Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,388,948	T→C	7.7%	Q598R (CAA→CGA)	PP_3865 ←	tail protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,388,948	0	T	C	7.7%	145.6 / 3.1	52	Q598R (CAA→CGA)	PP_3865	tail protein
Reads supporting (aligned to +/- strand):  ref base T (26/22);  new base C (2/2);  total (28/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.79e-01

TCCCATGGTTCGCCGCCCGACATTCGGCGTGATGGTCACGCCGGGCTGACTGGTTTTCACCGACTCGACACGCAGGCCAGGCGGCGAGTTATCGAAGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCGGTGCGGGCAGCGGGGTCGCCGCACGCAACAGCGCCTCAGGGCTTACCCCAAAGGCTTGCTCGCGCGCCGCCTGGACGCCCTGCGC  >  NC_002947/4388800‑4389090                                                                                                                                                      |                                                                                                                                                tCCCATGGTTCGCCGCCCGACATTCGGCGTGATGGTCCCGCCGGGCTGACTGGTTTTCACCGACTCGACACGCAGGCCAGGCGGCGAGTTATCGAAGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAt‑t                                                                                                                                                 >  4:259137/1‑149 (MQ=255)  cccATGGTTCGCCGCCCGACATTCGGGGTGATGGTCACGCCGGGCTGACTGGTTTTCACCGACTCGACACGCAGGCCAGGCGGCGAGTTATCGAAGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAt‑t                                                                                                                                                 >  1:198448/1‑148 (MQ=255)    cctGGTTCGCCGCCCGTCTATCGGCGTGATGGTCACGCCGGGCTGACTGGTGTTCACCGACTCGACACGCAGGCCAGGCGGCGAGTTATCGAAGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGAc                                                                                                                                              <  8:146489/147‑1 (MQ=255)     aTGGTTCGCCGCCCGACATTCGGCGTGATGGGCACGCCGGGCTGACTGGTTTTCACCGACTCGACACGCAGGCCAGGCGGCGAGTTATCGAAGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACg                                                                                                                                             <  7:247501/149‑1 (MQ=255)        gTTCGCCGCCCGACATTCGGCGTGATGGTCACGCCGGGCTGACTGGTTTTCACCGACTCGACACGCAGGCCAGGCGGCGAGTTATCGAAGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCa                                                                                                                                           <  4:67467/148‑1 (MQ=255)            gccgccCGACATTCGGCGTGATGGTCACGCCGGGCTGACTGGTTTTCACCGACTCGACACGCAGGCCAGGCGGCGAGTTATCGAAGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTa                                                                                                                                        >  5:130004/1‑147 (MQ=255)            gccgccCGACATTCGGCGGGATGGTCACGCCGGGCTGTCTGGTTTTCACCGACTCGACACGCAGGCCAGGCGGCGAGTTATCGAAGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTaa‑a                                                                                                                                     <  4:200813/149‑1 (MQ=255)               gccCGACATTCGGCGTGATGGTCACGCCGGGCTGACTGGTTTTCACCGACTCGACACGCAGGCCAGGCGGCGAGTTATCGAAGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGTCAAT‑CGGCGCAggtgggtg                                                                                                                                   <  6:233324/149‑8 (MQ=255)               gccCGACATTCGGCGTGATGGTCACGCCGGGCTGACTGGTTTTCACCGACTCGACACGCAGGCCAGGCGGCGAGTTATCGAAGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGcc                                                                                                                                  >  2:121267/1‑149 (MQ=255)                      aTTCGGCGTGATGGTCACGCCGGGCTGACTGGTTTTCACCGACTCGACACGCAGGCCAGGCGGCGAGTTATCGAAGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGTCAAT‑CGGCGCAggtggg                                                                                                                                     <  2:27511/140‑6 (MQ=255)                      aTTCGGCGTGATGGTCACGCCGGGCTGACTGGTTTTCACCGACTCGACACGCAGGCCAGGCGGCGAGTTATCGAAGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGTCAAT‑CGGCGCAggtggg                                                                                                                                     >  1:27511/1‑135 (MQ=255)                      aTTCGGCGTGATGGTCACGCCGGGCTGACTGGTTTTCACCGACTCGACACGCAGGCCAGGCGGCGAGTTATCGAAGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCt                                                                                                                           >  3:155527/1‑149 (MQ=255)                           gCGTGATGGTCACGCCGGGCTGACTGGTTTTCACCGACTCGACACGCAGGCCAGGCGGCGAGTTATCGACGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGc                                                                                                                      <  4:316567/149‑1 (MQ=255)                                       cGCCGGGCTGACTGGTTTTCACCGACTCGACACGCAAGCCAGGCGGCGAGTTATCGAAGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCTGCTCGGGCAGTTGGCCGGAc                                                                                                          <  3:259137/149‑1 (MQ=255)                                               tGACTGGTTTTCACCGACTCGACACGCAGGCCAGGCGGCGAGTTATCGAAGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCgcag                                                                                                  >  3:136425/1‑149 (MQ=255)                                                gACTGGTTTTCACCGACTCGACACGCAGGCCAGGCGGCGAGTTATCGAAGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCgcag                                                                                                  >  1:69789/1‑148 (MQ=255)                                                 aCTGGTTTTCACCGACTCGACACGCAGGCCAGGCGGCGAGTTATCGAAGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCgcagca                                                                                                <  2:198448/149‑1 (MQ=255)                                                   tGGTTTTCACCGACTCGACACGCAGGCCAGGCGGCGAGTTATCGAAGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAgg                                                                                              >  5:115587/1‑149 (MQ=255)                                                     gTTTTCACCGACTCGACACGCAGGCCAGGCGGCGAGTTATCGAAGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGgcc                                                                                            >  2:54683/1‑149 (MQ=255)                                                           aCCGACTCGACACGCAGGCCAGGCGGCGAGTTATCGAAGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCgg                                                                                      >  1:19528/1‑149 (MQ=255)                                                           aCCGACTCGACACGCAGGCCAGGCGGCGAGTTATCGAAGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCgg                                                                                      >  6:244119/1‑149 (MQ=255)                                                                   gACACGCAGGCCAGGCGGCGAGTTATCGAAGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCGGTGCggg                                                                                >  6:217053/1‑147 (MQ=255)                                                                   gACACGCAGGCCAGGCGGCGAGTTATCGAAGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCACCGGGCGGCCTGCTGCGGGc                                                                               <  1:121267/148‑1 (MQ=255)                                                                        gCAGGCCAGGCGGCGAGTTATCGAAGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTAACAGCCCCCGGCTCGGGCAGTTGGCCGGAc                                                                                                          <  1:22996/117‑1 (MQ=255)                                                                        gCAGGCCAGGCGGCGAGTTATCGAAGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGAc                                                                                                          >  2:22996/1‑116 (MQ=255)                                                                        gCAGGCCAGGCGGCGAGTTATCGAAGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCGGTGCGGGCAGCggg                                                                         >  4:288676/1‑149 (MQ=255)                                                                               aggcGGCGAGTTATCGAAGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCGGTGCGGGCAGCGGGGTcgc                                                                    <  7:249251/147‑1 (MQ=255)                                                                               aggcGGCGAGTTATCGAAGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCGGTGCGGGCAGCGGGGTcgc                                                                    >  8:249251/1‑147 (MQ=255)                                                                                  cggcgAGTTATCGAAGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCGGTGCGGGCAGCGGGGTCGCcgcac                                                               <  1:51784/149‑1 (MQ=255)                                                                                  cggcgAGTTATCGAAGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCGGTGCGGGCAGCGGGGTCGCcgcac                                                               <  6:122449/149‑1 (MQ=255)                                                                                           aTCGAAGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCGGTGCGGGCAGCGGGGTCGCCGCACGCAACAgc                                                       <  4:136425/148‑1 (MQ=255)                                                                                               aaGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCGGTGCGGGCAGCGGGGTCGCCGCACGCAACAGCGCCt                                                   >  1:343415/1‑148 (MQ=255)                                                                                                  gCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCGGTGCGGGCAGCGGGGTCGCCGCACGCAACAGCGCCTCAgg                                               >  4:16669/1‑149 (MQ=255)                                                                                                  gCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCGGTGCGGGCAGCGGGGTCGCCGCACGCAACAGCGCCTCAgg                                               <  4:155527/149‑1 (MQ=255)                                                                                                   ccACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCGGTGCGGGCAGCGGGGTCGCCGCACGCAACAGCGCCTCAggg                                              <  2:265944/149‑1 (MQ=255)                                                                                                       ccGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGATGTGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCGGTGCGGGCAGCGGGGTCGCCGCACGCAACAGCGCCTCAGGGCt                                            >  1:273436/1‑148 (MQ=255)                                                                                                                 ccTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCGGTGCGGGCAGCGGGGTCGCCGCACGCAACAGCGCCTCAGGGCTTACCCCAAAGGc                                >  2:107088/1‑149 (MQ=255)                                                                                                                 ccTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCGGTGCGGGCAGCGGGGTCGCCGCACGCAACAGCGCCTCAGGGCTTACCCCAAAGGc                                <  3:288676/149‑1 (MQ=255)                                                                                                                      cAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCGGTGCGGGCAGCGGGGTCGCCGCACGCAACAGCGCCTCAGGGCTTACCCCAAAGGCTTGCt                           <  3:16669/149‑1 (MQ=255)                                                                                                                      cAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCGGTGCGGGCAGCGGGGTCGCCGCACGCAACAGCGCCTCAGGGCTTACCCCAAAGGCTTGCt                           >  7:179676/1‑149 (MQ=255)                                                                                                                          tgctgctTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCGGTGCGGGCAGCGGGGTCGCCGCACGCAACAGCGCCTCAGGGCTTACCCCAAAGGCTTGCTcgcg                       >  6:68987/1‑149 (MQ=255)                                                                                                                              gctTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCGGTGCGGGCAGCGGGGTCGCCGCACGCAACAGCGCCTCAGGGCTTACCCCAAAGGc                                <  4:61826/136‑1 (MQ=255)                                                                                                                              gctTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCGGTGCGGGCAGCGGGGTCGCCGCACGCAACAGCGCCTCAGGGCTTACCCCAAAGGc                                >  3:61826/1‑136 (MQ=255)                                                                                                                               ctTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCGGTGCGGGCAGCGGGGTCGCCGCACGCAACAGCGCCTCAGGGCTTACCCCAAAGGCTTGCTCGCGcgccg                  >  6:292293/1‑149 (MQ=255)                                                                                                                               ctTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCGGTGCGGGCAGCGGGGTCGCCGCACGCAACAGCGCCTCAGGGCTTACCCCAAAGGCTTGCTCGCGcgcc                   <  3:155598/148‑1 (MQ=255)                                                                                                                                ttGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCGGTGCGGGCAGCGGGGTCGCCGCACGCAACAGCGCCTCAGGGCTTACCCCAAAGGCTTGCTCGCGcgccgc                 >  4:205600/1‑149 (MQ=255)                                                                                                                                     acccaccTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCGGTGCGGGCAGCGGGGTCGCCGCACGCAACAGCGCCTCAGGGCTTACCCCAAAGGCTTGCTCGCGCGCCGCCTGGa            >  6:214944/1‑149 (MQ=255)                                                                                                                                     acccaccTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCGGTGCGGGCAGCGGGGTCGCCGCACGCAACAGCGCCTCAGGGCTTACCCCAAAGGCTTGCTCGCGCGCCGCCTGGa            >  7:113365/1‑149 (MQ=255)                                                                                                                                          acTGCGTCAAT‑CGGCGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCGGTGCGGGCAGCGGGGTCGCCGCACGCAACAGCGCCTCAGGGCTTACCCCAAAGGCTTGCTCGCGCGCCGCCTGGACGccc       >  3:336131/2‑149 (MQ=255)                                                                                                                                              cgcCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCGGTGCGGGCAGCGGGGTCGCCGCACGCAACAGCGCCTCAGGGCTTACCCCAAAGGCTTGCTCGCGCGCCGCCTGGACGCCCTgc    <  6:115587/148‑1 (MQ=255)                                                                                                                                               gcCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCGGTGCGGGCAGCGGGGTCGCCGCACGCAACAGCGCCTCAGGGCTTACCCCAAAGGCTTGCTCGCGCGCCGCCTGGACGCCCTgcgc  <  3:110804/149‑1 (MQ=255)                                                                                                                                               gcCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCGGTGCGGGCAGCGGGGTCGCCGCACGCAACAGCGCCTCAGGGCTTACCCCAAAGGCTTGCTCGCGCGCCGCCTGGACGCCCTgcgc  >  4:110804/1‑149 (MQ=255)                                                                                                                                                 cGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGccc                                                                                        >  4:337324/1‑61 (MQ=255)                                                                                                                                                 cGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGccc                                                                                        <  3:337324/61‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                TCCCATGGTTCGCCGCCCGACATTCGGCGTGATGGTCACGCCGGGCTGACTGGTTTTCACCGACTCGACACGCAGGCCAGGCGGCGAGTTATCGAAGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCGGTGCGGGCAGCGGGGTCGCCGCACGCAACAGCGCCTCAGGGCTTACCCCAAAGGCTTGCTCGCGCGCCGCCTGGACGCCCTGCGC  >  NC_002947/4388800‑4389090

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: ‑