Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,225,473	G→T	11.4%	intergenic (‑49/+97)	gltJ ← / ← gltI	glutamate/aspartate ABC transporter permease/glutamate/aspartate ABC transporter substrate‑binding protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,225,473	0	G	T	11.4%	129.3 / 7.0	44	intergenic (‑49/+97)	gltJ/gltI	glutamate/aspartate ABC transporter permease/glutamate/aspartate ABC transporter substrate‑binding protein
Reads supporting (aligned to +/- strand):  ref base G (21/17);  new base T (2/3);  total (24/20)
Fisher's exact test for biased strand distribution p-value = 6.50e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.37e-01

AGGCCGGTGATGTACCAGTCCAGATAGGTTTCGCTGCCCACGCCGGTGGACTTGAAGAACACGCCCCAGTCCCAGTTGTAATTCATCGGGATTTCCCCTCAGACGGTTGTTTCACGGGCACCTTCGAGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGACACTAATGAGTGGCCTGCAGAATTGATTCGTGCTCGTGAGCACCAGGCCACTATTTACTGAGGATCAGGACTTCTTCTCGTCCGCAGCCTTGTCGGTCGGCTCGGCGATCAGT  >  NC_002947/1225339‑1225618                                                                                                                                       |                                                                                                                                                  aGGCCGGTGATGTACCAGTCCAGATAGTTTTCGCTGCCCACGCCGGTGGAATTGAAGAACACGCCCCAGTCCCAGTTGTAATTCATCGGGATTTCCCCTCAGACGCTTGTATCACGGGCACCTTCGAGCATCCGCGGGCGCAAGGCGcc                                                                                                                                     >  4:148535/1‑149 (MQ=255)  ggCCGGTGATGTACCAGTCCAGATAGGTTTCGCTGCCCACGCCGGTGGACTTGAAGAACACGCCCCAGTCCCAGTTGTAATTCATCGGGATTTCCCCTCAGACGGTTGTTTCACGGGCACCTTCGAGCATCCGGGGGCGCAAGGCGcc                                                                                                                                     >  5:302536/1‑148 (MQ=255)    ccGGTGATGTACCAGTCCAGATAGGTTTCGCTGCCCACGCCGGTGGACTTGAAGAACACGCCCCAGTCCCAGTTGTAATTCATCGGGATTTCCCCTCAGACGGTTGTTTCACGGGCACCTTCGAGCATCCGTGGGCGCCTTGCGccccc                                                                                                                                  <  8:255386/149‑3 (MQ=255)          aTGTACCAGTCCAGATAGGTTTCGCTGCCCACGCCGGTGGACTTGAAGAACACGCCCCAGTCCCAGTTGTAATTCATCGGGATTTCCCCTCAGACGGTTGTTTCACGGGCACCTTCGAGCATCCGGGGGCGCAAGGCGCCCACGGATg                                                                                                                             >  3:5602/1‑148 (MQ=255)                                 ggtggccACGCCGGTGGACTTTAAGAACACGCCCCTGTCCCAGTTGTAATTCATCGGGATTTGCCCTCAGACGGTTGTTTCACGGGCACCTTCGAGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGACACTAATGAGTgg                                                                                                      <  4:110521/143‑1 (MQ=255)                                   tGCCCACGCCGGTGGACTTGAAGAACACGCCCCAGTCCCAGTTGTAATTCATCGGGATTTCCCCTCAGACGGTTGTTTCACGGGCACCTTCGAGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGACACTAATGAGTGGCCt                                                                                                   >  2:180631/1‑149 (MQ=255)                                     cccACGCCGGTGGACTTGAAGAACACGCCCCAGTCCCAGTTGTAATTCATCGGGATTTCCCCTCAGACGGTTGTTTCACGGGCACCTTCGAGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGACACTAATGAGTGGCCTg                                                                                                  >  1:98108/1‑148 (MQ=255)                                       cACGCCGGTGGACTTGAAGAACACGCCCCAGTCCCAGTTGTAATTCATCGGGATTTCCCCTCAGACGGTTGTTTCACGGGCACCTTCGAGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGACACTAATGAGTGGCCTg                                                                                                  >  7:123381/1‑146 (MQ=255)                                              gTGGACTTGAAGAACACGCCCCAGTCCCAGTTGTAATTCATCGGGATTTCCCCTCAGACGGTTGTTTCACGGGCACCTTCGAGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGACACTAATGAGTGGCCTGCAGAATTGAt                                                                                        <  2:98108/149‑1 (MQ=255)                                              gTGGACTTGAAGAACACGCCCCAGTCCCAGTTGTAATTCATCGGGATTTCCCCTCAGACGGTTGTTTCACGGGCACCTTCGAGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGACACTAATGAGTGGCCTGCAGAATTGAt                                                                                        <  8:123381/149‑1 (MQ=255)                                                  aCTTGAAGAACACGCCCCAGTCCCAGTTGTAATTCATCGGGATTTCCCCTCAGACGGTTGTTTCACGGGCACCTTCGAGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGACACTAATGAGTGGCCTGCAGAATTGATTCGt                                                                                    <  1:180631/149‑1 (MQ=255)                                                    ttGAAGAACACGCCCCAGTCCCAGTTGTAATTCATCGGGATTTCCCCTCAGACGGTTGTTTCACGGGCACCTTCGAGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTATACACTAATGAGTGGCCTGCAGAATTGATTCGTGc                                                                                  >  5:85244/1‑149 (MQ=255)                                                    ttGAAGAACACGCCCCAGTCCCAGTTGTAATTCATCGGGATTTCCCCTCAGACGGTTGTTTCACGGGCACCTTCGAGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGACACTAATGAGTGGCCTGCAGAATTGATTCGTGc                                                                                  >  1:177797/1‑149 (MQ=255)                                                      gaagaaCACGCCCCAGTCCCAGTTGTAATTCATCGGGATTTCCCCTCAGACGGTTGTTTCACGGGCACCTTCGAGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGACACTAATGAGTGGCCTGCAGAATTGATTCGTGCTc                                                                                >  2:15472/1‑149 (MQ=255)                                                                       cccagtTGTAATTCATCGGGATTTCCCCTCAGACGGTTGTTTCACGGGCACCTGCGAGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGACACTAATGAGTGGCCTGCAGAATTGATTCGTGCTCGTGAGCACCAGGCCAc                                                                >  1:87045/1‑148 (MQ=255)                                                                        ccagtTGTAATTCATCGGGATTTCCCCTCAGACGGTTGTTTCACGGGCACCTTCGAGCATCCGTGGGCGCCTTGCGccccc                                                                                                                                  <  6:268003/81‑3 (MQ=38)                                                                        ccagtTGTAATTCATCGGGATTTCCCCTCAGACGGTTGTTTCACGGGCACCTTCGAGCATCCGTGGGCGCCTTGCGccccc                                                                                                                                  >  5:268003/1‑79 (MQ=38)                                                                              gTAATTCATCGGGATTTCCCCTCAGACGGTTGTTTCACGGGCACCTTCGAGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGACACTAATGAGTGGCCTGCAGAATTGATTCGTGCTCGTGAGCACCAGGCCACTATTTAc                                                         <  6:302536/148‑1 (MQ=255)                                                                                aaTTCATCGGGATTTCCCCTCAGACGGTTGTTTCACGGGCACCTTCGAGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGACACTAATGAGTGGCCTGCAGAATTGATTCGTGCTCGTGAGCACCAGGCCACTATTTACt                                                        >  2:318219/1‑147 (MQ=255)                                                                                 aTTCATCGGGATTTCCCCTCAGACGGTTGTTTCACGGGCACCTTCGAGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGACACTAATGAGTGGCCTGCAGAATTGATTCGTGCTCCTGAGCACCAGGCCACTATTTACTGa                                                      <  7:274857/148‑1 (MQ=255)                                                                                 aTTCATCGGGATTTCCCCTCAGACGGTTGTTTCACGGGCACCTTCGAGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGACACTAATGAGTGGCCTGCAGAATTGATTCGTGCTCATGAGCACCAGGCCACTATTTACt                                                        >  8:274857/1‑146 (MQ=255)                                                                                      tCGGGATTTCCCCTCAGACGGTTGTTTCACGGGCACCTTCGAGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGACACTAATGAGTGGCCTGCAGAATTGATTCGTGCTCGTGAGCACCAGGCCACTATTTACTGAGGAt                                                  >  1:190606/1‑147 (MQ=255)                                                                                        gggATTTCCCCTCAGACGGTTGTTTCACGGGCACCTTCGAGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGaca                                                                                                                 >  6:273833/1‑82 (MQ=255)                                                                                        gggATTTCCCCTCAGACGGTTGTTTCACGGGCACCTTCGAGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGaca                                                                                                                 <  5:273833/82‑1 (MQ=255)                                                                                               ccccTCAGACGGTTGTTTCACGGGCACCTTCGAGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGACACTAATGAGTGGCCTGCAGAATTGATTCGTGCTCGTGAGCACCAGGCCACTATTTACTGAGGATCAGGActtct                                        >  4:111787/1‑148 (MQ=255)                                                                                                cccTCAGACGGTTGTTTCACGGGCACCTTCGAGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGACACTAATGAGTGGCCTGCAGAATTGATTCGTGCTCGTGAGCACCAGGCCACTATTTACTGAGGATCAGGACttcttc                                      <  3:148535/149‑1 (MQ=255)                                                                                                cccTCAGACGGTTGTTTCACGGGCACCTTCGAGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGACACTAATGAGTGGCCTGCAGAATTGATTCGTGCTCGTGAGCACCAGGCCACTATTTACTGAGGATCAGGACttcttc                                      <  1:318219/149‑1 (MQ=255)                                                                                                 ccTCAGACGGTTGTTTCACGGGCACCTTCGAGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGACACTAATGAGTGGCCTGCAGAATTGATTCGTGCTCGTGAGCACCAGGCCACTATTTACTGAGGATCAGGACTtcttct                                     >  2:37957/1‑149 (MQ=255)                                                                                                  cTCAGACGGTTGTTTCACGGGCACCTTCGAGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGACACTAATGAGTGGCCTGCAGAATTGATTCGTGCTCGTGAGCACCAGGCCACTATTTACTGAGGATCAGGACTTCTtctc                                    <  2:177797/149‑1 (MQ=255)                                                                                                   tCAGACGGTTGTTTCACGGGCACCTTCGAGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGACACTAATGAGTGGCCTGCAGAATTGATTCGTGCTCGTGAGCACCAGGCCACTATTTACTGAGGATCAGGACttcttc                                      <  1:313016/146‑1 (MQ=255)                                                                                                   tCAGACGGTTGTTTCACGGGCACCTTCGAGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGACACTAATGAGTGGCCTGCAGAATTGATTCGTGCTCGTGAGCACCAGGCCACTATTTACTGAGGATCAGGACttcttc                                      >  2:313016/1‑146 (MQ=255)                                                                                                           ttgttTCACGGGCACCTTCGAGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGACACTAATGAGTGGCCTGCAGAATTGATTCGTGCTCGTGAGCACCAGGCCACTATTTACTGAGGATCAGGACTTCTTCTCGTCCGCAGc                           >  8:165159/1‑149 (MQ=255)                                                                                                                      gCACCTTCGAGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGACACTAATGAGTGGCCTGCAGAATTGATTCGTGCTCGTGAGCACCAGGCCACTATTTa                                                          >  3:183431/1‑107 (MQ=255)                                                                                                                      gCACCTTCGAGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGACACTAATGAGTGGCCTGCAGAATTGATTCGTGCTCGTGAGCACCAGGCCACTATTTa                                                          <  4:183431/107‑1 (MQ=255)                                                                                                                      gCACCTTCGAGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGACACTAATGAGTGGCCTGCAGAATTGATTCGTGCTCGTGAGCACCAGGCCACTATTTACTGAGGATCAGGACTTCTTCTCGTCCGCAGCCTTgtcggtcg                >  3:112431/1‑149 (MQ=255)                                                                                                                      gCACCTTCGAGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGACACTAATGAGTGGCCTGCAGAATTGATTCGTGCTCGTGAGCACCAGGCCACTATTTACTGAGGATCAGGACTTCTTCTCGTCCGCAGCCTTgtcggtcg                >  7:43996/1‑149 (MQ=255)                                                                                                                           ttCGAGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGACACTAATGAGTGGCCTGCAGAATTGATTCGTGCTCGTGAGCACCAGGCCACTATTTACTGAGGATCAGGACTTCTTCTCGTCCGCAGCCTTGTCGGtcggctcg           >  5:63376/1‑149 (MQ=255)                                                                                                                             cGAGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGACACTAATGAGTGGCCTGCAGAATTGATTCGTGCTCGTGAGCACCAGGCCACTATTTACTGAGGATCAGGACTTCTTCTCGTCCGCAGCCTTGTCGGtcggctcgg          <  4:112431/148‑1 (MQ=255)                                                                                                                              tttcATCCGTGGGCGCCTTGCGCCCCCGGATGAAAGGTTAGACACTAATGAGTGGCCTGCAGAATTGATTCGt                                                                                    <  4:315503/70‑1 (MQ=21)                                                                                                                              tttcATCCGTGGGCGCCTTGCGCCCCCGGATGAAAGGTTAGACACTAATGAGTGGCCTGCAGAATTGATTCGt                                                                                    >  3:315503/4‑73 (MQ=21)                                                                                                                              gAGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGACACTAATGAGTGGCCTGCAGAATTGATTCGTGCTCGTGAGCACCAGGCCACTATTTACTGa                                                      <  4:30501/103‑1 (MQ=255)                                                                                                                               aGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGACACTAATGAGTGGCCTGCAGAATTGATTCGTGCTCGTGAGCACCAGGCCACTATTTACTGAGGATCAGGACTTCTTCTCGTCCGCAGCCTTGTCGGTCGGCTCGGCGa       <  2:87045/149‑1 (MQ=255)                                                                                                                                gCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGACACTAATGAGTGGCCTGCAGAATTGATTCGTGCTCGTGAGCACCAGGCCACTATTTACTGAGGATCAGGACTTCTTCTCGTCCGCAGCCTTGTCGGTCGGCTCGGCGAt      <  7:165159/149‑1 (MQ=255)                                                                                                                                     cGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGACACTAATGAGTGGCCTGCAGAATTGATTCGTGCTCGTGAGCACCAGGCCACTATTTACTGAGGATCAGGACTTCTTCTCGTCCGCAGCCTTGTCGGTCGGCTCGGCGATCAGt  <  6:63376/148‑1 (MQ=255)                                                                                                                                       |                                                                                                                                                  AGGCCGGTGATGTACCAGTCCAGATAGGTTTCGCTGCCCACGCCGGTGGACTTGAAGAACACGCCCCAGTCCCAGTTGTAATTCATCGGGATTTCCCCTCAGACGGTTGTTTCACGGGCACCTTCGAGCATCCGGGGGCGCAAGGCGCCCACGGATGAAAGGTTAGACACTAATGAGTGGCCTGCAGAATTGATTCGTGCTCGTGAGCACCAGGCCACTATTTACTGAGGATCAGGACTTCTTCTCGTCCGCAGCCTTGTCGGTCGGCTCGGCGATCAGT  >  NC_002947/1225339‑1225618

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑