Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,388,950	A→G	7.7%	R597R (CGT→CGC)	PP_3865 ←	tail protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,388,950	0	A	G	7.7%	146.6 / 2.6	52	R597R (CGT→CGC)	PP_3865	tail protein
Reads supporting (aligned to +/- strand):  ref base A (26/22);  new base G (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 = 3.54e-01

CATGGTTCGCCGCCCGACATTCGGCGTGATGGTCACGCCGGGCTGACTGGTTTTCACCGACTCGACACGCAGGCCAGGCGGCGAGTTATCGAAGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCGGTGCGGGCAGCGGGGTCGCCGCACGCAACAGCGCCTCAGGGCTTACCCCAAAGGCTTGCTCGCGCGCCGCCTGGACGCCCTGCGCGACCTGCA  >  NC_002947/4388803‑4389098                                                                                                                                                     |                                                                                                                                                      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                                                                            >  8:249251/1‑147 (MQ=255)                                                                            aggcGGCGAGTTATCGAAGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCGGTGCGGGCAGCGGGGTcgc                                                                            <  7:249251/147‑1 (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                                                       <  4:155527/149‑1 (MQ=255)                                                                                               gCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCGGTGCGGGCAGCGGGGTCGCCGCACGCAACAGCGCCTCAgg                                                       >  4:16669/1‑149 (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)                                                                                                                                                     aCGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCGGTGCGGGCAGCGGGGTCGCCGCACGCAACAGCGCCTCAGGGCTTACCCCAAAGGCTTGCTCGCGCGCCGCCTGGACGCCCTGCGCGACCTGCa  >  6:125200/1‑149 (MQ=255)                                                                                                                                                     |                                                                                                                                                      CATGGTTCGCCGCCCGACATTCGGCGTGATGGTCACGCCGGGCTGACTGGTTTTCACCGACTCGACACGCAGGCCAGGCGGCGAGTTATCGAAGGCCACCCGCACCTCCCCTTCCAGCTGCTGCTTGCCACCCACCTGCGCCGAT‑TGACGCAGTAA‑AGCCCCCGGCTCGGGCAGTTGGCCGGACGCCCGCAGCAGGCCGCCCGGTGCGGGCAGCGGGGTCGCCGCACGCAACAGCGCCTCAGGGCTTACCCCAAAGGCTTGCTCGCGCGCCGCCTGGACGCCCTGCGCGACCTGCA  >  NC_002947/4388803‑4389098

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: ‑