Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	2,420,353	A→G	67.6%	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	G	67.6%	42.6 / 33.1	51	intergenic (‑86/+135)	hisJ/argT	histidine/lysine/arginine/ornithine transporter subunit/lysine/arginine/ornithine transporter subunit
Reads supporting (aligned to +/- strand):  ref base A (8/8);  new base G (16/17);  total (25/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.05e-01

TTGCGCTGGAGAAGGCCAGAACCAGAGAGAGCGATAGCACCAGTTTTTTCATAATGTCCTCAACTGACAGTCTTTTTATAGGGAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAAATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACAAACCTGGCGTGCACCATGATGATCATTCCATCAGGTACAGCTTCCCAGCGACGTATCAGTCA  >  CP009273/2420216‑2420494                                                                                                                                          |                                                                                                                                              ttGCGCTGGAGAAGGCCAGAACCAGAGAGAGCGATAGCACCAGTTTTTTCATAATGTCCTCAACTGACAGTCTTTTTATAGGGAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAGATATccc                                                                                                                                        >  1:405616/1‑145 (MQ=255) ttGCGCTGGAGAAGGCCAGAACCAGAGAGAGCGATAGCACCAGTTTTTTCATAATGTCCTCAACTGACAGTCTTTTTATAGGGAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGAACATCAAAGCAAGATATccc                                                                                                                                        >  2:372616/1‑145 (MQ=255)            aaGGCCAGAACCAGAGAGAGCGATAGCACCAGTTTTTTCATAATGTCCTCAACTGACAGTCTTTTTATAGGGAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAGATATCCCGCCCCGTTAGa                                                                                                                             >  2:241641/1‑145 (MQ=255)            aaGGCCAGAACCAGAGAGAGCGATAGCACCAGTTTTTTCAGAATGTCCTCAACTGACAGTCTTTTTATAGGGAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAGATATCCCGCCCCGTTAGa                                                                                                                             <  1:383550/145‑1 (MQ=255)                       cAGAGAGAGCGATAGCACCAGTTTTTTCATAATGTCCTCAACTGACAGTCTTTTTATAGGGAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAAATATCCCGCCCCGTTAGACGTATTAtttt                                                                                                                  <  2:238920/145‑1 (MQ=255)                        agcgagagGGTTAGCACCAGTTTTTTCATAATGTCCTCAACTGACAGTCTTTTTATAGGGAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAAATATCCCGCCCCGTTAGACGTATTAttttt                                                                                                                 <  1:98870/142‑1 (MQ=255)                         gagagatCGATAGCACCAGTTTTTTCATAATTTCCTCAACTGACAGTCTTTTTATAGGGAATATTTACAGGCTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAGATATCCCGCCCCGTTAGACGTATTATTTTTc                                                                                                                <  1:54035/145‑1 (MQ=255)                                agATATCACAAGTTTATTCATAATATCCTCAACTGACAGTCTATTTATAGGGAATATTTACAGGTTTGTTACACTTATCTTGCTATAAAATTGTCCATCAAGGCCATATATTCCGCCCCCTTAGAAGTATTATGTTTCAtttaga                                                                                                         >  1:98473/2‑141 (MQ=255)                                      cACCAGTTTTTTCATAATGTCCTCAACTGACAGTCTTTTTATAGGGAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAGATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGttt                                                                                                   >  1:388189/1‑145 (MQ=255)                                        ccAGTTTTTTCATAATGTCCTCAACTGCGAATACAGATATTGGGAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCGTCAAGGCAAAATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCGTaa                                                                                                 >  1:408216/1‑145 (MQ=255)                                        ccAGTTTTTTCATAATGTCCTCAACTGACAGTCTTTTTATAGGGAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAGATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTaa                                                                                                 <  2:405616/145‑1 (MQ=255)                                         cAGTTTTTTCATAATGTGCTACACTGACAGGCTTTTTATAGGGAATATTTACAGGTTTGTTACACTTATCGTTCCATAAAATTGACCATCAAGGCAAGATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAg                                                                                                <  2:183162/145‑1 (MQ=255)                                                 tCATAATGTCCTCAACTGACAGTCTTTTTATAGGGAATATTTACAGGTTTGTTACACTTATCGTGCCATCAACTTGACCATCAAGGCAAGATATCCCGCCCCGTTATACGTATTATTTTTCATTAAAAATGCTTAAGTATGCAtt                                                                                        >  2:91785/1‑145 (MQ=255)                                                 tCATAATGTCCTCAACTGACAGTCTTTTTATAGGGAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGGAAGATATGCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCAtt                                                                                        <  2:188357/145‑1 (MQ=255)                                                    tAATGTCCTCAACTGACAGTCTTTTTATAGGGAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAGATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCa                                                                                     >  1:80313/1‑145 (MQ=255)                                                    tAATGTCCTCAACTGACAGTCTTTTTATAGGGAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAGATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCa                                                                                     <  2:343982/145‑1 (MQ=255)                                                      aTGTCCTCAACTGACAGTCTTTTTATAGGGAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAGATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCCTTTCatt                                                                                   >  1:98095/1‑143 (MQ=255)                                                       tGTCCTCAACTGACAGTCTTTTTATAGGGAATATTTACATGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAGATATCCCGCCCCGTTAGACGTATTACTTTTCATTAAAAATGCTTAAGTATGCATTTCAATg                                                                                  <  1:254728/145‑1 (MQ=255)                                                       tGTCCTCAACTGACAGTCTTTTTATAGGGAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAAATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATg                                                                                  >  1:141460/1‑145 (MQ=255)                                                           cTCAACTGACAGTCTTTTTATAGGGAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAGATATCCCGCCCCGTTAGAAGTATTATGTTTCATTAAAAATGCGTAAGTATGAATTTCCATAcacc                                                                              >  2:134005/1‑145 (MQ=255)                                                            tCAAGTGACAGTCTGTTTATAGGGAATATTTTCAGTTTTGTTACACTTATCGGGCCATAAAATTGACCATCAAGGCAAGATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGcacca                                                                             <  2:53105/145‑1 (MQ=255)                                                                cTGACAGTCTTTTTATAGGGAATAATTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAAATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGAt                                                                         >  2:316035/1‑145 (MQ=255)                                                                 tGACAGTCTTTTTATAGGGAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAGATATCCCGCCCCGTTAGACATATTATTTTTCATTAAAAATGCTTAAGTATGCAATTAAATGCACCACGATa                                                                        >  2:217817/1‑145 (MQ=255)                                                                 tGACAGTCTTTTTATAGGGAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAAATATCCCCCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTCAAGTATCCATTCCAATGCACCACGATa                                                                        >  1:99595/1‑145 (MQ=255)                                                                   aCAGTCTTTTTATAGGGAATATTTACAGGTTTGTTACCCTTATCGTGCCATAAAATTGACCATCAAAACAAGAAATCCCGCCCCGTTAAAAGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGGTAGt                                                                      >  2:17535/1‑145 (MQ=255)                                                                   aCAGTCTTTTTATAGGGAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAAATATCCCGCCCCGTTAGACGTATTATTTTTTATTAAATATGCTTAAGTATGCATTTCAATGCACCACGATAGt                                                                      >  1:254529/1‑145 (MQ=255)                                                                    cAGTCTTTTTATAGGGAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAGATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTg                                                                     <  2:375692/145‑1 (MQ=255)                                                                    cAGTCTTTTTATAGGGAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAAATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTg                                                                     <  2:141460/145‑1 (MQ=255)                                                                       tttttttATAGGGAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAAATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGcaa                                                                  <  2:252900/143‑1 (MQ=255)                                                                       tCTTTTTATAGGGAATATTTACCGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAGATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGcaa                                                                  <  2:171496/145‑1 (MQ=255)                                                                       tCTTTTTATAGGGAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAAATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACTACGATAGTGcaa                                                                  >  2:331313/1‑145 (MQ=255)                                                                       tCTTTTTACTAGGAAAATGTACAGGTTTGTTACACTTATCCTGCCCTAAACATGACCAGCAAGGCAAAATTTCTCTCCCTGTTCGACGTATTAATTTTAAAAAAAAATGCTTAATTATGCATTTCAATGCACCACGATAGTGcaa                                                                  <  1:107720/145‑1 (MQ=255)                                                                               taGGGAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAAATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACAAACCTg                                                          <  2:346291/145‑1 (MQ=255)                                                                                aGGGAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAAATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACAAACCTgg                                                         >  2:359915/1‑145 (MQ=255)                                                                                 atggtgcacgccAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAGATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACAAACCTGGc                                                        <  2:109529/134‑1 (MQ=255)                                                                                  ggAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAGATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACAAACCTGGCg                                                       >  2:357097/1‑145 (MQ=255)                                                                                  ggAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAGATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACAAACCTGGCg                                                       >  2:93461/1‑145 (MQ=255)                                                                                       atTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAAATATCACGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTACAACAAACCTGGCGTGCAc                                                  >  1:124523/1‑145 (MQ=255)                                                                                               gTTTGTTACACTTATCGTGCTATAAAATTGACCATCAAGGCAATATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACAAACCTGGCGTGCACCAtgatga                                          <  2:17813/145‑1 (MQ=255)                                                                                               gTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAGATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACAAACCTGGCGTGCACCAtgatga                                          <  2:341021/145‑1 (MQ=255)                                                                                                tttGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAGATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACAAACCTGGCGTGCACCATgatgat                                         >  1:342830/1‑145 (MQ=255)                                                                                                   gTTACACTTATCGTGCCATAAAATTTACCATCAAGGCAAAATATCCCGCCCCGTTAGACGTCTTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACAAACCTGGCGTGCACCATGATGATCAt                                      <  1:152342/145‑1 (MQ=255)                                                                                                      acacTTATCGTGCCATAAAATTGACCATCAAGGCAAGATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACAAACCTGGCGTGCACCATGATGATCATTcc                                   >  1:411846/1‑145 (MQ=255)                                                                                                         cTTATCGTGCCATAAAATTGACCATCAAGGCAAGATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACAAACCTGGCGTGCACCATGATGATCATTCCATc                                <  1:121936/145‑1 (MQ=255)                                                                                                                 gCCTTAAAATTGACCATAAAGGCAAGATATCCCGCCCCGTTAGACGTTTTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACAAACCTGGCGTGCACCATGATGATCATTCCATCAGGTACAg                        <  2:52641/145‑1 (MQ=255)                                                                                                                  ccATAAAATTGACCATCAAGGCAAGATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACCAACCTGGCGTGCACCATGATGATCATTCCATCAGGTACAGc                       >  1:99470/1‑145 (MQ=255)                                                                                                                       aaaTTGACCATCAAGGCAAAATATCCCGGCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACAAACCTGGCGTGCACCATGATGATCATTCCATCAGGTACAGCTTccc                  <  2:74958/145‑1 (MQ=255)                                                                                                                        aaTTGACCATCAAGGCAAGATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACAAACCTGGCGTGCACCATGATGATCATTCCATCAAGTACAGCTTCCCa                 >  1:381870/1‑145 (MQ=255)                                                                                                                           tgcccATCCAGCCAAGATAACCCGGCCCGTGAGCCGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACAACCCTGGCGTGCACCATGATGATCATTCCATCAGGTACAGCTTCCCAGCg              <  1:172772/142‑1 (MQ=255)                                                                                                                                 tCAAGGCAAGATGCCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACACACCTGGCGTGCACCATGATGATCATTCCATCAGGTACAGCTTCCCAGCGACGTAt        <  1:152812/145‑1 (MQ=255)                                                                                                                                 tCAAGGCAAGATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACAAACCTGGCGTGCACCATGATGATCATTCCATCAGGTACAGCTTCCCAGCGACGTAt        <  2:357320/145‑1 (MQ=255)                                                                                                                                 acaaagtaaaaTATCCCCCTCGGTCAAACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTGCAATGCACCACGATAGGGCAACTATCCTGGCGTGCACCATGATGATCATTCCATCAGGTACAGCTTCCCAGCGACGTAt        <  1:191237/138‑1 (MQ=255)                                                                                                                                       ccaaaTATCCCCCCCTGTTCGACGTATTATTTTTCCTTAAAAAGGCTTAAGTATGCAGTTCAATGCACCACGATAGTGCAACAAACCTGGCGTACCCCATGATGATCATTCCATCAGGTACAGCTTCCCAGCGACGTATCAGTCa  <  1:141432/143‑1 (MQ=255)                                                                                                                                          |                                                                                                                                              TTGCGCTGGAGAAGGCCAGAACCAGAGAGAGCGATAGCACCAGTTTTTTCATAATGTCCTCAACTGACAGTCTTTTTATAGGGAATATTTACAGGTTTGTTACACTTATCGTGCCATAAAATTGACCATCAAGGCAAAATATCCCGCCCCGTTAGACGTATTATTTTTCATTAAAAATGCTTAAGTATGCATTTCAATGCACCACGATAGTGCAACAAACCTGGCGTGCACCATGATGATCATTCCATCAGGTACAGCTTCCCAGCGACGTATCAGTCA  >  CP009273/2420216‑2420494

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: ‑