Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,740,474	C→A	18.8%	intergenic (+39/+32)	hutF → / ← PP_5037	formiminoglutamate deiminase/lipocalin family lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,740,474	0	C	A	18.8%	111.9 / 18.6	52	intergenic (+39/+32)	hutF/PP_5037	formiminoglutamate deiminase/lipocalin family lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (16/26);  new base A (3/7);  total (19/33)
Fisher's exact test for biased strand distribution p-value = 7.29e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.88e-01

GCGCGATGTGATGGTGAATGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACC‑‑‑GGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAGGCCGGCAG  >  NC_002947/5740327‑5740616                                                                                                                                                       |                                                                                                                                               gcgcGATGTGATGGTGAATGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACT‑‑‑GGGGTTGCGTTGCAGCCCTTCGCGTGCAAGccc                                                                                                                                               <  6:333224/149‑1 (MQ=255)       tgtgATGGTGAATGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACC‑‑‑GGGGTTGCGTTGCAACCCTTCGCGGGCTTGCACGCGAAg                                                                                                                                         <  8:335409/149‑1 (MQ=39)       tgtgATGGTGAATGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTGGCGCCAGCTTTTGGGCTGAGCGTACC‑‑‑GGGGTTGCGTTGCAACCCTTCGCGGGCTTGCACGCGAAg                                                                                                                                         <  6:111264/149‑1 (MQ=39)       tggcaTGGTGAATGGGCAATGTGTGGTGCGCCAGGGGCTGCATGCCCAGGAAGATGAAAGCTGGCGGGCGTTTTCCAAGGTGTTGCGCCAGCTTTTTGGCTGAGCGTACC‑‑‑GGTGTTGCGTTTCAGCCCTTCGCGTGCAAGCCCGCGAAg                                                                                                                                         <  5:6033/145‑1 (MQ=255)        gtgATGGTGAATGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACC‑‑‑GGGGTTGCGTTGCAACCCTTCGCGGGCTTGCACGCGAAg                                                                                                                                         <  4:184827/148‑1 (MQ=39)         tgATGGTGAATGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACC‑‑‑GGGGTTGCGTTGCCGCCCTTCGCGTGGAACCCCGCGCAggg                                                                                                                                       >  8:202293/1‑149 (MQ=255)         tgATGGTGAATGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACC‑‑‑GGGGTTGCGTTGCAGCCCTTCGCGGGCTTGCACGCGAAgg                                                                                                                                        <  4:257382/148‑1 (MQ=255)          gATGGTGAATGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCCTGGGGGTTGCGTTGGACCACATAGCGTGCAACCCCGCCAAg                                                                                                                                         >  1:126985/1‑149 (MQ=255)            tGGTGAATGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACC‑‑‑GGGGTTGCGTTTCAGCCCTTAGCGTGCAAGCCCGCGAAGGGTTg                                                                                                                                    >  6:357752/1‑149 (MQ=255)               tGAATGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACC‑‑‑GGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAGGGTTgcaa                                                                                                                                 <  8:271147/149‑1 (MQ=255)                            ggtggtGCGCCAGGGGCGGCATGCCCAGGAAGATGAACGCGGGCGGGCGTTGGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACC‑‑‑GGGGTGGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAGGGTTGCAACGCAACCCCaaa                                                                                                                     <  7:202293/148‑1 (MQ=255)                                 tgCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACC‑‑‑GGGGTTGCGTTGCAGCCCATAGCGTGCAACCCCGCGAAGGGTTGCAACGCAACCCCaaaaaaaa                                                                                                                >  8:191405/1‑146 (MQ=255)                                  gcgcCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACC‑‑‑GGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCTATGGGTTGCAACGCAACCCCAAAAAACTCa                                                                                                              <  2:251511/149‑1 (MQ=255)                                      cAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACC‑‑‑GGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAGGGTTgcaacgcaa                                                                                                                            <  2:332442/131‑1 (MQ=255)                                          ggcggcATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACC‑‑‑GGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCAttt                                                                                                      <  5:276600/149‑1 (MQ=255)                                                   cccATGAAGATGAATGGGGGGGGGCGTTTGCCAAGTTGTTGCGCCTTCTTTTGGGCTGAGGTTACC‑‑‑GGGGTTGGGTTGCTCCCGTTCGCTTGCAAGCCGGCGATGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTAtt                                                                                              <  2:126985/148‑1 (MQ=255)                                                    ccAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACC‑‑‑GGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAg                                                                                                                                         <  6:354188/104‑1 (MQ=255)                                                    ccAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACC‑‑‑GGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAg                                                                                                                                         >  5:354188/1‑104 (MQ=255)                                                                                      gtgtTGCTCCAGCTTTTGGGGTGAGCGTACG‑‑‑GGGGTTGCGTTGCAGGCCTTCGCGTGCATGGCGGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGgtg                                                          <  8:99302/149‑1 (MQ=255)                                                                                        gtTGCGCCAGCTTTTGGGCTGAGCGTACC‑‑‑GGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAGGTTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTc                                                        <  7:191405/149‑1 (MQ=255)                                                                                              ccAGCTTTTGGGCTGAGCTTACC‑‑‑GGGGTTGCGTTGCAGCCCTTCGCGTTCAAGCCCGATAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATAccc                                                  <  7:136240/149‑1 (MQ=255)                                                                                                        ggCTGAGCGTACC‑‑‑GTGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGGGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCcgc                                        <  2:294726/149‑1 (MQ=255)                                                                                                        ggCTGAGCGTACC‑‑‑GGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCcgc                                        <  1:235186/149‑1 (MQ=255)                                                                                                         gCTGAGCGTACC‑‑‑GGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTc                                                        <  5:110495/132‑1 (MQ=255)                                                                                                          cTGAGCGTACC‑‑‑GGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCgcgc                                      <  5:368397/149‑1 (MQ=255)                                                                                                                ttACC‑‑‑GGGTTTCCGTTGCAGCCGTTCGCGGGAAAGCCCGCTAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGa                                <  7:320705/148‑1 (MQ=255)                                                                                                                         gggTTGCTTTGCAGCCCTTGGCGTACAAGCCCGCTATGGTTTGAAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGAcagcag                          <  3:269557/149‑1 (MQ=255)                                                                                                                          ggTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAgg                         <  7:64448/149‑1 (MQ=255)                                                                                                                              gcgttgcAGCCCTTCGCGTGCAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTg                                                             <  4:70231/109‑1 (MQ=255)                                                                                                                              gcgttgcAGCCCTTCGCGTGCAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTg                                                             >  3:70231/1‑109 (MQ=255)                                                                                                                                gttgcAACCCTTCGCGGGCTTGCACGCGAAGGGCTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGAc                               >  8:4122/1‑137 (MQ=37)                                                                                                                                gttgcAACCCTTCGCGGGCTTGCACGCGAAGGGCTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGAc                               <  7:4122/137‑1 (MQ=37)                                                                                                                                  tgcAGCCCTTCGCGTGCAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGAcagcag                          <  3:79263/140‑1 (MQ=255)                                                                                                                                  tgcAGCCCTTCGCGTGCAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGAcagcag                          >  4:79263/1‑140 (MQ=255)                                                                                                                                    caacccTTCGCGGGCTTGCACGCGAAGGGCTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCt               >  2:52086/4‑149 (MQ=38)                                                                                                                                     aGCCCTTCGCGTGCAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTc              >  3:28999/1‑149 (MQ=255)                                                                                                                                      gCCCTTCGCGTGCAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAAGTCAGTGGATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTcc             >  1:95042/1‑149 (MQ=255)                                                                                                                                      acccTTCGCGTGCAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTtc                      >  1:286955/2‑140 (MQ=255)                                                                                                                                      acccTTCGCGTGCAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTtc                      <  2:286955/139‑1 (MQ=255)                                                                                                                                       cccTTCGCGGGCTTGCACGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCt                                   >  8:61490/1‑126 (MQ=255)                                                                                                                                       cccTTCGCGGGCTTGCACGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCt                                   <  7:61490/126‑1 (MQ=255)                                                                                                                                         cTTCGCGTGCAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTc              >  3:87427/1‑145 (MQ=255)                                                                                                                                         cTTCGCGTGCAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTc              <  4:87427/145‑1 (MQ=255)                                                                                                                                         cTTCGCGTGCAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCCGCCGCGCCCTGGAcagca                           <  5:370501/132‑1 (MQ=255)                                                                                                                                         cTTCGCGTGCAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCAGCCGCGCCCTGGAcagca                           >  6:370501/1‑132 (MQ=255)                                                                                                                                          ttCGCGGGCTTGCACGCGAAGGGCTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTg                                  <  2:172783/124‑1 (MQ=38)                                                                                                                                           tCGCGTGCAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGAcagc                            <  5:301867/129‑1 (MQ=255)                                                                                                                                           tCGCGTGCAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGAcagc                            >  6:301867/1‑129 (MQ=255)                                                                                                                                               gTGCAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCAc                  >  3:374467/1‑135 (MQ=255)                                                                                                                                               gTGCAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCAc                  <  4:374467/135‑1 (MQ=255)                                                                                                                                               gTGCAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAGGCCgg     >  1:165440/1‑148 (MQ=255)                                                                                                                                                tGCAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAGGCCGGCa   <  5:357752/149‑1 (MQ=255)                                                                                                                                                 gCAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAGGCCGGCAg  >  3:160115/1‑149 (MQ=255)                                                                                                                                                       |                                                                                                                                               GCGCGATGTGATGGTGAATGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACC‑‑‑GGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAGGCCGGCAG  >  NC_002947/5740327‑5740616

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑