Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP002416	2,704,360	(T)5→6	intergenic (‑891/+1396)	Clo1313_2294 ← / ← Clo1313_2296	two component transcriptional regulator, winged helix family/flavin reductase domain protein FMN‑binding protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP002416	2,704,360	1	.	T	100.0%	45.8 / NA	25	intergenic (‑891/+1396)	Clo1313_2294/Clo1313_2296	two component transcriptional regulator, winged helix family/flavin reductase domain protein FMN‑binding protein
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base T (16/9);  total (16/9)

TTTCATCAAGATATCTGCTAACTGTTTTTCTATTAAGCCCGGTACGCCTGGATATCTCTCTATTACTCAAACCTATTCCCTTTAACTCCCGCACCTCATTTACACGTTCCATTTTTTGCTTTACTCTTTCTTCATGTATGATCATCTTTTT‑GTCTGGAATGACTTTTCCCTTTTTC  >  CP002416/2704210‑2704385                                                                                                                                                        |                          tttCATCAAGATATCTGCTAACTGTTTTTCTATTAAGCCCGGTACGCCTGGATATCTCTCTATTACTCAAACCTATTCCCTTTAACTCCCGCACCTCATTTACACGTTCCATTTTTTGCTTTACTCTTTCTTCATGTATGATCATCttttt                            <  1:142371/151‑1 (MQ=38)  ttCATCAAGATATCTGCTAACTGTTTTTCTATTAAGCCCGGTACGCCTGGATATCTCTCTATTACTCAAACCTATTCCCTTTAACTCCCGCACCTCATTTACACGTTCCATTTTTTGCTTTACTCTTTCTTCATGTATGATCATCtttttt                           >  1:1291888/1‑150 (MQ=38)  ttCATCAAGATATCTGCTAACTGTTTTTCTATTAAGCCCGGTACGCCTGGATATCTCTCTATTACTCAAACCTATTCCCTTTAACTCCCGCACCTCATTTACACGTTCCATTTTTTGCTTTACTCTTTCTTCATGTATGATCATCtttttt                           >  1:3420510/1‑150 (MQ=38)      tcaAGATATCTGCTAACTGTTTTTCTATTAAGCCCGGTACGCCTGGATATCTCTCTATTACTCAAACCTATTCCCTTTAACTCCCGCACCTCATTTACACGTTCCATTTTTTGCTTTACTCTTTCTTCATGTATGATCATCttttttgtct                       >  1:981922/1‑146 (MQ=21)        aaGATATCTGCTAACTGTTTTTCTATTAAGCCCGGTACGCCTGGATATCTCTCTATTACTCAAACCTATTCCCTTTAACTCCCGCACCTCATTTACACGTTCCATTTTTTGCTTTACTCTTTCTTCATGTATGATCATCTTTTTTGTCTgg                     <  1:2576667/151‑1 (MQ=18)        aaGATATCTGCTAACTGTTTTTCTATTAAGCCCGGTACGCCTGGATATCTCTCTATTACTCAAACCTATTCCCTTTAACTCCCGCACCTCATTTACACGTTCCATTTTTTGCTTTACTCTTTCTTCATGTATGATCATCTTTTTTGTCTgg                     <  1:1424264/151‑1 (MQ=18)         aGATATCTGCTAACTGTTTTTCTATTAAGCCCGGTACGCCTGGATATCTCTCTATTACTCAAACCTATTCCCTTTAACTCCCGCACCTCATTTACACGTTCCATTTTTTGCTTTACTCTTTCTTCATGTATGATCATCTTTTTTGTCTGGa                    >  1:1613164/1‑151 (MQ=18)          gATATCTGCTAACTGTTTTTCTATTAAGCCCGGTACGCCTGGATATCTCTCTATTACTCAAACCTATTCCCTTTAACTCCCGCACCTCATTTACACGTTCCATTTTTTGCTTTACTCTTTCTTCATGTATGATCATCTTTTTTGTCTGGaa                   >  1:3469411/1‑151 (MQ=18)           atatCTGCTAACTGTTTTTCTATTAAGCCCGGTACGCCTGGATATCTCTCTATTACTCAAACCTATTCCCTTTAACTCCCGCACCTCATTTACACGTTCCATTTTTTGCTTTACTCTTTCTTCATGTATGATCATCTTTTTTGTCTGGAAt                  >  1:1194283/1‑151 (MQ=18)           atatCTGCTAACTGTTTTTCTATTAAGCCCGGTACGCCTGGATATCTCTCTATTACTCAAACCTATTCCCTTTAACTCCCGCACCTCATTTACACGTTCCATTTTTTGCTTTACTCTTTCTTCATGTATGATCATCTTTTTTGTCTGGAAt                  >  1:1423731/1‑151 (MQ=18)             atCTGCTAACTGTTTTTCTATTAAGCCCGGTACGCCTGGATATCTCTCTATTACTCAAACCTATTCCCTTTAACTCCCGCACCTCATTTACACGTTCCATTTTTTGCTTTACTCTTTCTTCATGTATGATCATCTTTTTTGTCTGGAATGa                >  1:2796746/1‑151 (MQ=18)              tCTGCTAACTGTTTTTCTATTAAGCCCGGTACGCCTGGATATCTCTCTATTACTCAAACCTATTCCCTTTAACTCCCGCACCTCATTTACACGTTCCATTTTTTGCTTTACTCTTTCTTCATGTATGATCATCTTTTTTGTCTGGAATGAc               >  1:124104/1‑151 (MQ=18)                tGCTAACTGTTTTTCTATTAAGCCCGGTACGCCTGGATATCTCTCTATTACTCAAACCTATTCCCTTTAACTCCCGCACCTCATTTACACGTTCCATTTTTTGCTTTACTCTTTCTTCATGTATGATCATCTTTTTTGTCTGGAATGACtt             >  1:250519/1‑151 (MQ=17)                 gCTAACTGTTTTTCTATTAAGCCCGGTACGCCTGGATATCTCTCTATTACTCAAACCTATTCCCTTTAACTCCCGCACCTCATTTACACGTTCCATTTTTTGCTTTACTCTTTCTTCATGTATGATCATCTTTTTTGTCTGGAATGACttt            >  1:2936574/1‑151 (MQ=14)                 gCTAACTGTTTTTCTATTAAGCCCGGTACGCCTGGATATCTCTCTATTACTCAAACCTATTCCCTTTAACTCCCGCACCTCATTTACACGTTCCATTTTTTGCTTTACTCTTTCTTCATGTATGATCATCTTTTTTGTCTGGAATGACttt            >  1:2132361/1‑151 (MQ=14)                 gCTAACTGTTTTTCTATTAAGCCCGGTACGCCTGGATATCTCTCTATTACTCAAACCTATTCCCTTTAACTCCCGCACCTCATTTACACGTTCCATTTTTTGCTTTACTCTTTCTTCATGTATGATCATCTTTTTTGTCTGGAATGACttt            <  1:2438028/151‑1 (MQ=14)                 gCTAACTGTTTTTCTATTAAGCCCGGCACGCCTGGATATCTCTCTATTACTCAAACCTATTCCCTTTAACTCCCGCACCTCATTTACACGTTCCATTTTTTGCTTTACTCTTTCTTCATGTATGATCATCTTTTTTGTCTGGAATGACttt            >  1:1125565/1‑151 (MQ=9)                  cTAACTGTTTTTCTATTAAGCCCGGTACGCCTGGATATCTCTCTATTACTCAAACCTATTCCCTTTAACTCCCGCACCTCATTTACACGTTCCATTTTTTGCTTTACTCTTTCTTCATGTATGATCATCTTTTTTGTCTGGAATGACtttt           <  1:336787/151‑1 (MQ=14)                    aaCTGTTTTTCTATTAAGCCCGGTACGCCTGGATATCTCTCTATTACTCAAACCTATTCCCTTTAACTCCCGCACCTCATTTACACGTTCCATTTTTTGCTTTACTCTTTCTTCATGTATGATCATCTTTTTTGTCTGGAATGACTTTTcc         <  1:2862952/151‑1 (MQ=14)                    aaCTGTTTTTCTATTAAGCCCGGTACGCCTGGATATCTCTCTATTACTCAAACCTATTCCCTTTAACTCC‑GCACCTCATTTACACGTTCCATTTTTTGCTTTACTCTTTCTTCATGTATGATCATCTTTTTTGTCTGGAATGACTTTTccc        >  1:2012805/1‑151 (MQ=9)                     aCTGTTTTTCTATTAAGCCCGGTACGCCTGGATATCTCTCTATTACTCAAACCTATTCCCTTTAACTCCCGCACCTCATTTACACGTTCCATTTTTTGCTTTACTCTTTCTTCATGTATGATCATCTTTTTTGTCTGGAATGACTTTTccc        <  1:2890604/151‑1 (MQ=14)                       tGTTTTTCTATTAAGCCCGGTACGCCTGGATATCTCTCTATTACTCAAACCTATTCCCTTTAACTCCCGCACCTCATTTACACGTTCCATTTTTTGCTTTACTCTTTCTTCATGTATGATCATCTTTTTTGTCTGGAATGACTTTTCCCtt      >  1:240704/1‑151 (MQ=14)                       tGTTTTTCTATTAAGCCCGGTACGCCTGGATATCTCTCTATTACTCAAACCTATTCCCTTTAACTCCCGCACCTCATTTACACGTTCCATTTTTTGCTTTACTCTTTCTTCATGTATGATCATCTTTTTTGTCTGGAATGACTTTTCCCtt      >  1:1656211/1‑151 (MQ=14)                        gTTTTTCTATTAAGCCCGGTACGCCTGGATATCTCTCTATTACTCAAACCTATTCCCTTTAACTCCCGCACCTCATTTACACGTTCCATTTTTTGCTTTACTCTTTCTTCATGTATGATCATCTTTTTTGTCTGGAATGACTTTTCCCttt     >  1:666816/1‑151 (MQ=14)                         tttttCTATTAAGCCCGGTACGCCTGGATATCTCTCTATTACTCAAACCTATTCCCTTTAACTCCCGCACCTCATTTACACGTTCCATTTTTTGCTTTACTCTTTCTTCATGTATGATCATCTTTTTTGTCTGGAATGACTTTTCCCtttt    <  1:2529398/151‑1 (MQ=14)                          ttttCTATTAAGCCCGGTACGCCTGGATATCTCTCTATTACTCAAACCTATTCCCTTTAACTCCCGCACCTCATTTACACGTTCCATTTTTTGCTTTACTCTTTCTTCATGTATGATCATCTTTTTTGTCTGGAATGACTTTTCCCttttt   >  1:1359011/1‑151 (MQ=14)                           tttCTATTAAGCCCGGTACGCCTGGATATCTCTCTATTACTCAAACCTATTCCCTTTAACTCCCGCACCTCATTTACACGTTCCATTTTTTGCTTTACTCTTTCTTCATGTATGATCATCTTTTTTGTCTGGAATGACTTTTCCCtttttt  >  1:1938399/1‑150 (MQ=11)                           tttCTATTAAGCCCGGTACGCCTGGATATCTCTCTATTACTCAAACCTATTCCCTTTAACTCCCGCACCTCATTTACACGTTCCATTTTTTGCTTTACTCTTTCTTCATGTATGATCATCTTTTTTGTCTGGAATGACTTTTCCCtttttt  <  1:951894/151‑2 (MQ=11)                           tttCTATTAAGCCCGGTACGCCTGGATATCTCTCTATTACTCAAACCTATTCCCTTTAACTCCCGCACCTCATTTACACGTTCCATTTTTTGCTTTACTCTTTCTTCATGTATGATCATCTTTTTTGTCTGGAATGACTTTTCCCtttttt  <  1:1544577/151‑2 (MQ=11)                                                                                                                                                        |                          TTTCATCAAGATATCTGCTAACTGTTTTTCTATTAAGCCCGGTACGCCTGGATATCTCTCTATTACTCAAACCTATTCCCTTTAACTCCCGCACCTCATTTACACGTTCCATTTTTTGCTTTACTCTTTCTTCATGTATGATCATCTTTTT‑GTCTGGAATGACTTTTCCCTTTTTC  >  CP002416/2704210‑2704385

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑