Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,857,611	T→G	8.9%	L63L (CTT→CTG)  noncoding (69/224 nt)	PP_3407 → PP_mr41 →	hypothetical protein Cobalamin regulatory region

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,857,611	0	T	G	8.9%	165.0 / 8.0	56	L63L (CTT→CTG)  noncoding (69/224 nt)	PP_3407 PP_mr41	hypothetical protein Cobalamin regulatory region
Reads supporting (aligned to +/- strand):  ref base T (27/24);  new base G (2/3);  total (29/27)
Fisher's exact test for biased strand distribution p-value = 6.64e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.53e-01

ACTTCAGGCCTGAGCCTGTCGTACCTGCTGTTCGACAGCCTCGCACGCTGTATGACATTGACGCCAAGCCCGCCCCATGCTCTCCTTATGCCTCGCGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGAGTGAAGCGTCTGTACCACTGTGCCTCGTAGTACGGCATGGGAAGGTGACGCGTTCCAGGAGCCCAGCTCTTCCTCGCAAGCCCGGAGACCGGCCTGGCGT  >  NC_002947/3857463‑3857757                                                                                                                                                     |                                                                                                                                                   aCTTCAGGCCTGAGCCTGTCGTACCTGCTGTTCGACAGCCTCGCACGCTGTATGACATTGACGCCAAGCCCGCCCCATGCTCTCCTTATGCCTCCCGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCtt                                                                                                                                                    <  3:303076/149‑1 (MQ=255)      aGGCCTGAGCCTGTCGTACCTGCTGTTCGACAGCCTCGCACGCTGTATGACATTGACGCCAAGCCCGCCCCATGCTCTCCTTATGCCTCGCGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTcag                                                                                                                                                 >  1:44197/1‑147 (MQ=255)      aGGCCGGAGCCTGTCGTACCTGCTGTTCGACAGCGTCGCACGCTGTATGACATTGACGCCAAGCCCGCCCCATGCTCTCCTTATGCCTCGCGTTCTGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTcagc                                                                                                                                                <  6:35574/148‑1 (MQ=255)          cTGAGCCTGTCGTACCTGCTGTTCGACAGCCTCGCACGCTGTATGACATTGACGCCAAGCCCGCCCCATGCTCTCCTTATGCCTCGCGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAggg                                                                                                                                            <  8:321292/148‑1 (MQ=255)          cTGAGCCTGTCGTACCTGCTGTTCGACAGCCTCGCACGCTGTATGACATTGACGCCAAGCCCGCCCCATGCTCTCCTTATGCCTCGCGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAggg                                                                                                                                            >  7:321292/1‑148 (MQ=255)             aGCCTGTCGTACCTGCTGTTCGACAGCCTCGCACGCTGTATGACATTGACGCCAAGCCCGCCCCATGCTCTCCTTATGCCTCGCGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGcc                                                                                                                                          <  7:21828/147‑1 (MQ=255)              gCCTGTCGTACCTGCTGTTCGACAGCCTCGCACGCTGTATGACATTGACGCCAAGCCCGCCCCATGCTCTCCTTATGCCTCGCGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTGCTGAAGGGcctgg                                                                                                                                       <  4:313099/149‑4 (MQ=255)                       aCCTGCTGTTCGACAGCCTCGCACGCTGTATGACATTGACGCCAAGCCCGCCCCATGCTCTCCTTATGCCTCGCGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCgg                                                                                                                              >  8:86888/1‑149 (MQ=255)                          tgctgTTCGACATCCTCGCACGCTGTATGACATTGACGCCAAGCCCGCCCCATGCTCTCCTTATGCCTCGCGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGc                                                                                                                                 <  6:96806/143‑1 (MQ=255)                          tgctgTTCGACAGCCTCGCACGCTGTATGACATTGACGCCAAGCCCGCCCCATGCTCTCCTTATGCCTCGCGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGc                                                                                                                                 >  5:96806/1‑143 (MQ=255)                           gctgTTCGACAGCCTCGCACGCTGTATGACATTGACGCCAAGCCCGCCCCATGCTCTCCTTATGCCTCGCGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGtgct                                                                                                                          >  5:148583/1‑149 (MQ=255)                             tgTTCGACAGCCTCGCACGCTGTATGACATTGACGCCAAGCCCGCCCCATGCTCTCCTTATGCCTCACGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGa                                                                                                                                       <  6:275866/134‑1 (MQ=255)                             tgTTCGACAGCCTCGCACGCTGTATGACATTGACGCCAAGCCCGCCCCATGCTCTCCTTATGCCTCACGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGa                                                                                                                                       >  5:275866/1‑134 (MQ=255)                                  gACAGCCTCGCACGCTGTATGACATTGACGCCAAGCCCGCCCCATGCTCTCCTTATGCCTCGCGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCg                                                                                                                   >  8:111106/1‑149 (MQ=255)                                      gCCTCGCACGCTGTATGACATTGACGCCAAGCCCGCCCCATGCTCTCCTTATGCCTCGCGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAAc                                                                                                               <  7:86888/149‑1 (MQ=255)                                             aCGCTGTATGACATTGACGCCAAGCCCGCCCCATGCTCTCCTTATGCCTCGCGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGc                                                                                                        >  6:162329/1‑149 (MQ=255)                                                 tGTATGACATTGACGCCAAGCCCGCCCCATGCTCTCCTTATGCCTCGCGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCCGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGAGt                                                                                                    >  4:86365/1‑149 (MQ=255)                                                   tATGACATTGACGCCAAGCCCGCCCCATGCTCTCCTTATGCCTCGCGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGAGt                                                                                                    <  7:111106/147‑1 (MQ=255)                                                      gACATTGACGCCAAGCCCGCCCCATGCTCTCCTTATGCCTCGCGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGAGTGAAGc                                                                                               >  6:168207/1‑149 (MQ=255)                                                       aCATTGACGCCAAGCCCGCCCCATGCTCTCCTTATGCCTCGCGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGAGTGAAGCg                                                                                              >  3:224012/1‑149 (MQ=255)                                                        cATTGACGCCAAGCCCGCCCCATGCTCTCCTTATGCCTCGCGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGAGTGAAGCGt                                                                                             >  6:204862/1‑149 (MQ=255)                                                                ccAAGCCCGCCCCATGCTCTCCTTATGCCTCGCGTTCAGGTGCACCTCAGGGGGTGAAACAGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGAGTGAAGCGTCTGTACCa                                                                                     >  1:275244/1‑149 (MQ=255)                                                                 cAAGCCCGCCCCATGCTCTCCTTATGCCTCGCGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTGCTGAAGGGcct                                                                                                                                         <  4:294572/96‑2 (MQ=39)                                                                 cAAGCCCGCCCCATGCTCTCCTTATGCCTCGCGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTGCTGAAGGGcct                                                                                                                                         >  3:294572/1‑95 (MQ=39)                                                                 cAAGCCCGCCCCATGCTCTCCTTATGCCTCGCGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTGCTGAAGGGcct                                                                                                                                         <  2:215539/96‑2 (MQ=39)                                                                 cAAGCCCGCCCCATGCTCTCCTTATGCCTCGCGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTGCTGAAGGGcct                                                                                                                                         >  1:215539/1‑95 (MQ=39)                                                                    gcccgcccCATGCTCTCCTTATGCCTCGCGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGAGTGAAGCGTCTGTACCACtgt                                                                                 >  7:239078/1‑149 (MQ=255)                                                                     cccgcccCATGCTCTCCTTATGCCTCGCGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGAGTGAAGCGTCTGTACCACtgtg                                                                                <  3:260359/149‑1 (MQ=255)                                                                       cgcccCATGCTCTCCTTATGCCTCGCGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGAGTGAAGCGTCTGTACCACTGTGcc                                                                              <  8:239078/149‑1 (MQ=255)                                                                            cATGCTCTCCTTATGCCTCGCGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGAGTGAAGCGTCTGTACCACTGTGCCTCgta                                                                         <  5:162329/149‑1 (MQ=255)                                                                                     cTTATGCCTCGCGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGAGTGAAGCGTCTGTACCACTGTGCCTCGTAGTACGGCAt                                                                <  8:185847/149‑1 (MQ=255)                                                                                        aTGCCTCGCGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGAGt                                                                                                    <  1:316916/110‑1 (MQ=255)                                                                                        aTGCCTCGCGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGAGt                                                                                                    >  2:316916/1‑110 (MQ=255)                                                                                           ccTCGCGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGAGTGAAGCGTCTGTACCACTGTGCCTCGTAGTACGGCATGGGAAg                                                          <  6:58098/149‑1 (MQ=255)                                                                                           ccTCGCGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGAGTGAAGCGTCTGTACCACTGTGCCTCGTAGTACGGCATGGGAAg                                                          >  5:58098/1‑149 (MQ=255)                                                                                             tCGCGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGa                                                                                                      >  1:242548/1‑103 (MQ=255)                                                                                             tCGCGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGa                                                                                                      <  2:242548/103‑1 (MQ=255)                                                                                               gcgTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGAGTGAAGCGTCTGTACCACTGTGCCTCGTAGTACGGCATg                                                               >  7:218352/1‑140 (MQ=255)                                                                                               gcgTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGAGTGAAGCGTCTGTACCACTGTGCCTCGTAGTACGGCATg                                                               <  8:218352/140‑1 (MQ=255)                                                                                                cgTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGAGTGAAGCGTCTGTACCACTGTGCCTCGTAGTACGGCATGGGAAGGTGAc                                                     <  4:224012/149‑1 (MQ=255)                                                                                                          ccccTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCGGGCAACGGTAAGCGAGTGAAGCGTCTGTACCACTGTGCCTCGTAGTACGGCATGGGAAGGTGACGCGTTCCAg                                            <  6:148583/148‑1 (MQ=255)                                                                                                          ccccTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGAGTGAAGCGTCTGTACCACTGTGCCTCGTAGTACGGCATGGGAAGGTGACGCGTTCCAg                                            <  2:275244/148‑1 (MQ=255)                                                                                                            ccTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGAGTGAAGCGt                                                                                             >  7:241081/1‑97 (MQ=255)                                                                                                            ccTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGAGTGAAGCGt                                                                                             <  8:241081/97‑1 (MQ=255)                                                                                                            ccTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGAGTGAAGCGTCTGTACCACTGTGCCTCGTAGTACGGCATGGGAAGGTGACGCGTTCCAGGAg                                         <  5:204862/149‑1 (MQ=255)                                                                                                                  ggggTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGAGTGAAGCGTCTGTACCACTGTGCCTCGTAGTACGGCATGGGAAGGTGACGCGTTCCAGGAGCCCAGc                                   >  8:77833/1‑149 (MQ=255)                                                                                                                        aaaCGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGc                                                                                                        >  6:53871/1‑74 (MQ=255)                                                                                                                        aaaCGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGc                                                                                                        <  5:53871/74‑1 (MQ=255)                                                                                                                          aCGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGAGTGAAGCGTCTGTACCACTGTGTCTCGTAGTACGGCATGGGAAGGTGACGCGTTCCAGGAGCCCAGCTCTTCCTc                           >  5:127044/1‑149 (MQ=255)                                                                                                                                 aCCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGAGTGAAGCGTCTGTACCACTGTGCCTCGTAGTACGGCATGGGAAGGTGACGCGTTCCAGGAGCCCAGCTCTTCCTCGCAAGcc                    >  2:67887/1‑149 (MQ=255)                                                                                                                                    ggTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGAGTGAAGCGTCTGTACCACTGTGCCTCgta                                                                         >  7:308210/1‑93 (MQ=255)                                                                                                                                    ggTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGAGTGAAGCGTCTGTACCACTGTGCCTCgta                                                                         <  8:308210/93‑1 (MQ=255)                                                                                                                                     gTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGAGTGAAGCGTCTGTACCACTGTGCCTCGTAGTACGGCATGGGAAGGTGACGCGTTCCAGGAGCCCAGCTCTTCCTCGCAAGCCCg                  >  3:287156/1‑147 (MQ=255)                                                                                                                                         gTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGAGTGAAGCGTCTGTACCACTGTGCCTCGTAGTACGGCATGGGAAGGTGACGCGTTCCAGGAGCCCAGCTCTTCCTCGCAAGCCCGGAGAcc            >  7:262553/1‑149 (MQ=255)                                                                                                                                           cccAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGAGTGAAGCGTCTGTACCACTGTGCCTCGTAGTACGGCATGGGAAGGTGACGCGTTCCAGGAGCCCAGCTCTTCCTCGCAAGCCCGGAGACCgg          >  3:143650/1‑149 (MQ=255)                                                                                                                                               ggCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGAGTGAAGCGTCTGTACCACTGTGCCTCGTAGTACGGCATGGGAAGGTGACGCGTTCCAGGAGCCCAGCTCTTCCTCGCAAGCCCGGAGACCGGCCTg      <  4:143650/149‑1 (MQ=255)                                                                                                                                                   cTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGAGTGAAGCGTCTGTACCACTGTGCCTCGTAGTACGGCATGGGAAGGTGACGCGTTCCAGGAGCCCAGCTCTTCCTCGCAAGCCCGGAGACCGGCCTGGCGt  <  2:44197/149‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                   ACTTCAGGCCTGAGCCTGTCGTACCTGCTGTTCGACAGCCTCGCACGCTGTATGACATTGACGCCAAGCCCGCCCCATGCTCTCCTTATGCCTCGCGTTCAGGTGCCCCTCAGGGGGTGAAACGGGAAACCGGTGCGTCCCAGGCCCTTCAGCAGGGCCGGACAATGCCGGTGCTGCCCCCGCAACGGTAAGCGAGTGAAGCGTCTGTACCACTGTGCCTCGTAGTACGGCATGGGAAGGTGACGCGTTCCAGGAGCCCAGCTCTTCCTCGCAAGCCCGGAGACCGGCCTGGCGT  >  NC_002947/3857463‑3857757

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: ‑