Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,417,788	(C)6→7	coding (69/120 nt)	BW25113_RS26130 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,417,782	1	.	C	96.7%	90.9 / ‑2.7	30	coding (75/120 nt)	BW25113_RS26130	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base C (12/17);  total (13/17)
Fisher's exact test for biased strand distribution p-value = 4.33e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.29e-01

TCGTCGTCGGTTGCACATCAAAGCAGTCTGTCAGTCAGTGCGTGAAGCCACCACCGCCTCCGGCGTGGATAATGCAGCCT‑CCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCCGGGAACGACTGGTAATGATGCAGGCCCAACTTGAAGG  >  NZ_CP009273/1417703‑1417864                                                                                 |                                                                                   tcgtcgtcgGTTGCACATCAAAGCAGTCTGTCAGTCAGTGCGTGAAGCCACCACCGCCTCCGGCGTGGATAATGCAGCCT‑cccccccgac                                                                          <  2:1034009/90‑5 (MQ=18) tcgtcgtcgGTTGCACATCAAAGCAGTCTGTCAGTCAGTGCGTGAAGCCACCACCGCCTCCGGCGTGGATAATGCAGCCT‑cccccccgac                                                                          <  2:353072/90‑5 (MQ=18)         ggTTGCACACCAAAGCAGTCTGTCAGTCAGTGCGTGAAGCCACCACCGCCTCCGGCGTGGATAATGCAGCCTCCCCCCCGACTGGCAGac                                                                   <  2:760840/90‑1 (MQ=11)                        cAGTCTGTCAGTCAGTGCGTGAAGCCACCACCGCCTCCGGCGTGGATAATGCAGCCTCCCCCCCGACTGGCAGACACCGCTGAACGGGat                                                    <  2:277080/90‑1 (MQ=255)                        cAGTCTGTCAGTCAGTGCGTGAAGCCACCACCGCCTCCGGCGTGGATAATGCAGCCTCCCCCCCGACTGGCAGACACCGCTGAACGGGat                                                    <  1:491797/90‑1 (MQ=255)                        cAGTCTGTCAGTCAGTGCGTGAAGCCACCACCGCCTCCGGCGTGGATAATGCAGCCTCCCCCCCGACTGGCAGACACCGCTGAACGGGat                                                    <  2:134367/90‑1 (MQ=255)                        cAGTCTGTCAGTCAGTGCGTGAAGCCACCACCGCCTCCGGCGTGGATAATGCAGCCTCCCCCCCGACTGGCAGACACCGCTGAACGGGat                                                    <  2:554640/90‑1 (MQ=255)                          gTCTGTCAGTCAGTGCGTGAAGCCACCACCGCCTCCGGCGTGGATAATGCAGCCTCCCCCCCGACTGGCAGACACCGCTGAACGGGatta                                                  >  2:849709/1‑90 (MQ=255)                          gTCTGTCAGTCAGTGCGTGAAGCCACCACCGCCTCCGGCGTGGATAATGCAGCCTCCCCCCCGACTGGCAGACACCGCTGAACGGGatta                                                  >  1:882517/1‑90 (MQ=255)                          gTCTGTCAGTCAGTGCGTGAAGCCACCACCGCCTCCGGCGTGGATAATGCAGCCTCCCCCCCGACTGGCAGACACCGCTGAACGGGatta                                                  >  2:410065/1‑90 (MQ=255)                          gTCTGTCAGTCAGTGCGTGAAGCCACCACCGCCTCCGGCGTGGATAATGCAGCCT‑cccccc                                                                              >  1:197807/1‑61 (MQ=37)                          gTCTGTCAGTCAGTGCGTGAAGCCACCACCGCCTCCGGCGTGGATAATGCAGCCT‑cccccc                                                                              <  2:197807/61‑1 (MQ=35)                                 agtcagtGCGTGAAGCCACCACCGCCTCCGGCGTGGATAATGCAGCCTCCCCCCCGACTGGCAGACACCGCTGAAc                                                         <  2:752388/76‑1 (MQ=255)                                 agtcagtGCGTGAAGCCACCACCGCCTCCGGCGTGGATAATGCAGCCTCCCCCCCGACTGGCAGACACCGCTGAAc                                                         >  1:752388/1‑76 (MQ=255)                                 agtcagtGCGTGAAGCCACCACCGCCTCCGGCGTGGATAATGCAGCCTCCCCCCCGACTGGCAGACACCCCTGAACGGGATTATTTCAcc                                           >  2:647805/1‑90 (MQ=11)                                    cagtGCGTGAAGCCACCACCGCCTCCGGCGTGGATAATGCAGCCTCCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTc                                        <  2:798777/90‑1 (MQ=255)                                      gtGCGTGAAGCCACCACCGCCTCCGGCGTGGATAATGCAGCCTCCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCCg                                      >  1:1236474/1‑90 (MQ=255)                                        gCGTGAAGCCACCACCGCCTCCGGCGTGGATAATGCAGCCT‑CCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCCGGGa                                   >  1:602122/1‑90 (MQ=255)                                           tGACGCCACCCCCGCCTCCGGCGTGGATAATGCAGCCTCCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCCGGGAAc                                 <  1:1078610/90‑1 (MQ=14)                                           tGAACCCCCCCCCGCCTCCGGCGTGGATAATGCAGCCTCCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCCCCCTCCGGGAAc                                 <  2:777134/90‑1 (MQ=14)                                               gCCACCACCGCCTCCGGCGTGGATAATGCAGCCTCCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCCGGGAACGACt                             <  2:962867/90‑1 (MQ=255)                                               gCCACCACCGCCTCCGGCGTGGATAATGCAGCCTCCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCCGGGAACGACt                             <  1:251307/90‑1 (MQ=255)                                                ccaccaCCGCCTCCGGCGTGGATAATGCAGCCTCCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCCGGGAAc                                 >  2:840631/1‑85 (MQ=255)                                                ccaccaCCGCCTCCGGCGTGGATAATGCAGCCTCCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCCGGGAAc                                 <  1:840631/85‑1 (MQ=255)                                                    caccGCCTCCGGCGTGGATAATGCAGCCTCCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCCGGGAACGACTGGTaa                        >  1:823176/1‑90 (MQ=255)                                                        gCCTCCGGCGTGGATAATGCAGCCTCCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCCGGGAAc                                 >  2:610878/1‑77 (MQ=255)                                                        gCCTCCGGCGTGGATAATGCAGCCTCCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCCGGGAAc                                 <  1:610878/77‑1 (MQ=255)                                                        gCCTCCGGCGTGGATAATGCAGCCTCCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCCGGGAACGACTGGTAatgat                    >  2:1189584/1‑90 (MQ=255)                                                                cGTGGATAATGCAGCCTCCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCCGGGAACGACTGGTAATGATGCAGGccc            <  1:1189584/90‑1 (MQ=255)                                                                cGTGGATAATGCAGCCTCCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCCGGGAACGACTGGTAATGATGCAGGccc            <  2:463177/90‑1 (MQ=255)                                                                cGTGGATAATGCAGCCTCCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCCGGGAACGACTGGTAATGATGCAGGccc            <  1:919443/90‑1 (MQ=255)                                                                        aTGCAGCCTCCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCCGGGAACGACTGGTAATGATGCAGGCCCAACTTGaa    >  2:794033/1‑90 (MQ=255)                                                                        aTGCAGCCTCCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCCGGGAACGACTGGTAATGATGCAGGCCCAACTTGaa    >  2:991077/1‑90 (MQ=255)                                                                          gCAGCCTCCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCCGGGAACGACTGGTAATGATGCAGGCCCAACTTGAAgg  <  2:280920/90‑1 (MQ=255)                                                                                 |                                                                                   TCGTCGTCGGTTGCACATCAAAGCAGTCTGTCAGTCAGTGCGTGAAGCCACCACCGCCTCCGGCGTGGATAATGCAGCCT‑CCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCCGGGAACGACTGGTAATGATGCAGGCCCAACTTGAAGG  >  NZ_CP009273/1417703‑1417864

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑