Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,414,942	C→T	11.9%	A56T (GCA→ACA)	PP_3027 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,414,942	0	C	T	11.9%	80.9 / 3.4	34	A56T (GCA→ACA)	PP_3027	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (16/13);  new base T (2/2);  total (18/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.11e-01

GCGCCTGACTCGCTCCGGGCTGTGAACCCGGTGCTGACCGTAGCTGATAGTTTCGCGCCGACGAGGGTGGGATTAGGCACTGCAGTTTTCATTCGCTATCTCCCGGGCGGGCTATGGTCCGTTTACTCAATGCTCGTTTTGCGGCCACGTTG‑‑GCCATGTAGGCTGCCCACTTACCACCCTCCCGGCGTTGGCGGATCTGGCTGCATTTCATGTGTCGACGGGTTGA‑CCTGCCTTCGCCGCAAACATCGCAAATCGCGGGCAAGTCGAGGCTGTGGGAGGC  >  NC_002947/3414801‑3415080                                                                                                                                              |                                                                                                                                              gcgcCTGACTCGCTCCGGGCTGTGAACCCGGTGCTGACCGTAGCTGATAGTTTCGCGCCGACGAGGGTGGGATTAGGCACTGCAGTTTTCATTCGCTATCTCCCGGGCGGGCTATGGTCCGTTTACTCAATGCTCGTTTTGc                                                                                                                                               >  1:1337/1‑142 (MQ=255) gcgcCTGACTCGCTCCGGGCTGTGAACCCGGTGCTGACCGTAGCTGATAGTTTCGCGCCGACGAGGGTGGGATTAGGCACTGCAGTTTTCATTCGCTATCTCCCGGGCGGGCTATGGTCCGTTTACTCAATGCTCGTTTTGc                                                                                                                                               <  2:1337/142‑1 (MQ=255)   gcCTGACTCGCTCCGGGCTGTGAACCCGGTGCTGACCGTAGCTGATAGTTTCGCGCCGACGAGGGTGGGATTAGGCACTGCAGTTTTCATTCGCTATCTCCCGGGCGGGCTATGGTCCGTTTACTCAATGCTCGTTTTGCGGCCACGtt                                                                                                                                      >  6:346887/1‑149 (MQ=255)     cTGACTCGCTCCGGGCTGTGAACCCGGTGCTGACCGTAGCTGATAGTTTCGCGCCGACGAGGGTGGGATTAGGCACTGCAGTTTTCATTCGCTATCTCCCGGGCGGGCTATGGTCCGTTTACTCAATGCTCGTTTTGTGGCCAc                                                                                                                                         >  6:38123/1‑144 (MQ=255)     cTGACTCGCTCCGGGCTGTGAACCCGGTGCTGACCGTAGCTGATAGTTTCGCGCCGACGAGGGTGGGATTAGGCACTGCAGTTTTCATTCGCTATCTCCCGGGCGGGCTATGGTCCGTTTACTCAATGCTCGTTTTGTGGCCAc                                                                                                                                         >  6:33031/1‑144 (MQ=255)     cTGACTCGCTCCGGGCTGTGAACCCGGTGCTGACCGTAGCTGATAGTTTCGCGCCGACGAGGGTGGGATTAGGCACTGCAGTTTTCATTCGCTATCTCCCGGGCGGGCTATGGTCCGTTTACTCAATGCTCGTTTTGTGGCCAc                                                                                                                                         <  5:38123/144‑1 (MQ=255)     cTGACTCGCTCCGGGCTGTGAACCCGGTGCTGACCGTAGCTGATAGTTTCGCGCCGACGAGGGTGGGATTAGGCACTGCAGTTTTCATTCGCTATCTCCCGGGCGGGCTATGGTCCGTTTACTCAATGCTCGTTTTGTGGCCAc                                                                                                                                         <  5:33031/144‑1 (MQ=255)       gACTCGCGCCGGGCGGTGAACGCGGTGCGGCCCGTCGCTGATAGTTTCGCGCCGACGCGGGTGGGAGTAGGCACGGCAGTTGTCATTCGCTATCTCCCGGGCGGGCTCTGGGCCGGGTACTCAATGCTCGTTTTGCGGCCACGTTG‑‑Gcc                                                                                                                                <  5:251312/149‑1 (MQ=255)          tCGCTCCGGGCTGTGAACCCGGTGCTGACCGTAGCTGATAGTTTCGCGCCGACGAGGGTGGGATTAGGCACTGCAGTTTTCATTCGCTATCTCCCGGGCGGGCTATGGTCCGTTTACTCAATGCTCGTTTTGCGGCCACGTTG‑‑GCCATg                                                                                                                             >  8:152066/1‑149 (MQ=255)                                           gCTGATAGTTTCGCGCCGACGAGGGTGGGATTAGGCACTGCAGTTTTCATTCGCTATCTCCCGGGCGGGCTATGGTCCGTTTACTCAATGCTCGTTTTGCGGCCACGTTG‑‑GCCATGTAGGCTGCCCACTTACCACCCTCCCGGCGTTgg                                                                                            <  7:152066/149‑1 (MQ=255)                                              gATAGTTTCGCGCCGACGAGCGTGGGAATAGGCACTGCAGTTTTCATTCGCTATCTCCCGGGCGGCCTATGGTCCGTTTACTCAATGCTCGTTTTGCGGACACGTTG‑‑GCCATGTAGGCTGACCACTTACCACCCTCCCGGCGTTGGCg                                                                                          >  2:115491/1‑148 (MQ=255)                                                tAGTTTCGCGCCGACGAGGGTGGGATTAGGCACTGCAGTTTTCATTCGCTATCTCCCGGGCGGGCTATGGTCCGTTTACTCAATGCTCGTTTTGCGGCCACGTTG‑‑GCCATGTAGGCTGCCCACTTACCACCCTCCCGGCGTTGGCGGa                                                                                        <  8:253157/148‑1 (MQ=255)                                                     tCGCGCCGACGAGGGTGGGATTAGGCACTGCAGTTTTCATTCGCTATCTCCCGGGCGGGCTATGGTCCGTTTACTCAATGCTCGTTTTGCGGCCACGTTG‑‑GCCATGTAGGCTGCCCACTTACCACCCTCCCGGCGTTGGCGGATCTgg                                                                                   >  1:256363/1‑148 (MQ=255)                                                     tCGCGCCGACGAGGGTGGGATTAGGCACTGCAGTTTTCATTCGCTATCTCCCGGGCGGGCTATGGTCCGTTTACTCAATGCTCGTTTTGCGGCCACGTTG‑‑GCCATGTAGGCTGCCCACTTACCACCCTCCCGGCGTTGGCGGATCTgg                                                                                   <  2:256363/148‑1 (MQ=255)                                                      cgcgCCGACGAGGGTGGGATTAGGCACTGCAGTTTTCATTCGCTATCTCCCGGGCGGGCTATGGTCCGTTTACTCAATGCTCGTTTTGCGGCCACGTTG‑‑GCCATGTAGGCTGCCCACTTACCACCCTCCCGGCGTTGGCGGATCTGGc                                                                                  <  5:346887/148‑1 (MQ=255)                                                                  ggTGGGATTAGGCACTGCAGTTTTCATTCGCTATCTCCCGGGCGGGCTATGGTCCGTTTACTCAATGCTCGTTTTGCGGCCACGTTG‑‑GCCATGTAGGCTGCCCACTTACCACCCTCCCGGCGTTGGCGGATc                                                                                      >  3:49454/1‑132 (MQ=255)                                                                  ggTGGGATTAGGCACTGCAGTTTTCATTCGCTATCTCCCGGGCGGGCTATGGTCCGTTTACTCAATGCTCGTTTTGCGGCCACGTTG‑‑GCCATGTAGGCTGCCCACTTACCACCCTCCCGGCGTTGGCGGATc                                                                                      <  4:49454/132‑1 (MQ=255)                                                                         ttAGGCACTGCAGTTTTCATTCGCTATCTCCCGGGCGGGCTATGGTCCGTTTACTCAATGCTCGTTTTGCGGCCACGTTG‑‑GCCATGTAGGCTGCCCACTTACCACCCTCCCGGCGTTGGCGGATCTGGCTGCATTTCATGTGTCGACgg                                                              >  7:84349/1‑149 (MQ=255)                                                                             ggaCTGCAGTTTTCATTCGCTATCTCCCGGGCGGGCTATGGTCCGTTTACTCAATGCTCGTTTTGCGGCCACGTTG‑‑GCCATGTAGGCTGCCCACTTACCACCCTCCCGGCGTTGGCGGATCTGGCTGCATTTCATGTGTCGACGGGTTg                                                          <  2:283620/147‑1 (MQ=255)                                                                               aCTGCAGTTTTCATTCGCTATCTCCCGGGCGGGCTATGGTCCGTTTACTCAATGCTCGTTTTGCGGCCACGTTG‑‑GCCATGTAGGCTGCCCACTTACCACCCTCCAGGCGTTGGCGGATCTGGCTGCATTTCATGTTTCGACGTGTTGA‑c                                                       >  4:124409/1‑149 (MQ=255)                                                                                   cAGTTTTCATTCGCTATCTCCCGGGCGGGCTATGGTCCGTTTACTCAATGCTCGTTTTGCGGCCACGTTG‑‑GCCATGTAGGCTGCCCACTTACCACCCTCCCGGCGTTGGCGGATCTGGCTGCATTTCATGTGTCGACGGGTTGA‑CCTGc                                                   >  3:241084/1‑149 (MQ=255)                                                                                      ttttCATTCGCTATCTCCCGGGCGGGCTATGGTCCGTTTACTCAATGCTCGTTTTGCGGCCACGTTG‑‑GCCATGTAGGCTGCCCACTTACCACCCTCCCGGCGTTGGCGGATCTGGCTGCATTTCATGTGTCGACGGGTTGA‑c                                                       >  4:148994/1‑142 (MQ=255)                                                                                      ttttCATTCGCTATCTCCCGGGCGGGCTATGGTCCGTTTACTCAATGCTCGTTTTGCGGCCACGTTG‑‑GCCATGTAGGCTGCCCACTTACCACCCTCCCGGCGTTGGCGGATCTGGCTGCATTTCATGTGTCGACGGGTTGA‑c                                                       <  3:148994/142‑1 (MQ=255)                                                                                       tttCATTCGCTATCTCCCGGGCGGGCTATGGTCCGTTTACTCAATGCTCGTTTTGCGGCCACGTTG‑‑GCCATGTAGGCTGCCCACTTACCACCCTCCCGGCGTTGGCGGATCTGGCTGCATTTCATGTGTCGACGGGTTGA‑CCTGCCTTc                                               >  7:293164/1‑149 (MQ=255)                                                                                            ttCGCTATCTCCCGGGCGGGCTATGGTCCGTTTACTCAATGCTCGTTTTGCGGCCACGTTG‑‑GCCATGTAGGCTGCCCACTTACCACCCTCCCGGCGTTGGCGGATCTGGCTGCATTTCATGTGTCGACGGGTTGA‑CCTGCCTTcgccg                                           >  4:97426/1‑148 (MQ=255)                                                                                                       ccGGGCGGGCTATGGTCCGTTTACTCAATGCTCGTTTTGCGGCCACGTTG‑‑GCCATGTAGGCTGCCCACTTACCACCCTCCCGGCGTTGGCGGATCTGGCTGCATTTCATGTGTCGACGGGTTGA‑CCTGCCTTCGCCGCAAACAt                                    <  5:148194/144‑1 (MQ=255)                                                                                                       ccGGGCGGGCTATGGTCCGTTTACTCAATGCTCGTTTTGCGGCCACGTTG‑‑GCCATGTAGGCTGCCCACTTACCACCCTCCCGGCGTTGGCGGATCTGGCTGCATTTCATGTGTCGACGGGTTGA‑CCTGCCTTCGCCGCAAACAt                                    >  6:148194/1‑144 (MQ=255)                                                                                                             gggcTATGGTCCGTTTACTCAATGCTCGTTTTGCGGCCACGTTG‑‑GCCATGTAGGCTGCCCACTTACCACCCTCCCGGCGTTGGCGGATCTGGCTGCATTTCATGTGTCGACGGGTTGACCCTGCCTTCGCCGCAAACATCGCAAATcgc                          <  1:31031/149‑1 (MQ=255)                                                                                                              ggcTATTGTCCGTTTACTCAATGCTCGTGTTGCGGCCACGGTGTTGCCATGTAGGCTGCCCACTTACCACCCTCCCGGCGTTGGCGGATCTGGCTGCATTTCATGTGTCGACGGGTTGA‑CCTGCCAGCGCCGCAAACATCGCAAATcgc                          <  1:115491/149‑1 (MQ=255)                                                                                                              ggcTATGGTCCGTTTACTCAATGCTCGTTTTGCGGCCACGTTG‑‑GCCATGTAGGCTGCCCACTTACCACCCTCCCGGCGTTGGCGGATCTGGCTGCATTTCATGTGTCGACGGGTTGA‑CCTGCCTTCGCCGCAAACATCGCAAATCGCgg                        <  4:241084/149‑1 (MQ=255)                                                                                                                cTATGGTCCGTTTACTCAATGCTCGTTTTGCGGCCACGTTG‑‑GCCATGTAGGCTGCCCACTTACCACCCTCCCGGCGTTGGCGGATCTGGCTGCATTTCATGTGTCGACGGGTTGA‑CCTGCCTTCGCCGCAAACATCGCAAATCGCggg                       >  4:6115/1‑148 (MQ=255)                                                                                                                          tttACTCAATGCTCGTTTTGCGGCCACGTTG‑‑GCCATGTAGGCTGCCCACTTACCACCCTCCCGGCGTTGGCGGATCTGGCTGCATTTCATGTGTCGACGGGTTGA‑CCTGCCTTCGCCGCAAACATCGCAAATCGCGGGCAAGTCGAGGc            >  2:211116/1‑149 (MQ=255)                                                                                                                             aCTCAATGCTCGTTTTGCGGCCACGTTG‑‑GCCATGTAGGCTGCCCACTTACCACCCTCCCGGCGTTGGCGGATCTGGCTGCATTTCATGTGTCGACGGGTTGA‑CCTGCCTTCGCCGCAAACATCGCAAATCGCGGGCAAGTCGAGGCtgt         >  8:200836/1‑149 (MQ=255)                                                                                                                              cTCAATGCTCGTTTTGCGGCCACGTTG‑‑GCCATGTAGGCTGCCCACTTACCACCCTCCCGGCGTTGGCGGATCTGGCTGCATTTCATGTGTCGACGGGTTGA‑CCTGCCTTCGCCGCAAACATCGCAAATCGCGGGCAAGTCGAGGCtgt         <  7:200836/148‑1 (MQ=255)                                                                                                                                 attGCTCGTTTTGAGGCCACGTTG‑‑GCCTTGTAGGCTGCCCACTTAGCACCCTCCCGGCGTTGGCGGATCTGGCTGCATTTCATGTGTCGACGGGTTGA‑CCTGCCTTCGCCGCAAACATCGCAAATCGCGGGCAAGTCGAGGCTGTgg       <  3:124409/145‑1 (MQ=255)                                                                                                                                    gCTCGTTTTGCGGCCACGTTG‑‑GCCATGTAGGCTGCCCACTTACCACCCTCCCGGCGTTCGCGGATCTGGCTGCATTTCATGTGTCGACGGGTTGA‑CCTGCCTTCGCCGCAAACATCGCAAATCGCGGGCAAGTCGAGGCTGTGGGAGGc  >  3:231103/1‑149 (MQ=255)                                                                                                                                              |                                                                                                                                              GCGCCTGACTCGCTCCGGGCTGTGAACCCGGTGCTGACCGTAGCTGATAGTTTCGCGCCGACGAGGGTGGGATTAGGCACTGCAGTTTTCATTCGCTATCTCCCGGGCGGGCTATGGTCCGTTTACTCAATGCTCGTTTTGCGGCCACGTTG‑‑GCCATGTAGGCTGCCCACTTACCACCCTCCCGGCGTTGGCGGATCTGGCTGCATTTCATGTGTCGACGGGTTGA‑CCTGCCTTCGCCGCAAACATCGCAAATCGCGGGCAAGTCGAGGCTGTGGGAGGC  >  NC_002947/3414801‑3415080

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑