TB-Profiler result

Run: SRR17567930
Summary

Run ID: SRR17567930

Sample name:

Date: 03-04-2023 18:01:59

Number of reads: 273342

Percentage reads mapped: 6.82

Strain: lineage4.4.1.1

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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 0.99
lineage4.4.1.1 Euro-American S;Orphans None 0.95
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
pncA 2288788 c.446_453delATGGCTTG frameshift_variant 1.0 pyrazinamide, pyrazinamide
pncA 2288824 p.Arg140Ser missense_variant 1.0 pyrazinamide
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
rpoB 762872 p.Met1022Ile missense_variant 0.33
rpoB 762878 p.Ile1024Met missense_variant 0.4
rpoB 762879 p.Met1025Leu missense_variant 0.4
rpoC 762896 c.-474G>C upstream_gene_variant 0.6
rpoC 762917 c.-453C>G upstream_gene_variant 0.67
rpoC 762923 c.-447C>G upstream_gene_variant 0.67
rpoB 762925 p.Thr1040Ile missense_variant 0.67
rpoC 762929 c.-441G>C upstream_gene_variant 0.75
rpoB 762939 p.Met1045Leu missense_variant 0.77
rpoB 762942 p.Ile1046Val missense_variant 0.77
rpoC 762965 c.-405T>C upstream_gene_variant 0.69
rpoC 762980 c.-390T>C upstream_gene_variant 0.75
rpoC 762989 c.-381G>C upstream_gene_variant 0.74
rpoC 762995 c.-375G>T upstream_gene_variant 0.71
rpoB 763005 p.Cys1067Val missense_variant 0.56
rpoC 763013 c.-357C>G upstream_gene_variant 0.5
rpoB 763014 p.Met1070Leu missense_variant 0.5
rpoB 763017 p.Gln1071Glu missense_variant 0.5
rpoC 763028 c.-342T>C upstream_gene_variant 0.54
rpoC 763031 c.-339T>G upstream_gene_variant 0.46
rpoC 763040 c.-330C>G upstream_gene_variant 0.42
rpoB 763050 p.Leu1082Met missense_variant 0.31
rpoC 763053 c.-317T>C upstream_gene_variant 0.2
rpoC 764428 c.1059G>C synonymous_variant 0.3
rpoC 764431 c.1062G>C synonymous_variant 0.33
rpoC 764434 c.1065A>G synonymous_variant 0.33
rpoC 764435 c.1066A>C synonymous_variant 0.33
rpoC 764446 p.Asp359Glu missense_variant 0.38
rpoC 764450 p.Gly361Arg missense_variant 0.33
rpoC 764461 p.Glu364Asp missense_variant 0.27
rpoC 764468 p.Val367Ile missense_variant 0.27
rpoC 764471 p.Asn368Arg missense_variant 0.3
rpoC 764485 c.1116G>C synonymous_variant 0.3
rpoC 764491 c.1122G>T synonymous_variant 0.25
rpoC 764497 c.1128A>G synonymous_variant 0.25
rpoC 764498 p.Ser377Ala missense_variant 0.25
rpoC 764506 c.1137C>T synonymous_variant 0.23
rpoC 764575 c.1206T>C synonymous_variant 0.25
rpoC 764576 p.Ser403Ala missense_variant 0.25
rpoC 764581 c.1212T>C synonymous_variant 0.33
rpoC 764582 p.Leu405Met missense_variant 0.38
rpoC 764587 c.1218C>G synonymous_variant 0.41
rpoC 764605 c.1236G>C synonymous_variant 0.6
rpoC 764611 c.1242G>C synonymous_variant 0.62
rpoC 764632 c.1263T>C synonymous_variant 0.73
rpoC 764650 c.1281G>C synonymous_variant 0.74
rpoC 764672 p.Gln435Glu missense_variant 0.79
rpoC 764677 c.1308C>G synonymous_variant 0.79
rpoC 764695 c.1326T>C synonymous_variant 0.73
rpoC 764701 c.1332C>G synonymous_variant 0.68
rpoC 764705 p.Leu446Lys missense_variant 0.6
rpoC 764716 c.1347G>C synonymous_variant 0.57
rpoC 764735 p.Val456Met missense_variant 0.17
rpoC 766817 p.His1150Asn missense_variant 0.2
rpoC 766843 c.3474T>C synonymous_variant 0.2
rpoC 766846 c.3477C>G synonymous_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303911 c.981G>A synonymous_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472089 n.244C>T non_coding_transcript_exon_variant 0.38
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.78
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.88
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.88
rrs 1472129 n.284G>A non_coding_transcript_exon_variant 0.88
rrs 1472135 n.290C>T non_coding_transcript_exon_variant 0.88
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.88
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.88
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.88
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.87
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.89
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.93
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.92
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.85
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.79
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.79
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.75
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.74
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.74
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.74
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.69
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.22
rrs 1472698 n.853A>C non_coding_transcript_exon_variant 0.43
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.73
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.75
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.76
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.77
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.76
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.76
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.76
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.74
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.75
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.81
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.25
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.25
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.25
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.22
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.22
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.22
rrl 1474770 n.1113G>A non_coding_transcript_exon_variant 0.18
rrl 1474774 n.1117A>T non_coding_transcript_exon_variant 0.22
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.22
rrl 1474780 n.1123C>A non_coding_transcript_exon_variant 0.22
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.22
rrl 1474801 n.1145delT non_coding_transcript_exon_variant 0.5
rrl 1474825 n.1168G>C non_coding_transcript_exon_variant 0.55
rrl 1474828 n.1171G>C non_coding_transcript_exon_variant 0.5
rrl 1474832 n.1176delG non_coding_transcript_exon_variant 0.55
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.5
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.42
rrl 1474875 n.1218G>A non_coding_transcript_exon_variant 0.38
rrl 1474876 n.1219T>A non_coding_transcript_exon_variant 0.38
rrl 1474883 n.1226T>C non_coding_transcript_exon_variant 0.36
rrl 1475791 n.2134A>G non_coding_transcript_exon_variant 0.57
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.44
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.44
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.5
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.5
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.88
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.89
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.88
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.88
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.91
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.91
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.92
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.91
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.93
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.93
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.94
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.92
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.93
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.93
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.91
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.83
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.78
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.5
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.73
rrl 1476569 n.2912G>A non_coding_transcript_exon_variant 0.73
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.73
rrl 1476584 n.2927C>G non_coding_transcript_exon_variant 0.69
rrl 1476586 n.2929C>G non_coding_transcript_exon_variant 0.69
rrl 1476588 n.2931A>T non_coding_transcript_exon_variant 0.69
rrl 1476595 n.2938C>G non_coding_transcript_exon_variant 0.69
rrl 1476602 n.2945G>C non_coding_transcript_exon_variant 0.73
rrl 1476607 n.2950C>G non_coding_transcript_exon_variant 0.73
rrl 1476608 n.2951C>T non_coding_transcript_exon_variant 0.73
rrl 1476611 n.2954T>A non_coding_transcript_exon_variant 0.73
rrl 1476613 n.2956G>C non_coding_transcript_exon_variant 0.73
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.69
rrl 1476621 n.2964C>T non_coding_transcript_exon_variant 0.69
rrl 1476624 n.2967T>A non_coding_transcript_exon_variant 0.69
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.69
rrl 1476630 n.2973A>G non_coding_transcript_exon_variant 0.69
rrl 1476645 n.2988A>G non_coding_transcript_exon_variant 0.65
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2155002 c.1110G>T synonymous_variant 0.67
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.92
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
rpoA 3878413 p.Tyr32Phe missense_variant 0.4
clpC1 4040032 p.Val225Ile missense_variant 0.5
clpC1 4040033 c.672G>C synonymous_variant 0.5
clpC1 4040045 c.660C>G synonymous_variant 0.5
clpC1 4040066 c.639G>C synonymous_variant 0.44
clpC1 4040090 c.615T>G synonymous_variant 0.43
clpC1 4040093 c.612C>G synonymous_variant 0.43
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248495 p.Pro661Gln missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0