Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	2,420,353	A→C	75.1%	intergenic (‑86/+135)	hisJ ← / ← argT	histidine/lysine/arginine/ornithine transporter subunit/lysine/arginine/ornithine transporter subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	2,420,353	0	A	C	75.1%	37.1 / 12.4	29	intergenic (‑86/+135)	hisJ/argT	histidine/lysine/arginine/ornithine transporter subunit/lysine/arginine/ornithine transporter subunit
Reads supporting (aligned to +/- strand):  ref base A (4/3);  new base C (13/8);  total (18/11)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.51e-01

AGAAGGCCAGAACCAGAGAGAGCGATAGCACCAGTTTTTTCATAATGTCCTCAACTGACAGTCTTTTTATAGGGAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAAATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACAAACCTGGCGTGCACCATGATGATCATTCCATCAGGTACAGCTTCCCAGCGACGTATCAGT  >  CP009273/2420225‑2420492                                                                                                                                 |                                                                                                                                            agaAGGCCAGAACCAGAGAGAGCGATAGCACCAGTTTTTTCATAATGTCCTCAACTGACAGTCTTTTTATAGGGAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAACATATCCCGCCCCGTTAg                                                                                                                            >  2:219229/1‑146 (MQ=255)    aGGCCAGAACCAGAGAGAGCGATAGCACCAGTTTGTTCATAATGTCCTCAACTGACAGTCTTTTTATAGGGAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCCTCAAGGCAACATATACGGCCCGGTTAGACg                                                                                                                         >  2:114133/1‑146 (MQ=255)     ggCCAGAACCAGAGAGAGCGATAGCACCAGTTTTTTCATAATGTCCTCAACTGACAGTCTTTTTATAGGGAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAACATATCCCGCCCCGTTAGACGt                                                                                                                        >  2:198530/1‑146 (MQ=255)                  gcgagCGATATCACCAATTCTTTCATAATGTCCTTAACTGACAGTCTTTTTATAGGGCAGATTTACGGGTTTTTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAACATATCCCGCCCCGTTAGACGTATTATTTTTCAtt                                                                                                           <  2:25550/144‑1 (MQ=255)                            gCACCAGTTTTTTCATAATGTCCTCAACTGACAGTCTTTTTATAGGGAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAAATATCCCGCCCCGTTAGACGTCTTATTTTTCATTAAAAATGCTTAAGt                                                                                             >  1:242331/1‑150 (MQ=255)                             cACCAGTTTTTTCATAATGTCCTCAACTGACAGTCTTTTTATAGGGAATATTTACAGGTTTGTTACCCTTATCGTGCCATAAAATTGACCATCAAGGCAAAATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTa                                                                                            >  1:71065/1‑150 (MQ=255)                                  gTTTTTTCATAATGTCCTCAACTGACAGTCTTTTTATAGGGAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAAATATCCCGCCCAGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCAt                                                                                       <  1:55975/150‑1 (MQ=255)                                         cATAATGCCCTCCACTGACAGTCTTTTCATAGGGAATATTTACAGGTTCGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAACATATCCCGCCCCGTTAGACGTATTATTTTTCATCAAACATGCTTAAGTATGCATTTc                                                                                    <  2:119066/146‑1 (MQ=255)                                                          aCAGTCTTTTTATAGGGAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAAATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGcaac                                                               <  1:162389/150‑1 (MQ=255)                                                              ggcttttAGAGGCAATCGTTACAGGTTTGTTACACTTCTCGTGCCATAAAATTGACCATCAAGGCAACATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGcaac                                                               <  2:62834/143‑1 (MQ=255)                                                                   ttATAGGGAATATTTACAGGTTTGTTACACTTATCGTGACATAATAGTGACCATCAAGGCAACATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACAAACCTGGc                                                      <  1:246004/150‑1 (MQ=255)                                                                           aaTATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAAATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACAAACCTGGCGtac                                                  >  2:122523/1‑144 (MQ=255)                                                                           aaTATTTAAAGCGTTGTTACACTTATCGTGCCATAAAATTGACTATCAAGGCAGAATATCCCGCCGCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGAATTTCAATGCACCACGATAGTGCAACAAACATGGCGTGc                                                  >  2:117045/1‑146 (MQ=255)                                                                                   cAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAACATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACAAACCTGGCGTGCACCATGATGATc                                      >  1:17055/1‑150 (MQ=255)                                                                                     ggTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAACATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACAAACCTGGCGTGCACCATGATGATCag                                    >  1:202318/1‑149 (MQ=255)                                                                                         tGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAAATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACAAACCTGGCGTGCACCATGATGATCATTCCa                                <  1:154193/150‑1 (MQ=255)                                                                                         agTTATACTTATACTGACAACAAATGGACCATCAAGGCAACAAATTCTCCCCCGTTAGACGTATTATTTTTCATTAAAAATTCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACAAACCTGGCGTGCACCATGATGATCAt                                    <  2:160053/145‑1 (MQ=255)                                                                                          gTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAGCATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACAAACCTGGCGTGCACCATGATGATCATTCCAt                               >  1:170373/1‑150 (MQ=255)                                                                                          gTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAACATATCCCGCCCCGTTCGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCAGTTCAATGCACCACGATAGTGCAACAAACCTGGCGTGCACCATGATGAGCATTCCAt                               >  1:29776/1‑150 (MQ=255)                                                                                          gTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAACATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACAAACCTGGCGTGCACCATGATGATCATTCCAt                               >  1:29761/1‑150 (MQ=255)                                                                                            tACACTTATCGTGCCATAAAATTGACCATCAGCATCGGGCTTCTCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACAAACCTGGCGAGCACCATGATGATCATTCCATCa                             >  1:261362/1‑150 (MQ=255)                                                                                             acacTTATCGTGCCATAAAATTGACCATCAAGGCAACATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACAAACCTGGCGTGCACCATGATGATCATTCCa                                <  2:190266/146‑1 (MQ=255)                                                                                                   aTCGTGCCATAAAATTGACAATCAGGGCAACATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGATTAAGTATGCATTTCAATGCACAACGATAGTGCAACAACACTGTCGTGCACCACGATGATCATTCCATCAGGTACAg                      >  1:172175/1‑150 (MQ=255)                                                                                                         ccATAAAATTTACCATCAAGTCAACATCCCCCGCCCCGTTAGACGTATTATTTTTCATTCAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACAAACCTGGCGTGCACCATGATGATCATTCCATCAGGTACAGCt                    <  2:119550/146‑1 (MQ=255)                                                                                                         ccATAAAATTGACCATCAAGGCAACATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACAAACCTGGCGTGCACCATGATGATCGTTCCATAAGGTACGGCTTcac                >  1:121132/1‑148 (MQ=255)                                                                                                                aTTGACCATCAAGGCAACATATCCCGCCCCGTTAGACGTATTATTTTTCATTAGAAGTGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACAAACCTGGCGTGCACCATGATGATCATTCCATCAGGTACAGCTTCCCAGCGACg         >  1:237890/1‑150 (MQ=255)                                                                                                                    aCCGTCAAGGCAACATATCCCGCCCCGTTCGACGTATTATTTTTCATTCAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACAAACCTGGCGTGCACCATGATGATCATTCCATCAGGTACAGCTTCCCAGCGACg         <  2:126445/146‑1 (MQ=255)                                                                                                                      cATTAAGGCAACATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACAAACCTGGCGTGCACCATGATGATCATTCCATCAGGTACCGCTTCCCAGCGCCGTATcga   >  1:230764/1‑148 (MQ=255)                                                                                                                       aTCAAGGCAACATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAGCAAACCTGGCGTGCACCATGATGATCATTCCATCAGGTACAGCTTCCCAGCGACGTATCAGt  >  1:177589/1‑150 (MQ=255)                                                                                                                                 |                                                                                                                                            AGAAGGCCAGAACCAGAGAGAGCGATAGCACCAGTTTTTTCATAATGTCCTCAACTGACAGTCTTTTTATAGGGAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAAATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACAAACCTGGCGTGCACCATGATGATCATTCCATCAGGTACAGCTTCCCAGCGACGTATCAGT  >  CP009273/2420225‑2420492

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑