Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,903,165	A→C	18.8%	intergenic (‑129/‑139)	PP_5175 ← / → PP_5176	HlyD family secretion protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,903,165	0	A	C	18.8%	77.9 / 10.9	49	intergenic (‑129/‑139)	PP_5175/PP_5176	HlyD family secretion protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (14/25);  new base C (4/5);  total (19/30)
Fisher's exact test for biased strand distribution p-value = 7.11e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01

GACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGA‑GCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCGAATGC  >  NC_002947/5903021‑5903307                                                                                                                                                 |                                                                                                                                                gACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCTA‑Gccc                                                                                                                                            >  5:300562/1‑149 (MQ=255) gACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGC‑Gccc                                                                                                                                            >  5:356186/1‑149 (MQ=255)     cATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCTC‑GCCCGCGa                                                                                                                                        <  5:363709/149‑1 (MQ=255)      aTCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGC‑GCCcgcg                                                                                                                                         >  2:320497/1‑147 (MQ=255)      aTCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGA‑GCCcgcg                                                                                                                                         >  6:120035/1‑147 (MQ=255)      aTCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGA‑GCCCGCGaa                                                                                                                                       <  4:314316/149‑1 (MQ=255)       tCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGa                                                                                                                                                 <  5:321291/139‑1 (MQ=255)       tCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGa                                                                                                                                                 >  6:321291/1‑139 (MQ=255)       tCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGA‑GCCcgcg                                                                                                                                         >  5:71166/1‑146 (MQ=255)       tCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTAGCGGGGGG‑Gcccccc                                                                                                                                         >  1:153918/1‑143 (MQ=255)       tCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCATAGCGGGCGA‑GCCCGCCaa                                                                                                                                       >  8:301408/1‑148 (MQ=255)        cAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCTC‑GCCCGCGAaga                                                                                                                                     <  3:71645/149‑1 (MQ=255)         aaCGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCTC‑GCCCGCGAagag                                                                                                                                    <  1:320497/149‑1 (MQ=255)          aCGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGCGGCCCATGATGGCATTTTTCTTGCCTGAGGGGGCCTCATAGCGGGCGA‑GCCCCAGAAGAgg                                                                                                                                   >  1:315251/1‑149 (MQ=255)              cATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGA‑GCCCGCGaa                                                                                                                                       <  1:21873/141‑1 (MQ=255)              cATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGA‑GCCCGCGaa                                                                                                                                       >  2:21873/1‑141 (MQ=255)                  atGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGA‑GCCCGCGAAGAGGCCTCcaca                                                                                                                           <  6:303329/148‑1 (MQ=255)                   tGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTAGCCGGCGA‑GCCCCCGCAGAGGCCTCCACAg                                                                                                                          >  1:279396/1‑149 (MQ=255)                         cttgcttgTCCACAATTTATTTGTGGTATGCTACTGTCAGCGTAGTTCAGGGTGCGATAAACATCACTGACGGGGGCCATGGGGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGA‑GCCCGCTAAGAGGCCTCCACAGCCATGt                                                                                                                    <  4:140008/149‑1 (MQ=255)                             cttgTGCACAAATGATTTGTGGGTTGCGCCTTTTCGCGTTGTTCTGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGGGGGCGA‑GCCCGCGAAGAGGCCTCCACAGCCATGTATCa                                                                                                                <  8:332599/149‑1 (MQ=255)                             cttgTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGA‑GCCCGCGAAGAGGCCTCCACAGCCATGTATCa                                                                                                                <  5:120035/149‑1 (MQ=255)                                gtgCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGA‑GCCCGCGAAGAGGCCTCCACAGCCATGTATCAGt                                                                                                              <  7:271316/148‑1 (MQ=255)                                gtgCAAATATGTTTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCTATAAACATCACTGACGGGGGCCATGCTGGAATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGA‑GCCCGCGAAGAGGCCTCCACAGCCATGTATCAGt                                                                                                              <  2:279396/148‑1 (MQ=255)                                   cacaAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTATTAGCGGGCGA‑GCCCGCGAAACGGCCGCCACAGCCATGTATCAggta                                                                                                            >  3:67718/1‑144 (MQ=255)                                    acaAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTAGCGGGCGA‑GCCCGCGAAGAGGCCTCCACAGCCAAGTATAAGTATCTg                                                                                                         >  5:190239/1‑149 (MQ=255)                                    acaAATCA‑TTGGGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGA‑GCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGc                                                                                                        <  1:325573/149‑1 (MQ=255)                                           aTTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGTGGAGGCCTCTTCGCGGGCTC‑GCCCGCGAaga                                                                                                                                     <  1:259272/114‑1 (MQ=38)                                           aTTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGTGGAGGCCTCTTCGCGGGCTC‑GCCCGCGAaga                                                                                                                                     >  2:259272/1‑114 (MQ=38)                                                       ggACTGTGAGGGTAGTTCAGGGTTCTATAAACATCAGTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGGGGGGGCGTCTTCGCGGGCGA‑GCCCGGGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCa                                                                                      <  6:190239/148‑1 (MQ=255)                                                       cGACTGTGAGCGTTTTTCAGGGTGCTATAAACATCACTGACGGGGGCCATGCTGGAATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGA‑GCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATc                                                                                       <  7:315449/148‑1 (MQ=255)                                                                        cAGGGTTCGATAAACATCACTGACGGGGTCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGA‑GCCCGCTAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATcccc                                                                      <  3:161701/148‑1 (MQ=255)                                                                            gTTGGATAAACATCACTCACGGCGGCCATGCGGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGA‑GCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTcc                                                                 <  6:356186/149‑1 (MQ=255)                                                                                  tAACCATCACTGACGGGGGCCTGGCTGGATTTTTGGGTGCCGGCGGGGGCCTCTGCGCGGGCGC‑GCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAAcc                                                             <  5:225822/147‑1 (MQ=255)                                                                                    aaCATCACTGACGGGGGCCATGGTGGCTTTTTTGGTGCGTGCGGGGGCCTTTTCGCGGGCGA‑TGCCGCTAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTa                                                         <  2:315251/149‑1 (MQ=255)                                                                                     aCATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGA‑GCCCGCGAagag                                                                                                                                    >  8:343811/1‑73 (MQ=255)                                                                                     aCATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGA‑GCCCGCGAagag                                                                                                                                    <  7:343811/73‑1 (MQ=255)                                                                                     aCATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGA‑GCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTAc                                                        <  6:71166/149‑1 (MQ=255)                                                                                       aTCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCGCTTCGCGGGCGC‑GGCCGCGCAGAGGGCGCCCCCGCCAGGTATCAGGTTATGCCATATGCAGAAAACCTCAGGCAGCGGGCCTCCCCCTTCCTACCGcg                                                          >  8:319813/1‑144 (MQ=255)                                                                                          aCTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGA‑GCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATc                                                                                                  >  7:231985/1‑102 (MQ=255)                                                                                          aCTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGA‑GCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATc                                                                                                  <  8:231985/102‑1 (MQ=255)                                                                                              aCGGGGGCCATGCTGGCTTTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGA‑GCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAg                                               <  2:231791/149‑1 (MQ=255)                                                                                                     ccATGCTGGCATTTTTGGTGCCTGCGGGGGCCACTTAGCCGGCGA‑GCCCGCGAACAGGCCGACCCACCCCAGTAACAGTATAATCCATATACCGAAACCAAAACGCCTACGCCAACCCCGGTCCCACCGCTACCATTAACAAggcggcg                                        >  2:119781/1‑148 (MQ=255)                                                                                                            ggCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGA‑GCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAg                                               <  6:286033/135‑1 (MQ=255)                                                                                                            ggCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGA‑GCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAg                                               >  5:286033/1‑135 (MQ=255)                                                                                                                tttttGGCGCCGGGGGGCGCTTCTGCGGGGTCGACGCGCTCTTAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCaa                               <  1:119781/148‑1 (MQ=255)                                                                                                                   ttGGTGCCTGCGGGGGACTCTTCGCGGGCGA‑GCCCGCTAAGAGGCCTACACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGaa                           <  7:301408/148‑1 (MQ=255)                                                                                                                             ggggggCGTGTTCGCGGGCGA‑CCCCGAGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGGAGATCAAAATGc                <  3:3422/148‑1 (MQ=255)                                                                                                                                       ttCGCGGGCGA‑GCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGtt            <  7:89673/143‑1 (MQ=255)                                                                                                                                       ttCGCGGGCGA‑GCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGtt            >  8:89673/1‑143 (MQ=255)                                                                                                                                          gcgGGCGA‑GCCCGCTAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCGAAt    <  3:177149/148‑1 (MQ=255)                                                                                                                                           cgGGCGA‑GCCCGCGAAGAGGCCGCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCGAATGc  <  4:67718/149‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                GACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGA‑GCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCGAATGC  >  NC_002947/5903021‑5903307

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: ‑