Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	2,279,621	T→A	9.3%	intergenic (+6/‑69)	yejM → / → proL	essential inner membrane DUF3413 domain‑containing protein; lipid A production and membrane permeability factor/tRNA‑Pro

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	2,279,621	0	T	A	9.3%	117.5 / 2.9	42	intergenic (+6/‑69)	yejM/proL	essential inner membrane DUF3413 domain‑containing protein; lipid A production and membrane permeability factor/tRNA‑Pro
Reads supporting (aligned to +/- strand):  ref base T (18/19);  new base A (2/2);  total (20/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

AAAGACGCTGGTACTGAACAATAACGGTAAATACCGCACTTACAACTTACGTGGTGAAAGAGTGAAAGATGAAAAACCACAGTTAAGTTTGTTATTGCAAGTGCTGACAGACGAGAAGCGTTTTATCGCTAACTGATTAATTATAAATCAGTTAGCGAAATATCTTACTTGCAATCGGTGTGGAAAACGGTAGTATTAGCAGCCACGAGTCGGCACGTAGCGCAGCCTGGTAGCGCACCGTCATGGGGTGTCGGGGGTCGGAGGTTCAAATCCTCTCGTGCCGACCAAA  >  CP009273/2279480‑2279768                                                                                                                                              |                                                                                                                                                    aaaGACGCTGGTACTGAACAATAACGGTAAATACCGCACTTACAACTTACGTGGTGAAAGAAAAAAAAATGAAAAACCACAGTTAAGTTTGTTATTGCAAGTGCTGACAGACGAGAAGCGTTTTATCGCTAACTGattaatta                                                                                                                                                    <  1:136891/143‑1 (MQ=255)  aaGACGCTGGTACTGAACAATAACGGTAAATACCGCACTTACAACTTACGTGGTGAAAGAGTGAAAGATGAAAAACCACAGTTAAGTTTGTTATTGCAAGTGCTGACAGACGAGAAGCGTGTTATCGCTAACTGATTAATTATAAATCa                                                                                                                                             <  2:340165/149‑1 (MQ=255)      cGCTGGTACTGAACAATAACGGTAAATACCGCACTTACAACTTACGTGGTGAAAGAGTGAAAGATGAAAAACCACAGTTAAGTTTGTTATTGCAAGTGCTGACAGACGAGAAGCGTTTTATCGCTAACTGATTAATTATAAATCAGTTa                                                                                                                                         <  2:24086/149‑1 (MQ=255)       gCTGGGAATGAAAAATAACGGTAAATACCGCACTTACAACTTACGTGGTGAAAGAGTGAAAGATGAAAAACCACAGTTAAGTTTGTTATTGCAAGTGCTGACAGACGAGAAGCGTTTTATCGCTAACTGATTTATAATTAATCAGTTAg                                                                                                                                        <  2:97134/149‑1 (MQ=255)            tACTGACCAATAACGGTAAATACCGCACTTACAACTTACGTGGTGAAAGAGTGAAAGATGAAAAACCACAGTTAAGTTTGTTATTGCAAGTGCTGACAGACGAGAAGCGTTTTATCGCTAACTGATTAATTATAAATCAGTTa                                                                                                                                         <  1:447533/143‑1 (MQ=255)            tACTGAACAATAACGGTAAATTCCGCACTTACAAGGTACGTGGTGAAAGAGTGAAAGATGAAAAACCACAGTTAAGTTTGTTATTGCAAGTGCTGACAGACGAGAAGCGTTTTATCGCTAACTGATTAATCATAAATCAGTTa                                                                                                                                         <  1:214654/143‑1 (MQ=255)            tACTGAACAATAACGGTAAATACCGCACTTACAACTTACGTGGTGAAAGAGTGAAAGATGAAAAACCACAGTTAAGTTTGTTATTGCAAGTGCTGACAGACGAGAAGCGTTTTATCGCTAACTGATTTATAATTAATCAGTTa                                                                                                                                         <  1:134425/143‑1 (MQ=255)               tGAACAATAACGGTAAATACCGCACTTACAACTTACGTGGTGAAAGAGTGAAAGATGAAAAAACACAGGTAAGTTTGTTATTGCAAGTGCTGACAGACGCGAAGAATTTTCTCGATAACTGATTAATAATCAATCACTTAGCGaacgat                                                                                                                                >  2:449585/1‑145 (MQ=255)                 aaCAATAACGGTAAATACCGCACTTACAACGTATGTGCTGCAGGAGTGAAAGATGAAAAACCACAGTTAAGTTTGTTATTGCAAGTGCTGACAGACGAGAAGCGTTTTATCGCTAACTGATTAATTATAAATCAGTTAGCGAAATATCt                                                                                                                              <  2:432998/149‑1 (MQ=255)                    aaTAACGGTAAATACCGCACTTACAACTTACGTGGTGAAAGAGTGAAAGATGAAAAACCACAGTTAAGTTTGTTATTGCAAGTGCTGACAGACGAGAAGCGTTTTATCGCTAACTGATTAATTCTACAGCAGTTAGCGAAata                                                                                                                                 <  1:207834/143‑1 (MQ=255)                    aaTAACGGTAAATACCGCACTTACAACTTACGTGGTGAAAGAGTGAAAGATGAAAAACCACAGTTAAGTTTGTTATTGCAAGTGCTGACAGACGAGAAGCGTTTTATCGCTAACTGATTAATTATCCATCAGTTAGCGAAata                                                                                                                                 <  1:207830/143‑1 (MQ=255)                      tAACGGTAAATACCGCACTTACAACTTACGTGGTGAAAGAGTGAAAGATGAAAAACCACAGTTAAGTTTGTTATTGCAAGTGCTGACAGACGAGAAGCGTTTTATCGCTAACTGATTAATTATAAATCAGTTAGCGAAATATCTTACtt                                                                                                                         <  2:336836/149‑1 (MQ=255)                                     cACTTACAACTTACGTTGTGAAAGCGTGAACGCTGATGACGCGCGGCGCGGTCGGGTAGGGCAAGTGCTGCCAGACCTGAAGCGTTTTATCGCTAACTGATTAATTATAAATCAGTTAGCGAAATATCTTACTTGCAATCGgt                                                                                                                <  1:402093/143‑1 (MQ=255)                                       cTTACAACTTACGTGGTGAAAGAGTGAAAGATGAAAAACCACAGTTAAGTTTGTTATTGCAAGTGCTGACAGACGAGAAGCGTTTTATCGCTAACTGATTAATTATAAATCAGTTAGCGAAATATCTTACTTGCAATCGgtgt                                                                                                              <  1:4484/143‑1 (MQ=255)                                             aCTTACGTGGTGAAAGAGTGAAAGATGAAAAACCACAGTTAAGTTTGTTATTGCAAGTGCTGACAGACGAGAAGCGTTTTATCGCTAACTGATTAATTATAAATCAGTTAGCGAAATATCTTACTTGCAATCGGTGTGGaaaa                                                                                                        >  1:454667/1‑143 (MQ=255)                                               ttACGTGGTGAAAGAGTGAAAGATGAAAAACCACAGTTAAGTTTGTTATTGCAAGTGCTGACAGACGAGAAGCGTTTTATCGCTAACTGATTAATTATAAATCAGTAAGCGCAATTTCTTACTTGCATTCGGGTTGGGAAAct                                                                                                      >  1:542860/1‑142 (MQ=255)                                                 aCGTGGTGAAAGAGTGAAAGATGAAAAACCACAGTTAAGTTTGTTATTGCAAGTGCTGACAGACGAGAAGCGTTTTATCGCTAACTGATTAATTATAAATCAGTTAGCGAAATATCTTACTTGCAATCGGTGTGGAAAACGgt                                                                                                    >  1:210879/1‑143 (MQ=255)                                                   gtggtgAAAGAGTGAAAGATGAAAAACCACAGTTAAGTTTGTTATTGCAAGTGCTGACAGACGAGAAGCGTTTTATCGCTAACTGATTAATTATAAATCAGTTAGCGAAATATCTTACTTGCAATCGGTGTGGAAAACGgtag                                                                                                  >  1:289388/1‑143 (MQ=255)                                                      gtgaaagagtgaaagaTGAAACACCACAGTTAAGTTTGTTATTGCAAGTGCTGACAGACGAGAAGCGTTTTATCGCTAACTGATTAATTATAAATCAGTTAGCGAAATATCTTACTTGCAATCGGTGTGGAAAACGGTAGTAt                                                                                               >  1:433344/1‑143 (MQ=255)                                                       tgaaagagtgaaagaTGAAAAACCACAGTTAAGTTTGTTATTGCAAGTGATGACAGAGGTGATGCGTTTTATCGCTAACTGATTAATTATAAATCAGTTAGCGAAATATATTACTTGCAATCGGTGTGGAAAACGGTGGTAtt                                                                                              >  1:95012/1‑143 (MQ=255)                                                       acaaagagtgaaagaTGAAAAACCACAGTTAAGTTTGTTATTGCAAGTGCTGACAGACGAGAAGCGTTTTATCGCTAACTGATTAATTATAAATCAGTTAGCGAAATATCTTACTTGCAATCGGTGTGGAAAACGGTAGTATTagcagc                                                                                        <  2:143118/147‑1 (MQ=255)                                                           agagtgaaagaTGAAAAACCACAGTTAAGTTTGTTATTGCAAGTGCTGACAGACGAGAAGCGTTTTATCGCTAACTGATTAATTATAAATCAGTTAGCGAAATATCTTACTTGCAATCGGTGTGGAAAACGGTAGTATTagca                                                                                          <  1:572573/143‑1 (MQ=255)                                                               tgaaagaTGAAAAACCACAGTTAAGTTTGTTATTGCAAGTGCTGACAGACGAGAAGCGTTTTATCGCTAACTGATTAATTATAAATCAGTTAGCGAAATATCTTACTTGCAATCGGTGTGGAAAACGGTAGTATTAGCAGCCa                                                                                      >  1:75999/1‑143 (MQ=255)                                                                gaaagaTGAAAAACCACAGTTAAGTTTGTTATTGCAAGTGCTGACAGACGAGAAGCGTTTTATCGCTAACTGATTAATTATAAATCAGTTAGCGAAATATCTTACTTGCAATCGGTGTGGAAAACGGTAGTATTAGCAGCCACGAGTCg                                                                               >  2:324787/1‑149 (MQ=255)                                                                      tGAAAAACCACAGTTAAGTTTGTTATTGCAAGTGCTGACAGACGAGAAGCGTTTTATCGCTAACTGATTAATTATAAATCAGTTAGCGAAATATCTTACTTGCAATCGGTGTGGAAAACGGTAGTATTAGCAGCCACGAGTCGGCACGt                                                                         >  2:585199/1‑149 (MQ=255)                                                                              cacaGTTAAGTTTGTTATTGCAAGTGCTGACAGACGAGAAGCGTTTTCTCGCTAACTGATTAATTATAAATCAGTTAGCGCAATATCTTACTTGCAATCGGTGGGGAAAACGGTAGTATTAGCAGCCCCGCGTCGGGACGTAgcgtgtg                                                                 >  2:250254/1‑145 (MQ=255)                                                                              atcaGTTAAGGTTGTGATTGCAAGTGCTGACAGACGAGAAGCGTTTTATCGCTAACTGATTAATTAGAAATCAGTTAGCGAAATATCTTACTTGCAATCGGTGTGGAAAACGGTAGTATTAGCAGCCACGAGTCGGCACGTAGCGCAGc                                                                 <  2:23781/147‑1 (MQ=255)                                                                                    tAAGTTTGTTATTGCAAGTGCTGACAGACGAGAAGCGTTTTATCGCTAACTGATTAATTATAAATCAGTTAGCGAAATATCTTACTTGCAATCGGTGTGGAAAACGGTAGTATTAGCAGCCACGAGTCGGCACGTAGCGCAGc                                                                 <  1:478907/143‑1 (MQ=255)                                                                                     aaGTTTGTTATTGCAAGTGCTGACAGACGAGAAGCGTTTTATCGCTAACTGATTAATTATAAATCAGTTAGCGAAATATCTTACTTGCAATCGGTGTGGAAAACGGTAGTATTAGCAGCCACGAGTCGGCACGTAGCGCAGcc                                                                >  1:575594/1‑143 (MQ=255)                                                                                       gTTTGTTATTGCAAGTGCTGACAGACGAGAAGCGTTTTATCGCTAACTGATTAATTATAAATCAGTTAGCGAAATATCTTACTTGCAATCGGTGTGGAAAACGGTAGTATTAGCAGCCACGAGTCGGCACGTAGCGCAGCCTg                                                              <  1:304147/143‑1 (MQ=255)                                                                                       gTTTGCTATTGCAAGTGCTGACAGACGAGAAGCGTTTTATCGCTAACTGATTAATTATAAATCAGTTAGCGAAATATCTTACTTGCAATCGGTGTGGAAAACGGTAGTATTAGCAGCCACGAGTCGGCACGTAGCGCAGCCTGGTAgcg                                                        <  2:488894/149‑1 (MQ=255)                                                                                        tttGTTATTGCAAGTGCTGACAGACGAGAAGTGTTTTATCGCTAACTGATTAATTATAAATCAGTTAGCGAAATATCTTACTTGCAATCGGTGTGGAAAACGGTAGTATTAGCAGCCACGAGTCGGCACGTAGCGCAGCCTgg                                                             >  1:370371/1‑143 (MQ=255)                                                                                        tttGTTATTGCAAGGGCTGACAGACGAGAAGCGTTTTATCGCTAACTGATTAATTATAAATCAGTTAGCGAAATATCTTACTTGCAATCGGTGTGGAACACGGTAGTATTAGCAGCCACGAGTCGGCACGTAGCGCAGCCTGGTAgcgc                                                       <  2:604468/149‑1 (MQ=255)                                                                                            ttATTGCAAGTGCTGACAGACGAGAAGCGTTTTATCGCTAACTGATTAATTATAAATCAGTTAGCGAAATATCTTACTTGCAATCGGTGTGGAAAACGGTAGTATTAGCAGCCACGAAGCGGCACGTAGCGCAGCCTGGTAGCGCACCg                                                   >  2:546938/1‑149 (MQ=255)                                                                                                 gCAAGTGCTGACAGACGAGAAGCGTTTTATCGCTAACTGATTAATTATAAATCAGTTAGCGAAATATCTTACTTGCAATCGGTGTGGAAAACGGTAGTATTAGCAGCCACGAGTCGGCACGTAGCGCAGCCTGGTAGCGCAcc                                                    >  1:111769/1‑143 (MQ=255)                                                                                                         tGACAGACGAGAAGCGTTTTAACGCTAACTGATTAATTATAAATCAGTTAGCGAAATATCTTACTTGCAATCGGTGTGGAAAACGGTAGTATTAGCAGCCACGAGTCGGCACGTAGCGCAGCCTGGTAGCGCACCGTCATGGGGTGTCg                                      <  2:230780/149‑1 (MQ=255)                                                                                                          gACAGACGAGAAGCGTTTTATCGCTAACTGATTAATTATAAATCAGTTAGCGAAATATCTTACTTGCAATCGGTGTGGAAAACGGTAGTATTAGCAGCCACGAGTCGGCACGTAGCGCAGCCTGGTAGCGCACCGTCATgggg                                           >  1:528734/1‑143 (MQ=255)                                                                                                             aGACGAGAAGCGTTTTATCGCTAACTGATTAATTATAAATCAGTTAGCGAAATATCTTACTTGCAATCGGTGTGGAAAACGGTAGTATTAGCAGCCACGAGTCGGCACGTAGCGCAGCCTGGTAGCGCACCGTCATGGGGTGTCggggg                                  >  2:102696/1‑149 (MQ=255)                                                                                                                cGAGAAGCGTTTTATCGCTAACTGATTAATTATAAGTCAGTTAGCGAAATATCTTACTTGCAATCGGTGTGGAAAACGGTAGTATTAGCAGCCACGAGTCGGCACGTAGCGCAGCCTGGTAGCGCACCGTCATGGGGTGTCgg                                     <  1:240838/143‑1 (MQ=255)                                                                                                                   gaAGCGTTGTATCGCTAACTGATTAATTATAAATCAGTTAGCGAAATATCTTACTTGCAATCGGTGTGGAAAACGGTAGTATTAGCAGCCACGAGTCGGCACGTAGCGCAGCCTGGTAGCGCACCGTCATGGGGTGTCGGGGGTCGGAg                            <  2:229122/149‑1 (MQ=255)                                                                                                                            tATCGCTAACTGATTAATTATAAATCAGTTAGCGAAATATCTTACTTGCAATCGGTGTGGAAAACGGTAGTATTAGCAGCCACGAGTCGGCACGTAGAGCAGCCTGGTAGCGCACAGTCATGGGGTGTCGGGGGACGGAGGTTCatatg                   >  2:161715/1‑148 (MQ=255)                                                                                                                                 cTAACTGATTAATTATAAATCAGTTAGCGAAATATCTTACTTGCAATCGGTGTGGAAAACGGTAGTATTAGCAGCCACGAGTCGGCACGTAGCGCAGCCTGGTAGCGCACCGTCATGGGGTGTCGGGGGCCGGAGGTTCAAATCctcgc              >  2:632225/1‑147 (MQ=255)                                                                                                                                  tAACTGATTTATAATTAATCAGTTAGCGAAATATCTTACTTGCAATCGGTGTGGAAAACGGTAGTATTAGCAGCCACGAGTCGGCACGTAGCGCAGCCTGGTAGCGCACCGTCATGGGGTGTCGGGGGTCGGAGGTTCAAATCCTCTCg             >  2:410767/1‑149 (MQ=255)                                                                                                                                             ttaTAAATCAGTTAGCGAAATATCTTACTTGCAATCGGTGTGGAAAACGGTAGTATTAGCAGCCACGAGTCGGCACGTAGCGCAGCCTGGTAGCGCACCGTCATGGGGTGTCGGGGGTTGGAGATTCAAATCCTCTCGTGCCGACCaaa  <  2:328347/149‑1 (MQ=255)                                                                                                                                              |                                                                                                                                                    AAAGACGCTGGTACTGAACAATAACGGTAAATACCGCACTTACAACTTACGTGGTGAAAGAGTGAAAGATGAAAAACCACAGTTAAGTTTGTTATTGCAAGTGCTGACAGACGAGAAGCGTTTTATCGCTAACTGATTAATTATAAATCAGTTAGCGAAATATCTTACTTGCAATCGGTGTGGAAAACGGTAGTATTAGCAGCCACGAGTCGGCACGTAGCGCAGCCTGGTAGCGCACCGTCATGGGGTGTCGGGGGTCGGAGGTTCAAATCCTCTCGTGCCGACCAAA  >  CP009273/2279480‑2279768

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑