Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	2,419,720	T→C	68.1%	D183G (GAT→GGT)	hisJ ←	histidine/lysine/arginine/ornithine transporter subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	2,419,720	0	T	C	68.1%	30.5 / 13.8	28	D183G (GAT→GGT)	hisJ	histidine/lysine/arginine/ornithine transporter subunit
Reads supporting (aligned to +/- strand):  ref base T (5/4);  new base C (8/11);  total (13/15)
Fisher's exact test for biased strand distribution p-value = 6.89e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGCTTCGCGCAGTTCGTTATCTTCTTTACGCAGGCCCATGCCGGTCCCTACGCCAAACAGTTTTTCATCTTTAACAGACGGGCCACCGAATTTGTAATCTTTACCGACAGGTTGTTTGAGGAAACCTTCGCTGGCAGCGACCTCATCCTGGAACGCGGCATCAATACGTCCGGCAGTCAGGTCAGAATAAATGTTGTCCTGCCCCTGATACGAGACGATTTCAATGCCTTTTGGTGCCCAATGTTCATTACCGAACGTCTCCTGGGTGGTGCCCTGCAA  >  CP009273/2419575‑2419853                                                                                                                                                  |                                                                                                                                      tGCTTCGCGCAGTTCGTTATCTTCTTTACGCAGGCCCATGCCGGTCCCTACGCCAAACAGTTTTTCATCTTTAACAGACGGGCCACCGAATTTGTAATCTTTACCGACAGGTTGTTTGAGGAAACCTTCGCTGGCAGCGACCTCACCCt                                                                                                                                    <  1:67552/149‑1 (MQ=255)             ttCGTTATCTTCTTTACGCAGGCCCATGCCGGTCCCTACGCCAAACAGTTTTTCATCTTTAACAGACGGGCCACCGAATTTGTAATCTTTACCGACAGGTTGTTTGAGGAAACCTTCGCTGGCAGCGACCTCATCCTGGAAcgc                                                                                                                             >  2:117903/1‑144 (MQ=255)                   aTCTTCTTTACGCAGGCCCATGCCGGTCCCTACGCCAAACAGTTTTTCATCTTTAACAGACGGGCCACCGAATTTGTAATCTTTACCGACAGGTTGTTTGAGGAAACCTTCGCTGGCAGCGACCTCACCCTGGAACGCGGCATCAATAc                                                                                                                  <  1:364515/149‑1 (MQ=255)                      ttcttTCCGCAGGCCCATGCCGGTCCCTACGCCAAACCGTTTTTCATCTTTAACACACGGGCCACCGAATTTGTAATCTTTACCGACAGGTTGTTTGAGGAAACCTTCGCTGGCAGCGACCTCACCCTGGAACGCGGCATCAAt                                                                                                                    <  2:296668/144‑1 (MQ=255)                      ttctgTACACACGCCCTGGCCGGTCCCTACGACAAACAGTTTTTCATCTTTAACTGACGGGCCACCGAATTTGTAATCTTTACCGACAGGTTGTTTGAGGAAACCTTCGCTGGCAGCGACCTCACCCTGGAACGCGGCATCAAt                                                                                                                    <  2:66007/144‑1 (MQ=255)                                   cccATGCCGGTCCCTACGCCAAACAGTTTTTCATCTTTAACAGACGGGCCAACGAATTTGTAATCTTTACCGACAGGTTGTTTGAGGAAACCTTCGCTGGCAGCGACCTCACCCTGGAACGCGGCATCAATACGTCCGGCAgtc                                                                                                       >  2:145832/1‑144 (MQ=255)                                    ccATGCCGGTCCCTACGCCAAACAGTTTTTCATCTTTAACAGACGGGCCACCGAATTTGTAATCTTTACCGACAGGTTGTTTGAGGAACCCTAGGCGGTCTTTGGTCTCATCCTGGACCGCGGCATCAATACGTCCGGCAgtcacgtca                                                                                                 >  1:308552/1‑149 (MQ=255)                                    ccATGCCGGTCCCTACGCCAAACAGTTTTTCATCTTTAACAGACGGGCCACCGAATTTGTAATCTTTACCGACAGGTTGTTTGAGGAAACCTTCGCTGGCAGCGACCTCACCCTGGAACGCGGCATCAATACGTCCGGCAgtcaggtca                                                                                                 <  1:288733/149‑1 (MQ=255)                                                          cAGTTTTTCATCTTTAACAGACGGGCCACCGAATTTGTAATCTTTACCGACAGGTTGTTTGAGGAAACCTTCGCTGGCAGCGACCTCACCCTGGAACGCGGCATCAATACGTCCGGCAGTCAGGTCAGTATAAATGTTGTCCTGCCCCt                                                                           >  1:143669/1‑149 (MQ=255)                                                           aGTTTTTCATCTTTAACAGACGGGCCACCGAATTTGTAATCTTTACCGACAGGTTGTTTGAGGAAACCTTCGCTGGCAGCGACCTCACCCTGGAACGCGGCATCAATACGTCCGGCAGTCAGGTCAGAATAAATGTTGTCCTGc                                                                               <  2:307136/144‑1 (MQ=255)                                                              ttttCATCTTTAACAGGCGGGCCACCGAATTTGTAATCTTTACCGACAGGTTGTTTGAGGAAACCTTCGCTGGCAGCGACCTCATCCTGGAACGCGGCATCAATACGTCCGGCAGTCAGGTCAGAATAAATGTTGTCCTGcccc                                                                            <  2:21990/144‑1 (MQ=255)                                                                   aTCTTTAACAGACGGGCCACCGAATTTGTAATCTTTACCGACAGGTTGTTTGAGGAAACCTTCGCTGGCAGCGACCTCACACTGGAACGCGGCCTCAATACGTCCGGCAGTGAGGTCAGAAGACAGGTTGTCCTGCCCCTGATGCgaga                                                                  >  1:25835/1‑149 (MQ=255)                                                                       ttAACAGACGGGCCACCGAATTTGTAATCTTTACCGACAGGTTGTTTGAGGAAACCTTCGCTGGCAGCGACCTCATCCTGGAACGCGGCATCAATACGTCCGGCAGTCAGGTCAGAATAAATGTTGTCCTGCCCCTGATACGAGACGAt                                                              <  1:353445/149‑1 (MQ=255)                                                                                   ccACCGAATTTGTAATCTTTACCGACAGGTTGTTTGAGGAAACCTTCGCTGGCAGCGACCTCACCCTGGAACGCGGCATCGATACGTCCGGCAGTCAGGTCAGAATAAATGTTGTCCTGCCCCTGATACGCGCCGATTTCAATGCCttt                                                  >  1:188240/1‑149 (MQ=255)                                                                                   ccACCGAATTTGTAATCTTTACCGACAGGTTGTTTGAGGAAACCTTCGCTGGCAGCGACCTCACCCTGGAACGCGGCATCAATACGTCCGGCAGTCAGGTCAGAATAAATGTTGTCCTGCCCCTGATACGAGACGATTTCAATGCCttt                                                  >  1:338409/1‑149 (MQ=255)                                                                                   ccACCGAATTTGTAATCTTTACCGACAGGTTGTTTGAGGAAACCTTCGCTGGCAGCGACCTCACCCTGGAACGCGGCATCAATACGTCCGGCAGTCAGGTCAGAATAAATGTTGTCCTGCCCCTGATACGAGACGATTTAAATg                                                       >  2:37856/1‑144 (MQ=255)                                                                                           tttGTAATCTTTACCGACAGGTTGTTTGAGGAAACCTTCGCTGGCAGCGACCTCATCCTGGAACGCGGCATCAATACGTCCGGCAGTCAGGTCAGAATAAATGTTGTCCTGCCCCTGATACGAGACGATTTCAATGCCTTTTGGTGccc                                          <  1:143924/149‑1 (MQ=255)                                                                                               tAATCTTTACCGACAGGTTGTTTGAGGAAACCTTCGCTGGCAGCGACCTCATCCTGGAACGCGGCATCAATACGTCCGGCAGTCAGGTCAGAATAAATGTTGTCCTGCCCCTGATACGAGACGATTTCAATGCCTTTTGGTGCCCAATg                                      >  1:355087/1‑149 (MQ=255)                                                                                               tAATCTTTACCGACAGGTTGTTTGAGGAAACCTTCGCTGGCAGCGACCTCACCCTGGAACGCGGCATCAATACGTCCGGCAGTCAGGTCAGAATAAATGTTGTCCTGCCCCTGATACGAGACGATTTCAATGCCTTTTGGTGCCCAATg                                      <  1:299795/149‑1 (MQ=255)                                                                                                    tttcacGACCGCTTTTTTGAGGAAACCTCCGCTGGCAGCGACCTCACCCTGGAACGCGGCACCAATACTTCCGGCAGTCACGTCAGAATAAACGTTGTCCTGTCCCGGATACGAGACGATTTCAATTCCTTTTGGTGCCCAATGTTCAt                                 <  1:84520/144‑1 (MQ=255)                                                                                                         cggcAGGTTGTTTGACGACACCTTCGCTGGCAGCGACCTCACCCTGGAACGCGGCATCAATACGTCCGGCAGTCAGGTTAGAATAAATGTTGTCCTGCCCCTGATACGAGACGATTTCAATGCCTTTTGGTGCCCAATGTTCAt                                 <  2:160339/141‑1 (MQ=255)                                                                                                          gACAGGTTGTTTGAGGAAACCTTCGCTGGCAGCGACCTCACCCTGGAACGCGGCATCAATACGTCCGGCAGTCAGGTCAGAATAAATGTTGTCCTGCCCCTGATACGAGACGATTTCAATGCCTTTCGGTGCCCAATGTTCATTACCGa                           <  1:139391/149‑1 (MQ=255)                                                                                                               gttgttTGAGGAAACCTTCGCTGGCAGCGACCTCATCCTGGAACGCGGCATCAATACGTCCGGCAGTCAGGTCAGAATAAATGTTGTCCTGCCCCTGATACGAGACGATTTCAATGCCTTTTGGTGCCCAATGTTCATTACCGACCGtc                      >  1:108827/1‑149 (MQ=255)                                                                                                                        ggAAACCTTCGCTGGCAGCGACCTCACCCTGGAACGCGGCATCAATACGTCCGGCAGTCAGGTCAGAATAAATGTTGTCCTGCCCCTGATACGAGACGATTTCAATGCCTTTTGGTGCCCAATGTTCATTACCGAACGTCTCCTGggtg             <  1:344859/149‑1 (MQ=255)                                                                                                                               ttCGCTGGCAGCGACCTCACCCTGGAACGCGGCATCAATACGTCCGGCAGTCAGGTCAGAATAAATGTTGTCCTGCCCCTGATACGAGACGATTTCAATGCCTTTTGGTGCCCAATGTTCATTACCGAACGTCTCCTGggtggt           >  2:167014/1‑144 (MQ=255)                                                                                                                                   cgggCAGCGACCTCACCCTGGAACGCGGCATCAATACGTCCGGCAGTCAGGCCAGAATAAATGTTGTCCTGCCCCTGATACGAGACGATTTCAATGCCTTTTGGTGCCCAATGTTCGTTACCGAACGTCTCCTCGCTGATGccc       >  2:62505/3‑144 (MQ=255)                                                                                                                                   cTGGCAGCGACCTCATCCTGGAACCCGGCATCAATACGTCTGGCAGGCAGGTCAGAATAAATGTTGTCCTGCCCCTGATACGAGACGATTTCAATGCCTTTTGGTGCCCAATGTTCATTACCGAACGTCTCCTGGGTGGTGCCCTGCaa  <  1:208071/149‑1 (MQ=255)                                                                                                                                       cAGCGACCTCATCCTGGAACGCGGCATCAATACGTCCGGCAGTCAGGGCAGAATAAATGTTGTCCTGCCCCTGATACGAGACGATTTCAATGACTTTTGGTGCCCAATGTTCATTACCGAACGTCTCCTGGGTGGTGCCCTGCa   >  2:348119/1‑144 (MQ=255)                                                                                                                                                  |                                                                                                                                      TGCTTCGCGCAGTTCGTTATCTTCTTTACGCAGGCCCATGCCGGTCCCTACGCCAAACAGTTTTTCATCTTTAACAGACGGGCCACCGAATTTGTAATCTTTACCGACAGGTTGTTTGAGGAAACCTTCGCTGGCAGCGACCTCATCCTGGAACGCGGCATCAATACGTCCGGCAGTCAGGTCAGAATAAATGTTGTCCTGCCCCTGATACGAGACGATTTCAATGCCTTTTGGTGCCCAATGTTCATTACCGAACGTCTCCTGGGTGGTGCCCTGCAA  >  CP009273/2419575‑2419853

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑