Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	2,982,682	(A)8→7	coding (20/483 nt)	BW25113_RS14815 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,982,675	0	A	.	97.8%	190.6 / ‑1.9	45	coding (13/483 nt)	BW25113_RS14815	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base . (22/22);  total (23/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.53e-01

TCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCTTACCGTGAGGTTAATCGTGATTGATTATAAAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGTTTATTCTCTTCACTGTCTATTCTTACACTGCAGAAAAAATGATATATAACGAAACATGCACTGCAAATTGGGTAATTTTTAATGACCAGGG  >  NZ_CP009273/2982555‑2982805                                                                                                                         |                                                                                                                                   tCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCTTACCGTGAGGTTAATCGTGATTGATTAT‑AAAAAAACTTAttatttat                                                                                                                 >  1:794593/1‑139 (MQ=255)  cccTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCTTACCGTGAGGTTAATCGTGATTGATTAT‑AAAAAAACTTATtatttatt                                                                                                                >  1:179681/1‑139 (MQ=255)  cccTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCTTACCGTGAGGTTAATCGTGATTGATTAT‑AAAAAAACTTATtatttatt                                                                                                                >  1:664387/1‑139 (MQ=255)   ccTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCTTACCGTGAGGTTAATCGTGATTGATTAT‑AAAAAAACTTATTatttattt                                                                                                               <  1:534516/139‑1 (MQ=255)                 cTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCTTACCGTGAGGTTAATCGTGATTGATTAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAGt                                                                                                 >  2:24031/1‑139 (MQ=255)                    aCCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCTTACCGTGAGGTTAATCGTGATTGATTAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAGTg                                                                                                <  1:82298/137‑1 (MQ=255)                     ccGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCTTACCGTGAGGTTAATCGTGATTGATTAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGt                                                                                             <  1:1233135/139‑1 (MQ=255)                     ccGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCTTACCGTGAGGTTAATCGTGATTGATTAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGt                                                                                             <  2:851512/139‑1 (MQ=255)                     ccGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCTTACCGTGAGGTTAATCGTGATTGATTAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGt                                                                                             <  1:896904/139‑1 (MQ=255)                         ggATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCTTACCGTGAGGTTAATCGTGATTGATTAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGTTTAt                                                                                         >  1:305291/1‑139 (MQ=255)                           atgatTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCTTACCGTGAGGTTAATCGTGATTGATTAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGTTTATtc                                                                                       <  1:477952/139‑1 (MQ=255)                                  ttATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCTTACCGTGAGGTTAATCGTGATTGATTAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGTTTATTCTCTTCa                                                                                 <  1:901263/138‑1 (MQ=255)                                    aTGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCTTACCGTGAGGTTAATCGTGATTGATTAT‑AAAAAAACTTATTATTTATTTTAGTTGTTATCAGTGGGTTTATTCTCTTCACTg                                                                              >  2:1163283/1‑139 (MQ=255)                                       gCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCTTACCGTGAGGTTAATCGTGATTGATTAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGTTTATTCTCTTCACTGTc                                                                            <  2:812915/138‑1 (MQ=255)                                       gCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCTTACCGTGAGGTTAATCGTGATTGATTAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGTTTATTCTCTTCACTGTc                                                                            <  2:179681/138‑1 (MQ=255)                                                           ccAACATGAAGTGGCAAACTGTTTAACCCTGTCTTACCGTGAGGTTAATCGTGATTGATTAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGTTTATTCTCTTCACTGTCTATTCTTACACTGCAGaaaaa                                                       <  2:794593/139‑1 (MQ=255)                                                               cATGAAGTGGCAAACTGTTTAACCCTGTCTTACCGTGAGGTTAATCGTGATTGATTATAAAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGTTTATTCTCTTCACTGTCTATTCTTACACTGCAGAAAAAAt                                                     >  2:1010441/1‑138 (MQ=255)                                                                        gCAAACTGTTTAACCCTGTCTTACCGTGAGGTTAATCGTGATTGATTAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGTTTATTCTCTTCACTGTCTATTCTTACACTGCAGAAAAAATGATATATAAc                                           <  2:774889/138‑1 (MQ=255)                                                                                          tCTTACCGTGAGGTTAATCGTGATTGATTAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAg                                                                                                  >  2:99177/1‑65 (MQ=255)                                                                                          tCTTACCGTGAGGTTAATCGTGATTGATTAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAg                                                                                                  <  1:99177/65‑1 (MQ=255)                                                                                          tCTTACCGTGAGGTTAATCGTGATTGATTAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGTTTATtc                                                                                       >  2:1027162/1‑76 (MQ=255)                                                                                          tCTTACCGTGAGGTTAATCGTGATTGATTAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGTTTATtc                                                                                       <  1:1027162/76‑1 (MQ=255)                                                                                          tCTTACCGTGAGGTTAATCGTGATTGATTAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGTTTATTCTCTTCACTGTc                                                                            >  1:1231693/1‑87 (MQ=255)                                                                                          tCTTACCGTGAGGTTAATCGTGATTGATTAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGTTTATTCTCTTCACTGTc                                                                            <  2:1231693/87‑1 (MQ=255)                                                                                          tCTTACCGTGAGGTTAATCGTGATTGATTAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGTTTATTCTCTTCACTGTCTATTCTTACACTGc                                                              >  2:146237/1‑101 (MQ=255)                                                                                          tCTTACCGTGAGGTTAATCGTGATTGATTAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGTTTATTCTCTTCACTGTCTATTCTTACACTGc                                                              <  1:146237/101‑1 (MQ=255)                                                                                          tCTTACCGTGAGGTTAATCGTGATTGATTAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGTTTATTCTCTTCACTGTCTATTCTTACACTGCAGAAAAAATGATATATAACGAAACATGCACTGCAAAtt                        >  1:1175204/1‑139 (MQ=255)                                                                                          tCTTACCGTGAGGTTAATCGTGATTGATTAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGTTTATTCTCTTCACTGTCTATTCTTACACTGCAGAAAAAATGATATATAACGAAACATGCACTGCAAAtt                        >  2:657912/1‑139 (MQ=255)                                                                                          tCTTACCGTGAGGTTAATCGTGATTGATTAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGTTTATTCTCTTCACTGTCTATTCTTACACTGCAGAAAAAATGATATATAACGAAACATGCACTGCAAAtt                        >  1:1254301/1‑139 (MQ=255)                                                                                                    aGGTTAATCGTGATTGATTAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGTTTATTCTCTTCACTGTCTATTCTTACACTGCAGAAAAAATGATATATAACGAAACATGCACTGCAAATTGGGTAAtttt              >  1:826468/1‑139 (MQ=255)                                                                                                    aGGTTAATCGTGATTGATTAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGTTTATTCTCTTCACTGTCTATTCTTACACTGCAGAAAAAATGATATATAACGAAACATGCACTGCAAATTGGGTAAtttt              >  1:707160/1‑139 (MQ=255)                                                                                                    aGGTTAATCGTGATTGATTAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGTTTATTCTCTTCACTGTCTATTCTTACACTGCAGAAAAAATGATATATAACGAAACATGCACTGCAAATTGGGTAAtttt              >  1:997135/1‑139 (MQ=255)                                                                                                    aGGTTAATCGTGATTGATTAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGTTTATTCTCTTCACTGTCTATTCTTACACTGCAGAAAAAATGATATATAACGAAACATGCACTGCAAATTGGGTAAtttt              >  2:332455/1‑139 (MQ=255)                                                                                                      gTTAATCGTGATTGATTAT‑AAAAAAACTTGTTATTTATTTTAGTTTTTATCAGTGGGTTTATTCTCTTc                                                                                  >  2:489429/1‑69 (MQ=255)                                                                                                      gTTAATCGTGATTGATTAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGTTTATTCTCTTc                                                                                  <  1:489429/69‑1 (MQ=255)                                                                                                      gTTAATCGTGATTGATTAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGTTTATTCTCTTCACTGTCTATTCTTACACTGCAGAAAAAATGATATATAACGAAACATGCACTGCAAATTGGGTAAttttt             >  1:867039/1‑138 (MQ=255)                                                                                                      gTTAATCGTGATTGATTAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGTTTATTCTCTTCACTGTCTATTCTTACACTGCAGAAAAAATGATATATAACGAAACATGCACTGCAAATTGGGTAATTTTTa            <  2:1254301/139‑1 (MQ=255)                                                                                                      gTTAATCGTGATTGATTAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGTTTATTCTCTTCACTGTCTATTCTTACACTGCAGAAAAAATGATATATAACGAAACATGCACTGCAAATTGGGTAATTTTTa            <  2:664387/139‑1 (MQ=255)                                                                                                      gTTAATCGTGATTGATTAT‑AAAAAAACTTATTATTTATTTTAGTTGTTATCAGTGGGTTTATTCTCTTCACTGTCTATTCTTACACTGCAGAAAAAATGATATATAACGAAACATGCACTGCAAATTGGGTAATTTTTa            <  1:1163283/139‑1 (MQ=255)                                                                                                         aaTCGTGATTGATTAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGTTTATTCTCTTCACTGTCTATTCTTACACTGCAGAAAAAATGATATATAACGAAACATGCACTGCAAATTGGGTAATTTTTAAt          >  1:1088669/1‑138 (MQ=255)                                                                                                           tCGTGATTGATTAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGTTTATTCTCTTCACTGTCTATTCTTACACTGCAGAAAAAATGATATATAACGAAACATGCACTGCAAATTGGGTAATTTTTAATGAc       <  1:226858/139‑1 (MQ=255)                                                                                                                attgattAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGTTTATTCTCTTCACTGTCTATTCTTACACTGCAGAAAAAATGATATATAACGAAACATGCACTGCAAATTGGGTAATTTTTAATGACCAggg  <  1:24031/139‑1 (MQ=255)                                                                                                                attgattAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGTTTATTCTCTTCACTGTCTATTCTTACACTGCAGAAAAAATGATATATAACGAAACATGCACTGCAAATTGGGTAATTTTTAATGACCAgg   >  1:865564/1‑138 (MQ=255)                                                                                                                    attAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGTTTATTCTCTTCACTGTCTATTCTTACACTGCAGaaa                                                         >  2:1011618/1‑80 (MQ=255)                                                                                                                    attAT‑AAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGTTTATTCTCTTCACTGTCTATTCTTACACTGCAGaaa                                                         <  1:1011618/80‑1 (MQ=255)                                                                                                                         |                                                                                                                                   TCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCCTGTCTTACCGTGAGGTTAATCGTGATTGATTATAAAAAAAACTTATTATTTATTTTAGTTTTTATCAGTGGGTTTATTCTCTTCACTGTCTATTCTTACACTGCAGAAAAAATGATATATAACGAAACATGCACTGCAAATTGGGTAATTTTTAATGACCAGGG  >  NZ_CP009273/2982555‑2982805

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑