Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,762,504	T→C	11.3%	intergenic (+20/‑121)	gpmI → / → PP_5057	2,3‑bisphosphoglycerate‑independent phosphoglycerate mutase/M23/M37 family peptidase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,762,504	0	T	C	11.3%	134.5 / 7.8	53	intergenic (+20/‑121)	gpmI/PP_5057	2,3‑bisphosphoglycerate‑independent phosphoglycerate mutase/M23/M37 family peptidase
Reads supporting (aligned to +/- strand):  ref base T (19/28);  new base C (3/3);  total (22/31)
Fisher's exact test for biased strand distribution p-value = 6.83e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.79e-01

GGCAAGCGCAACGTGAAAGTGCGCGAGGGCGGCGTGCTGGCCGACGTGGCGCCAACCATGCTGAAGCTGCTGGGGCTGG‑AAAAGCCGGTGGAAATGA‑CCGGTACCTCGATTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGTTTTTTTTGCCTGCCCAGGCGGGCATACTAGGCCAGTCTCCATCCTTGGTACGCCAAACCCCATGCTTCGCGCCCTGATCCTC  >  NC_002947/5762359‑5762645                                                                                                                                                    |                                                                                                                                              ggCAAGCGCAACGTGAAAGTGCGCGAGGGCGGCGTGCTGGCCGACGTGGCGCCAACCATGCTGAAGCTGCTGGGGCTGG‑AAAAGCCGGTGGAAATGACCCGGTACCTCGATTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTg                                                                                                                                              <  1:276383/148‑1 (MQ=255)      gcgcAACGTGAAAGTGCGCGAGGGCGGCGTGCTGGCCGACGTGGCGCCAACCATGCTGAAGCTGCTGGGGCTGG‑AAAAGCCGGTGGAAATGA‑CCGGTACCTCGATTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCAGcccc                                                                                                                                       <  4:356709/149‑1 (MQ=255)          aaCGTGAAAGTGCGCGAGGGCGGCGTGCTGGCCGACGTGGCGCCAACCATGCTGAAGCTGCTGGGGCTGG‑AAAAGCCGGTGGAAATGA‑CCGGTACCTCGATTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAAtt                                                                                                                                   <  5:38912/149‑1 (MQ=255)             gTGAAAGGGCGCGAGGGCGGCGTGCTGGCCGACGTGGCGCCAACCATGCTGAAGGTGCTGGGGCTGG‑AAAATGCGGTTGAAATGA‑CCGGTACCTCGATTCTGGGCGACGCCTGAATGTCGAAAGGGGATGCGTTGCAGCCCCAATTGca                                                                                                                                <  3:49179/149‑1 (MQ=255)                aaaGTGCGCGAGGGCGGCGTGCTGGCCGACGTGGCGCCAACCATGCTGAAGCTGCTGGGGCTGG‑AAAAGCCGGTGGAAATGA‑CCGGTACCTCGATTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACAt                                                                                                                             <  4:17593/149‑1 (MQ=255)                       cggAGTGCGGCGTGCTGGCCGACGTGGCGCCAACCATGCTGAAGCTGCTGGGGCTGG‑AAAAGCCGGTGGAAATGA‑CCGGTACCTCGATTCTGGTCGACGCCTGAATGTCGATTGGGGCTGCTTTGCAGCCCCAATTGCACATGAATTcc                                                                                                                      <  4:269411/147‑1 (MQ=255)                              cagcgTGCTGGCCGACGTGGCGCCAACCATGCTGAAGCTGCTGGGGCTGG‑AAAAGCCGGTGGAAATGA‑CCGGTACCTCGATTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACaaa                                                                                                               <  4:223588/147‑1 (MQ=255)                                    gCTGGCCGACGTGGCGCCAACCATGCTGAAGCTGCTGGGGCTGG‑AAAAGCCGGTGGAAATGA‑CCGGTACCTCGATTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTcc                                                                                                                      >  8:190583/1‑136 (MQ=255)                                    gCTGGCCGACGTGGCGCCAACCATGCTGAAGCTGCTGGGGCTGG‑AAAAGCCGGTGGAAATGA‑CCGGTACCTCGATTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTcc                                                                                                                      <  7:190583/136‑1 (MQ=255)                                       ggCCGACGTGGCGCCAACCATGCTGAAGCTGCTGGGGCTGG‑AAAAGCCGGTGGAAATGA‑CCGGTACCTCGATTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCt                                                                                                      >  2:317884/1‑149 (MQ=255)                                                   gcCAACCATGCTGAAGCTGCTGGGGCTGG‑AAAAGCCGGTGGAAATGA‑CCGGTACCTCGATTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGc                                                                                           >  6:32872/1‑148 (MQ=255)                                                   gcCAACCATGCTGAAGCTGCTGGGGCTGG‑AAAAGCCGGTGGAAATGA‑CCGGTACCTCGATTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGc                                                                                           >  3:128813/1‑148 (MQ=255)                                                     cAACCATGCTGAAGCTGCTGGGGCTGG‑AAAAGCCGGTGGAAATGA‑CCGGTACCTCGATTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAg                                                                                        <  8:191397/149‑1 (MQ=255)                                                         cATGCTGAAGCTGCTGGGGCTGGAAAAAGCCGGTGGAAATGA‑CCGGTACCTCGATTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCg                                                                                     >  1:191547/1‑149 (MQ=255)                                                            gCTGAAGCTGCTGGGGCTGG‑AAAAGCCGGTGGAAATGA‑CCGGTACCTCGATTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGtttt                                                                                 >  6:153646/1‑149 (MQ=255)                                                                aaGCTGCTGGGGCTGG‑AAAAGCCGGTGGAAATGA‑CCGGTACCTCGATTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGtttttttt                                                                             <  2:27142/149‑1 (MQ=255)                                                                aaGCTGCTGGGGCTGG‑AAAAGCCGGTGGAAATGA‑CCGGTACCTCGATTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGtttttttt                                                                             >  1:284644/1‑149 (MQ=255)                                                                 aGCTGCTGTGGCTGG‑AAAAGCCGGTGGAAATGA‑CCGTTACCTCGATTCTGTTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGtttttttt                                                                             <  3:45772/148‑1 (MQ=255)                                                                 aGCTGCTGGGGCTGG‑AAAAGCCGGTGGAAATGA‑CCGGTACCTCGATTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGTTTTTTTtg                                                                            <  8:247404/149‑1 (MQ=255)                                                                 aGCTGCTGGGGCTGG‑AAAAGCCGGTGGAAATGA‑CCGGTACCTCGATTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGTTTTTTTtg                                                                            <  1:317884/149‑1 (MQ=255)                                                                  gctgctGGGGCTGG‑AAAAGCCGGTGGAAATGA‑CCGGTACCTCGATTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGTTTTTTTtgc                                                                           <  5:153646/149‑1 (MQ=255)                                                                              gg‑AAAAGCCGGTGGAAATGA‑CCGGTACCTCGATTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCg                                                                                               >  5:197146/1‑117 (MQ=255)                                                                              gg‑AAAAGCCGGTGGAAATGA‑CCGGTACCTCGATTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCg                                                                                               <  6:197146/117‑1 (MQ=255)                                                                                  aaaGCCGGTGGAAATGA‑CCGGTACCTCGATTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGTTTTTTTTGCCTGCCCAGGCGGGCa                                                            >  1:5255/1‑149 (MQ=255)                                                                                        ggTGGAAATGA‑CCGGTACCTCGATTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGTTTTTTTTGCCTGCCCAGGc                                                                 >  8:242683/1‑138 (MQ=255)                                                                                        ggTGGAAATGA‑CCGGTACCTCGATTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGTTTTTTTTGCCTGCCCAGGc                                                                 <  7:242683/138‑1 (MQ=255)                                                                                        ggTGGAAATGA‑CCGGTACCTCGATTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGTTTTTTTTGCCTGCCCAGGCGGGCATACTAg                                                      <  2:284644/149‑1 (MQ=255)                                                                                         gTGGAAATGA‑CCGGTACCTCGATTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGTTTTTTTTGCCTGCCCAGGCGGGCATACTAgg                                                     >  5:114117/1‑149 (MQ=255)                                                                                          tGGAAATGA‑CCGGTACCTCGATTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGTTTTTTTTGCCTGCCCAGGCGGGCATACTAGGc                                                    <  4:128813/149‑1 (MQ=255)                                                                                                     cGGTACCTCGATTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGTTTTTTTTGCCTGCCCAGGCGGGCATACTAGGCCAGtct                                              <  7:320265/145‑1 (MQ=255)                                                                                                     cGGTACCTCGATTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGTTTTTTTTGCCTGCCCAGGCGGGCATACTAGGCCAGtct                                              >  8:320265/1‑145 (MQ=255)                                                                                                        tACCTCGATTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGTTTTTTTTGCCTGCCCAGGCGGGCATACTAGGCCAGTCTCCATCCt                                       <  1:199633/149‑1 (MQ=255)                                                                                                           cTCGATTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCCGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATACGCACAGAGGCGTTTTTTTTTCCTGCCCCGGCCGGCATACTAGGGCAGTGTCCATACTTgg                                    >  6:42614/1‑149 (MQ=255)                                                                                                           cTCGATTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGTTTTTTTTGCCTGCCCAGGCGGGCATACTAGGCCAGTCTCCATCCTTgg                                    >  2:195963/1‑149 (MQ=255)                                                                                                           cTCGATTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGTTTTTTTTGCCTGCCCAGGCGGGCATACTAGGCCAGTCTCCATCCTTgg                                    >  2:190065/1‑149 (MQ=255)                                                                                                            tCGATTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGTTTTTTTTGCCTGCCCAGGCGGGCATACTAGGCCAGTCTCCATCCTTgg                                    >  5:356786/1‑148 (MQ=255)                                                                                                               aTTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGTTTTTTTTGCCTGCCCAGGCGGGCATACTAGGCCAGTCTCCATCCTTGGTACg                                >  6:23763/1‑149 (MQ=255)                                                                                                                          cGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGTTTTTTTTGCCTGCCCAGGCGGGCATACTAGGCCAGTCTCCATCCTTGGTACGCCAAACCCCAt                     <  5:32872/149‑1 (MQ=255)                                                                                                                          cGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGTTTTTTTTGCCTGCCCAGGCGGGCATACTAGGCCAGTCTCCATCCTTGGTACGCCAAACCCCAt                     <  1:190065/149‑1 (MQ=255)                                                                                                                          cGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGTTTTTTTTGCCTGCCCAGGCGGGCATACTAGGCCAGTCTCCATCCTTGGTACGCCAAACCCCAt                     <  1:195963/149‑1 (MQ=255)                                                                                                                               gAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGTTTTTTTTGCCTGCCCAGGCGGGCATACTAGGCCAGTCTCCAt                                          >  5:186168/1‑123 (MQ=255)                                                                                                                               gAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGTTTTTTTTGCCTGCCCAGGCGGGCATACTAGGCCAGTCTCCAt                                          <  6:186168/123‑1 (MQ=255)                                                                                                                                    tCGATAGGCGCGGCGTTGCAGCCCCAATTGCACAAGAATTCCAGACAAACGCCCCCCTGCTTCCGCAGCGAGGCGTTTTTTTTGCCTGCCCAGGCGGGCATACTAGGCCAGTCTCCATCCTTGGTACGCCAAACCCCATGCTTCgcgc            <  8:158126/148‑1 (MQ=255)                                                                                                                                     caattggggCTGCAACGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGTTTTTTTTGCCTGCCCAGGCGGGCATACTAGGCCAGTCTCCATCCTTGGTACGCCAAACCCCATGCTTCGCGccc          >  2:235151/6‑149 (MQ=255)                                                                                                                                     caattggggCTGCAACGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGTTTTTTTTGCCTGCCCAGGCGGGCATACTAGGCCAGTCTCCATCCTTGGTACGCCAAACCCCATGCTTCGCGccc          <  1:235151/144‑1 (MQ=255)                                                                                                                                      gAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGTTTTTTTTGCCTGCCCAGGCGGGCATACTAGGCCAGTCTCCATCCTTGGTACGCCAAACCCCATGCTTCGCGccc          <  1:70016/148‑1 (MQ=255)                                                                                                                                        ttggggCTGCAACGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGTTTTTTTTGCCTGCCCAGGCGGGCATACTAGGCCAGTCTCCATCCTTGGTACGCCaa                            <  1:47953/126‑1 (MQ=255)                                                                                                                                        ttggggCTGCAACGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGTTTTTTTTGCCTGCCCAGGCGGGCATACTAGGCCAGTCTCCATCCTTGGTACGCCaa                            >  2:47953/3‑128 (MQ=255)                                                                                                                                         tggggCTGCAACGCAGCCCCTATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGttt                                                                                  >  6:380198/2‑73 (MQ=38)                                                                                                                                         tggggCTGCAACGCAGCCCCTATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGttt                                                                                  <  5:380198/72‑1 (MQ=38)                                                                                                                                             gCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGTTTTTTTTGCCTGCCCAGGCGGGCATACTAGGCCAGTCTCCATCCTTGGTACGCCAAACCCCATGCTTCGCGCCCTGAtcctc  <  2:5255/149‑1 (MQ=255)                                                                                                                                              cTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGTTTTTTTTGCCTGCCCAGGCGGGCATACTAGGCCAGTCTCCATCCTTGGTACGCCAAACCCCATGCTTCGCGCCCTGAtcctc  >  6:211673/1‑148 (MQ=255)                                                                                                                                              cTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGTTTTTTTTGCCTGCCCAGGCGGGCATACTAGGCCAGTCTCCATCCTTGGTACGCCAAACCCCATGCTTCGCGCCCTGAtcctc  <  5:211673/148‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                              GGCAAGCGCAACGTGAAAGTGCGCGAGGGCGGCGTGCTGGCCGACGTGGCGCCAACCATGCTGAAGCTGCTGGGGCTGG‑AAAAGCCGGTGGAAATGA‑CCGGTACCTCGATTCTGGTCGACGCCTGAATGTCGAAAGGGGCTGCGTTGCAGCCCCAATTGCACATGAATTCCAGACAAACGCCCCCCTGCATCCGCAGCGAGGCGTTTTTTTTGCCTGCCCAGGCGGGCATACTAGGCCAGTCTCCATCCTTGGTACGCCAAACCCCATGCTTCGCGCCCTGATCCTC  >  NC_002947/5762359‑5762645

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: ‑