TB-Profiler result

Run: SRR13861575
Summary

Run ID: SRR13861575

Sample name:

Date: 03-04-2023 09:35:15

Number of reads: 277708

Percentage reads mapped: 27.8

Strain: lineage4.9

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
lineage4.9 Euro-American (H37Rv-like) T1 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
rrs 1472307 n.462C>T non_coding_transcript_exon_variant 0.17 streptomycin
ethA 4327340 p.Trp45* stop_gained 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 7637 c.336C>G synonymous_variant 0.17
gyrA 8646 p.Gln449Lys missense_variant 1.0
gyrA 8786 c.1485T>C synonymous_variant 0.18
gyrA 9138 p.Gln613Lys missense_variant 1.0
gyrA 9597 c.2296T>C synonymous_variant 0.25
gyrA 9604 p.Val768Ala missense_variant 0.89
mshA 575771 p.Val142Phe missense_variant 0.18
ccsA 620748 c.858T>G synonymous_variant 1.0
rpoB 761327 c.1521A>G synonymous_variant 0.25
rpoB 761373 p.Val523His missense_variant 0.22
rpoB 761414 c.1608A>G synonymous_variant 0.22
rpoB 761423 c.1617T>C synonymous_variant 0.22
rpoB 761853 p.Ile683Val missense_variant 0.89
rpoB 762053 c.2247T>C synonymous_variant 0.17
rpoB 762062 c.2256T>C synonymous_variant 0.17
rpoB 762065 c.2259T>C synonymous_variant 0.17
rpoB 762083 c.2277T>C synonymous_variant 0.14
rpoB 762086 c.2280G>C synonymous_variant 0.13
rpoC 763765 c.396T>C synonymous_variant 0.25
rpoC 764995 c.1626C>G synonymous_variant 0.18
rpoC 765625 c.2256C>G synonymous_variant 0.22
rpoC 765628 c.2259G>C synonymous_variant 0.22
rpoC 765631 p.Asp754Glu missense_variant 0.22
rpoC 765658 c.2289C>T synonymous_variant 0.18
rpoC 765700 c.2331T>C synonymous_variant 0.2
rpoC 765734 c.2365T>C synonymous_variant 0.25
rpoC 765739 c.2370G>C synonymous_variant 0.25
rpoC 765751 c.2382C>G synonymous_variant 0.22
rpoC 765753 p.Asp795Ala missense_variant 0.22
rpoC 767098 c.3729T>C synonymous_variant 0.18
rpoC 767119 c.3750A>G synonymous_variant 0.22
rpoC 767134 c.3765C>G synonymous_variant 0.18
rpoC 767158 c.3789T>C synonymous_variant 0.15
rpoC 767167 c.3798C>G synonymous_variant 0.17
rpoC 767180 p.Ala1271Gln missense_variant 0.17
rpoC 767191 c.3822C>G synonymous_variant 0.17
mmpL5 777509 c.972G>T synonymous_variant 1.0
mmpS5 779508 c.-603G>C upstream_gene_variant 1.0
rpsL 781898 c.339A>T synonymous_variant 0.12
rpsL 781916 c.357T>C synonymous_variant 0.13
rpsL 781929 p.Gly124Ser missense_variant 0.13
rplC 800814 c.6A>G synonymous_variant 0.29
rplC 800817 c.9A>T synonymous_variant 0.29
rplC 800844 c.36T>C synonymous_variant 0.29
rplC 800865 c.57A>G synonymous_variant 0.33
rplC 800867 p.Ser20Asn missense_variant 0.33
rplC 800874 c.66A>G synonymous_variant 0.4
rplC 800877 c.69A>C synonymous_variant 0.4
rplC 800880 c.72A>G synonymous_variant 0.4
rplC 800889 c.81C>G synonymous_variant 0.5
rplC 800907 c.99C>G synonymous_variant 0.4
rplC 800916 c.108A>G synonymous_variant 0.4
rplC 801301 c.493C>A synonymous_variant 0.17
Rv1258c 1406081 c.1260A>T stop_lost&splice_region_variant 0.17
Rv1258c 1406904 c.436dupT frameshift_variant 1.0
Rv1258c 1407127 p.Arg72Ser missense_variant 1.0
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 1.0
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.22
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.22
rrl 1474009 n.352A>G non_coding_transcript_exon_variant 0.22
rrl 1474012 n.355C>T non_coding_transcript_exon_variant 0.22
rrl 1474103 n.446A>T non_coding_transcript_exon_variant 0.33
rrl 1474104 n.447G>A non_coding_transcript_exon_variant 0.33
rrl 1474111 n.454T>C non_coding_transcript_exon_variant 0.33
rrl 1474112 n.455T>A non_coding_transcript_exon_variant 0.33
rrl 1475199 n.1542G>A non_coding_transcript_exon_variant 0.22
rrl 1475206 n.1549C>T non_coding_transcript_exon_variant 0.22
rrl 1475209 n.1552G>C non_coding_transcript_exon_variant 0.22
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.22
rrl 1475249 n.1592T>C non_coding_transcript_exon_variant 0.22
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.25
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.29
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.18
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.2
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.2
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.2
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.22
rrl 1475638 n.1981C>T non_coding_transcript_exon_variant 0.2
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.2
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.27
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.27
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.29
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.3
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.5
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.5
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.5
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.54
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.53
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.53
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.53
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.53
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.53
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.57
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.53
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.62
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.67
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.53
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.53
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.47
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.47
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.43
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.43
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.2
rrl 1476689 n.3032A>T non_coding_transcript_exon_variant 0.25
rrl 1476690 n.3033C>T non_coding_transcript_exon_variant 0.25
rrl 1476693 n.3036G>A non_coding_transcript_exon_variant 0.25
rrl 1476695 n.3038T>A non_coding_transcript_exon_variant 0.2
rrl 1476716 n.3059A>T non_coding_transcript_exon_variant 0.29
rrl 1476723 n.3066T>A non_coding_transcript_exon_variant 0.25
rrl 1476725 n.3068C>T non_coding_transcript_exon_variant 0.25
rrl 1476726 n.3069A>G non_coding_transcript_exon_variant 0.25
rrl 1476732 n.3075T>C non_coding_transcript_exon_variant 0.25
inhA 1674552 c.351C>G synonymous_variant 1.0
rpsA 1834079 p.Arg180Cys missense_variant 1.0
PPE35 2168448 p.Gln722Pro missense_variant 1.0
Rv1979c 2221876 p.Val430Glu missense_variant 1.0
kasA 2518036 c.-78delG upstream_gene_variant 0.95
kasA 2518088 c.-27T>A upstream_gene_variant 1.0
eis 2714449 p.Trp295Ser missense_variant 1.0
eis 2714773 p.Pro187Gln missense_variant 1.0
eis 2715525 c.-193G>T upstream_gene_variant 1.0
ahpC 2726611 c.419_420insA frameshift_variant 1.0
folC 2747455 c.144C>A synonymous_variant 1.0
pepQ 2859723 c.696T>C synonymous_variant 1.0
ribD 2987540 c.702G>T synonymous_variant 1.0
thyX 3067515 p.Ser144Thr missense_variant 0.29
thyX 3067526 c.420C>G synonymous_variant 0.29
thyX 3067530 p.Ala139Ser missense_variant 0.29
fbiD 3339321 c.204G>A synonymous_variant 1.0
fprA 3474339 p.Met111Ile missense_variant 1.0
fprA 3474353 c.348delT frameshift_variant 1.0
rpoA 3878040 c.468T>C synonymous_variant 0.21
rpoA 3878046 c.462T>C synonymous_variant 0.13
rpoA 3878049 c.459G>C synonymous_variant 0.14
rpoA 3878055 c.453A>G synonymous_variant 0.14
rpoA 3878061 c.447G>C synonymous_variant 0.14
rpoA 3878070 c.438T>C synonymous_variant 0.14
rpoA 3878082 c.426T>C synonymous_variant 0.12
rpoA 3878100 c.408C>G synonymous_variant 0.12
rpoA 3878103 c.405A>G synonymous_variant 0.12
rpoA 3878106 c.402G>C synonymous_variant 0.12
rpoA 3878118 c.390T>C synonymous_variant 0.12
rpoA 3878169 c.339G>C synonymous_variant 0.18
rpoA 3878184 c.324C>T synonymous_variant 0.2
rpoA 3878187 c.321C>G synonymous_variant 0.2
rpoA 3878193 c.315T>C synonymous_variant 0.22
rpoA 3878199 c.309T>C synonymous_variant 0.22
rpoA 3878202 c.306G>C synonymous_variant 0.22
rpoA 3878217 c.291A>G synonymous_variant 0.25
rpoA 3878220 c.288C>T synonymous_variant 0.25
rpoA 3878271 c.237T>C synonymous_variant 0.21
rpoA 3878284 p.Glu75Ala missense_variant 0.2
rpoA 3878292 c.216T>C synonymous_variant 0.21
rpoA 3878298 c.210A>G synonymous_variant 0.15
rpoA 3878304 c.204G>C synonymous_variant 0.17
rpoA 3878313 c.195G>C synonymous_variant 0.25
rpoA 3878322 c.186A>G synonymous_variant 0.18
rpoA 3878331 c.177A>G synonymous_variant 0.18
rpoA 3878334 c.174T>C synonymous_variant 0.18
rpoA 3878337 c.171T>C synonymous_variant 0.27
rpoA 3878346 c.162T>C synonymous_variant 0.17
clpC1 4038436 p.Ala757Ser missense_variant 1.0
clpC1 4039682 c.1023C>G synonymous_variant 0.14
clpC1 4039685 c.1020C>T synonymous_variant 0.15
clpC1 4039694 c.1011G>C synonymous_variant 0.2
clpC1 4039724 c.981A>G synonymous_variant 0.17
clpC1 4039748 c.957G>C synonymous_variant 0.17
clpC1 4039751 c.954A>G synonymous_variant 0.17
clpC1 4039757 c.948A>G synonymous_variant 0.17
clpC1 4039760 c.945T>C synonymous_variant 0.17
clpC1 4039766 c.939T>C synonymous_variant 0.17
clpC1 4039769 c.936C>G synonymous_variant 0.17
clpC1 4039778 c.927A>G synonymous_variant 0.18
clpC1 4039781 c.924G>C synonymous_variant 0.15
clpC1 4039787 c.916_918delTCGinsAGC synonymous_variant 0.17
clpC1 4039793 c.912C>G synonymous_variant 0.18
embC 4240706 p.Val282Met missense_variant 0.2
embC 4240819 c.957A>G synonymous_variant 0.15
embC 4240825 c.963G>A synonymous_variant 0.15
embC 4240831 c.969T>G synonymous_variant 0.15
embC 4240867 c.1005T>G synonymous_variant 0.15
embC 4240870 c.1008T>C synonymous_variant 0.15
embC 4240879 c.1017G>C synonymous_variant 0.14
embC 4240880 p.Ala340Thr missense_variant 0.15
embC 4240885 c.1023T>C synonymous_variant 0.14
embC 4240897 c.1035C>G synonymous_variant 0.15
embC 4240900 c.1038A>G synonymous_variant 0.15
embC 4240945 c.1083T>C synonymous_variant 0.18
embC 4240951 c.1089C>G synonymous_variant 0.18
embC 4240954 p.Ile364Met missense_variant 0.2
embC 4240996 c.1134G>C synonymous_variant 0.18
embC 4241017 c.1155T>C synonymous_variant 0.2
embC 4241023 c.1161T>G synonymous_variant 0.15
embC 4241026 c.1164C>G synonymous_variant 0.15
embC 4241035 c.1173G>A synonymous_variant 0.17
embC 4241050 c.1188T>G synonymous_variant 0.2
embC 4242635 p.Ala925Ser missense_variant 1.0
embB 4249145 c.2634delC frameshift_variant 1.0
embB 4249483 c.2970C>G synonymous_variant 0.12
embB 4249487 c.2974T>C synonymous_variant 0.12
embB 4249521 p.Ala1003Val missense_variant 0.12
embB 4249532 p.Ala1007Thr missense_variant 0.13
embB 4249558 c.3045A>C synonymous_variant 0.14
embB 4249564 c.3051C>T synonymous_variant 0.13
embB 4249568 p.Ser1019Thr missense_variant 0.13
ubiA 4269803 p.Ala11Pro missense_variant 1.0
ethA 4326689 p.Lys262Thr missense_variant 1.0
ethA 4326849 p.Pro209Thr missense_variant 1.0