43
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.44
rrl 1476491 n.2834T>C non_coding_transcript_exon_variant 0.34
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.17
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.15
rpsA 1833450 c.-92G>C upstream_gene_variant 0.12
rpsA 1833931 c.390C>G synonymous_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918526 p.Gly196Val missense_variant 0.12
ndh 2102463 p.Glu194Gln missense_variant 0.1
PPE35 2168330 c.2283G>T synonymous_variant 0.13
PPE35 2168465 c.2148C>G synonymous_variant 0.17
PPE35 2168483 c.2130C>T synonymous_variant 0.12
PPE35 2170454 c.159C>T synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288784 p.Thr153Ile missense_variant 0.17
pncA 2290167 c.-926G>A upstream_gene_variant 0.12
kasA 2518824 p.Phe237Ser missense_variant 0.14
folC 2746886 p.Val238Asp missense_variant 0.18
pepQ 2860209 p.Asp70Glu missense_variant 0.11
thyX 3067330 p.Val206Leu missense_variant 0.11
thyX 3067658 c.288C>T synonymous_variant 0.15
thyA 3073849 p.Ile208Thr missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474177 c.171C>T synonymous_variant 1.0
fprA 3474472 p.Gly156* stop_gained 0.13
Rv3236c 3612280 c.837C>G synonymous_variant 0.1
rpoA 3878659 c.-152A>G upstream_gene_variant 0.17
ddn 3987129 p.Pro96Ala missense_variant 0.11
clpC1 4039791 p.Ala305Asp missense_variant 0.12
embC 4241793 p.Ser644Cys missense_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4245962 c.-552G>A upstream_gene_variant 1.0
embB 4249688 p.Arg1059Gly missense_variant 0.15
aftB 4268519 c.318C>T synonymous_variant 1.0
ubiA 4269670 p.Val55Gly missense_variant 1.0
ethA 4328329 c.-856C>G upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407742 p.Arg154Gln missense_variant 1.0
gid 4407867 c.336T>C synonymous_variant 0.1