Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,649,989	C→A	14.6%	G309C (GGC→TGC)	PP_4113 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,649,989	0	C	A	14.6%	130.1 / 13.0	48	G309C (GGC→TGC)	PP_4113	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (23/18);  new base A (3/4);  total (26/22)
Fisher's exact test for biased strand distribution p-value = 6.87e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

TCGCGCGCGCCGACCCGGTGAATGCCCCAGCTCCAGTTCAGCACCCGCACGCCATCTTCGACCAGGTTCACCGAGGCAGCGATGTTGGCGGTGATACCGGCATCCGAGTTGCGCTCTACCATCACCTCGAAGCCAGGGCTGTGCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCGTGGCTTGCCGGGCGGTTACCGTCGCGAGCGTAGAGGCATGTCTGGCCTTGTTCGCAGCCCCCTCGATAATGGCTGAACCCCGGGGCGT  >  NC_002947/4649841‑4650135                                                                                                                                                     |                                                                                                                                                   tCGCGCGCGCCGACCCGGTGAATGCCCCAGCTCCAGTTCAGCACCCGCACGCCATCTTCGCCCAGGTTCACCGAGGCAGCGATGTTGGCGGTGATACCGGCATCCGAGTTGCGCTCTACCATCACCTCGAAGCCAGGGCTGTGCTTGcc                                                                                                                                                    >  7:296725/1‑149 (MQ=255)           cGACCCGGTGAATGCCCCAGCTCCAGTTCAGCACCCGCACGCCATCTTCGACCAGGTTCACCGAGGCAGCGATGTTGGCGGTGATACCGGCATCCGAGTTGCGCTCTACCATCACCTCGAAGCCGGGGCTGGGCAAGCACAGCCCTGGc                                                                                                                                          <  2:112643/149‑1 (MQ=255)                cGGTGAATGCCCCAGCTCCAGTTCAGCACCCGCACGCCATCTTCGACCAGGTTCACCGAGGCAGCGATGTTGGCGGTGATACCGGCATCCGAGTTGCGCTCTACCATCACCTCGAAGCCAGGGCTGGGCAAGCACAGccctg                                                                                                                                            <  6:194835/142‑3 (MQ=255)                cGGTGAATGCCCCAGCTCCAGTTCAGCACCCGCACGCCATCTTCGACCAGGTTCACCGAGGCAGCGATGTTGGCGGTGATACCGGCATCCGAGTTGCGCTCTACCATCACCTCGAAGCCAGGGCTGGGCAAGCACAGccctg                                                                                                                                            >  5:194835/1‑140 (MQ=255)                   tGAATGCCCCAGCTCCAGTTCAGCACCCGCACGCCATCTTCGACCAGGTTCACCGAGGCAGCGATGTTGGCGGTGATACCGGCATCCGAGTTGCGCTCTACCATCACCTCGAAGCCAGGGCTGTGCTTGCCCAGCCCCGGCAAAAAGcc                                                                                                                                  <  7:9153/149‑1 (MQ=255)                                  cAGTTCAGCACCCGCACGCCATCTTCGACCAGGTTCACCGAGGCAGCGATGTTGGCGGTGATACCGGCATCCGAGTTGCGCTCTACCATCACCTCGAAGCCAGGGCTGTGCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGc                                                                                                                   >  7:27169/1‑149 (MQ=255)                                   aGTTCAGCACCCGCACGCCATCTTCGACCAGGTTCACCGAGGCAGCGATGTTGGCGGTGATACCGGCATCCGAGTTGCGCTCTACCATCACCTCGAAGCCAGGGCTGTGCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCg                                                                                                                  <  3:239796/149‑1 (MQ=255)                                        aGCACCCGCACGCCATCATCGACCAGGTTCACCGAGGCAGCGATGTTGGCGGTGATACCGGCATCCGAGTTGCGCTCTACCATCACCTCGAAGCCAGGGCTGTGCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAAt                                                                                                             <  2:314241/149‑1 (MQ=255)                                               gCACGCCATCTTCGACCAGGTTCACCGAGGCAGCGATGTTGGCGGTGATACCGGCATCCGAGTTGCGCTCTACCATCACCTCGAAGCCAGGGCTGTGCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGc                                                                                                       >  8:227065/1‑148 (MQ=255)                                                         ttCGACCAGGTTCACCGAGGCAGCGATGTTGGCGGTGATACCGGCATCCGAGTTGCGCTCTACCATCACCTCGAAGCCAGGGCTGTGCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGc                                                                                            >  5:82089/1‑149 (MQ=255)                                                             aCCAGGTTCACCGAGGCAGCGATGTTGGCGGTGATACCGGCATCCGAGTTGCGCTCTACCATCACCTCGAAGCCAGGGCTGTGCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCGTg                                                                                        >  6:315960/1‑149 (MQ=255)                                                                  gTTCACCGAGGCAGCGATGTTGGCGGTGATACCGGCATCCGAGTTGCGCTCTACCATCACCTCGAAGCCAGGGCTGTGCTTGCCCAGCCCCGGCAAAAAGCCCTCAcc                                                                                                                            <  6:187485/108‑1 (MQ=255)                                                                  gTTCACCGAGGCAGCGATGTTGGCGGTGATACCGGCATCCGAGTTGCGCTCTACCATCACCTCGAAGCCAGGGCTGTGCTTGCCCAGCCCCGGCAAAAAGCCCTCAcc                                                                                                                            >  5:187485/1‑108 (MQ=255)                                                                   ttCACCGAGGCTTCGATGTTGGCGGTGATTCCGGCATCCGAGTTGCGCTCTACCATCACCTCGAAGCCAGGGCTGTGCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGATTGCCTGCGACATGGCTGCCGTGGCTTGc                                                                                  <  8:296725/149‑1 (MQ=255)                                                                      aCCGAGGCAGCGATGTTGGCGGTGATACCGGCATCCGAGTTGCGCTCTACCATCACCTCGAAGCCAGGGCTGTGCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCg                                                                                          <  3:204508/138‑1 (MQ=255)                                                                      aCCGAGGCAGCGATGTTGGCGGTGATACCGGCATCCGAGTTGCGCTCTACCATCACCTCGAAGCCAGGGCTGTGCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCg                                                                                          >  4:204508/1‑138 (MQ=255)                                                                          aGGCAGCGATGTTGGCGGTGATACCGGCATCCGAGTTGCGCTCTACCATCACCTCGAAGCCAGGGCTGTGCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCGTGGCTTGCCGGGCgg                                                                           <  3:230499/149‑1 (MQ=255)                                                                              aGCGATGTTGGCGGTGATACCGGCATCCGAGTTGCGCTCTACCATCACCTCGAAGCCAGGGCTGTGCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCGTGGCTTGCCGGGCGGTTAc                                                                       >  2:144798/1‑149 (MQ=255)                                                                                  aTGTTCGCGGTGATACCGGCATCCGAGATGCGCTCTACCATCACCAAGAAGCCAGGGCAGTGCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCGTGGCTTGCCGGGCGGTTACCGTc                                                                   >  6:314329/1‑149 (MQ=255)                                                                                     ttGGCGGTGATACCGGCATCCGAGTTGCGCTCTACCATCACCTCGAAGCCAGGGCTGTGCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCGTGGCTTGCCGGGCGGTTACCGTcgc                                                                 <  8:27169/148‑1 (MQ=255)                                                                                          ggTGATACCGGCATCCGAGTTGCGCTCTACCATCACCTCGAAGCCAGGGCTGTGCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCGTGGCTTGCCGGGCGGTTACCGTCGCGAGCGt                                                           <  3:6851/149‑1 (MQ=255)                                                                                                aCCGGCATCCGAGTTGCGCTCTACCATCACCTCGAAGCCAGGGCTGTGCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCGTGGCTTGCCGGGCGGTTACCGTCGCGAGCGTAGAgg                                                      >  1:23831/1‑148 (MQ=255)                                                                                                       tCCGAGTTGCGCTCTACCATCACCTCGAAGCCAGGGCTGTGCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCGTGGCTTGCCGGGCGGTTACCGTCGCGAGCGTAGAGGCATGTCTg                                              >  4:71763/1‑149 (MQ=255)                                                                                                        ccGAGTTGCGCTCTACCATCACCTCGAAGCCAGGGCTGTGCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCGTGGCTTGCCGGGc                                                                             >  5:79019/1‑117 (MQ=255)                                                                                                        ccGAGTTGCGCTCTACCATCACCTCGAAGCCAGGGCTGTGCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCGTGGCTTGCCGGGc                                                                             <  6:79019/117‑1 (MQ=255)                                                                                                               gcgcTCTACCATCACCTCGAAGCCAGGGCTGTGCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCGTGGCTTGCCGGGCGGTTACCGTCGCGAGCGTAGAGGCATGTCTGGCCTTGt                                       <  5:315960/148‑1 (MQ=255)                                                                                                                  ctctACCATCACCTCGAAGCCAGGGCTGTGCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCGTGGCTTGCCGGGCGGTTACCGTCGCGAGCGTAGAGGCATGTCTGGCCTTGTTCg                                    >  2:28204/1‑148 (MQ=255)                                                                                                                     tACCATCACCTCGAAGCCAGGGCTGTGCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCGTGGCTTGCCGGGCGGTTACCGTCGCGAGCGTAGAGGCATGTCTGGCCTTGTTCGCa                                  <  2:321499/147‑1 (MQ=255)                                                                                                                       ccATCACCTCGAAGCCAGGGCTGTGCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCGTGGCTTGCCGGGCGGTTACCGTCGCGAGCGTAGAGGCATGTCTGGCCTTGTTCGCAGccc                              >  5:326967/1‑149 (MQ=255)                                                                                                                              cTCGAAGCCAGGGCTGTGCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCGTGGCTTGCCGGGCGGTTACCGTCGCGAGCGTaga                                                        >  5:247355/1‑116 (MQ=255)                                                                                                                              cTCGAAGCCAGGGCTGTGCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCGTGGCTTGCCGGGCGGTTACCGTCGCGAGCGTaga                                                        <  6:247355/116‑1 (MQ=255)                                                                                                                              cTCGAAGCCAGGGCTGTGCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCGTGGCTTGCCGGGCGGTTACCGTCGCGAGCGTAGAGGCATGTCTGGCCTTGTTCGCAGCCCCCTCGa                        >  6:144129/1‑148 (MQ=255)                                                                                                                                cGAAGCCAGGGCTGTGCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCGTGGCTTGCCGGGCGGTTACCGTCGCGAGCGTAGAGGCATGTCTGGCCTTGTTCGCAGCCCCCTCGATaa                     >  7:121536/1‑149 (MQ=255)                                                                                                                                    gCCAGGGCTGTGCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCGTGGCTTGCCGGGCGGTTACCGTCGCGAGCGTAGAGGCATGTCTGGCCTTGTTCGCAGCCCCCTCGATAATGGc                 >  2:62982/1‑149 (MQ=255)                                                                                                                                     ccAGGGCTGTGCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCGTGGCTTGCCGGGCGGTTACCGTCGCGAGCGTAGAGGCATGTCTGGCCTTGTTCGCAGCCCCCTCGATAATGGCt                <  1:62982/149‑1 (MQ=255)                                                                                                                                      cggggCTGGGCAAGCACAGCCCTGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCGTGGCTTGCCGGGCGGTTACCGTCGCGAGCGTAGAGGCATGTCTGGCCTTGTTCGc                                   <  3:292556/127‑1 (MQ=255)                                                                                                                                      cggggCTGGGCAAGCACAGCCCTGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCAGTGGCTTGCCGGGCGGTTACCGTCGCGAGCGTAGAGGCATGTCTGGCCTTGTTCGc                                   >  4:292556/3‑129 (MQ=255)                                                                                                                                      cggggCTGGGCAAGCACAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCGTGGCTTGCCGGGCGGTTACCGTCGCGAGCGTAGAGGCATGTCTGGCCTTGTTCGCAGCCCCCTCGATAATGGCt                >  4:276771/3‑148 (MQ=255)                                                                                                                                      cggggCTGGGCAAGCACAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCGTGGCTTGCCGGGCGGTTACCGTCGCGAGCGTAGAGGCATGTCTGGCCTTGTTCGCAGCCCCCTCGATAATGGCTg               <  3:276771/147‑1 (MQ=255)                                                                                                                                      cAGGGCTGTGCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCGTGGCTTGCCGGGCGGTTACCGTCGCGAGCGTAGAGGCATGTCTGGCCTTGTTCGCa                                  >  1:64226/1‑130 (MQ=255)                                                                                                                                      cAGGGCTGTGCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCGTGGCTTGCCGGGCGGTTACCGTCGCGAGCGTAGAGGCATGTCTGGCCTTGTTCGCa                                  <  2:64226/130‑1 (MQ=255)                                                                                                                                            tgtgCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCGTGGCTTGCCGGGCGGTTACCGTCGCGAGCGTAGAGGCATGTCTGGCCTTGTTCGCAGCCCCCTCGATAATGGCTGAAcccc         <  8:121536/149‑1 (MQ=255)                                                                                                                                            tgtgCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCGTGGCTTGCCGGGCGGTTACCGTCGCGAGCGTAGAGGCATGTCTGGCCTTGTTCGCAGCCCCCTCGATAATGGCTGAAcccc         >  1:239215/1‑149 (MQ=255)                                                                                                                                              tgCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCGTGGCTTGCCGGGCGGTTACCGTCGCGAGCGTAGAGGCATGTCTGGCCTTGTTCGCAGCCCCCTCGATAATGGCTGAACCCCg        <  6:326967/148‑1 (MQ=255)                                                                                                                                               gCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCGTGGCTTGCCGGGCGGTTACCGTCGCGAGCGTAGAGGCATGTCTGGCCTTGTTCGCAGCCCCCTCGATAATGGCTGAACCCCggg      >  7:816/1‑149 (MQ=255)                                                                                                                                                cTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCGTGGCTTGCCGGGCGGTTACCGTCGCGAGCGTAGAGGCATGTCTGGCCTTGTTCGCAGCCCCCTCGATAATGGCTGAAccc          <  2:302886/144‑1 (MQ=255)                                                                                                                                                cTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCGTGGCTTGCCGGGCGGTTACCGTCGCGAGCGTAGAGGCATGTCTGGCCTTGTTCGCAGCCCCCTCGATAATGGCTGAAccc          >  1:302886/1‑144 (MQ=255)                                                                                                                                                cTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCGTGGCTTGCCGGGCGGTTACCGTCGCGAGCGTAGAGGCATGTCTGGCCTTGTTCGCAGCCCCCTCGATAATGGCTGAACCCCgggg     >  4:169058/1‑149 (MQ=255)                                                                                                                                                   gCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCGTGGCTTGCCGGGCGGTTACCGTCGCGAGCGTAGAGGCATGTCTGGCCTTGTTCGCAGCCACCTCGATAATGGCTGAACCCCGGGGCGt  >  7:97800/1‑149 (MQ=255)                                                                                                                                                     |                                                                                                                                                   TCGCGCGCGCCGACCCGGTGAATGCCCCAGCTCCAGTTCAGCACCCGCACGCCATCTTCGACCAGGTTCACCGAGGCAGCGATGTTGGCGGTGATACCGGCATCCGAGTTGCGCTCTACCATCACCTCGAAGCCAGGGCTGTGCTTGCCCAGCCCCGGCAAAAAGCCCTCACCCTGCGCAGCGAGAATGCCTGCGACATGGCTGCCGTGGCTTGCCGGGCGGTTACCGTCGCGAGCGTAGAGGCATGTCTGGCCTTGTTCGCAGCCCCCTCGATAATGGCTGAACCCCGGGGCGT  >  NC_002947/4649841‑4650135

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: ‑