Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_002947	1,419,549	+C	intergenic (‑38/+98)	PP_1242 ← / ← PP_1244	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,419,548	1	.	C	97.8%	145.0 / ‑3.1	45	intergenic (‑37/+99)	PP_1242/PP_1244	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base C (19/25);  total (20/25)
Fisher's exact test for biased strand distribution p-value = 4.44e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.72e-01

CTGGCAGGGGATGCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTC‑TTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCT‑GG‑CTCTTCGCGGGCACGC‑CCGCTCCCACA‑GGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGCGGGCGTGCCCGCGAAGAGGCCTGACCTGCTAATGCAAGGTGTGAGGCTCTGTGGGTAAATGCGACCGCA  >  NC_002947/1419401‑1419687                                                                                                                                                       |                                                                                                                                              cTGGCAGGGGATGCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTC‑TTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGggct‑gg‑c                                                                                                                                              >  6:348765/1‑149 (MQ=255) cTGGCAGGGGATGCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTC‑TTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGggct‑gg‑c                                                                                                                                              >  2:174580/1‑149 (MQ=255) cTGGCAGGGGATGCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTC‑TTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGggct‑gg‑c                                                                                                                                              <  2:172457/149‑1 (MQ=255)    gCAGGGGATGCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTC‑TTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGggct‑gg‑cctc                                                                                                                                           >  7:270700/1‑146 (MQ=255)    gCAGGGGATGCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTC‑TTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGggct‑gg‑cctc                                                                                                                                           <  7:29050/149‑4 (MQ=255)        gggATGCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTC‑TTGCCGACTGTGGGGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCT‑GGCCTCTTcg                                                                                                                                        >  1:239567/1‑149 (MQ=255)          gATGCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTC‑TTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCT‑GGCCTCTTcgcg                                                                                                                                      >  5:162458/1‑149 (MQ=255)             ggcGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCGTGGTAGAAGCAGGTC‑TTGCGGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTGTGGGTTGCCTGGGCT‑GGCCTCTTCGCggg                                                                                                                                    >  5:284209/3‑148 (MQ=255)             gCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTC‑TTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCT‑GGCCTCTTCGCggg                                                                                                                                    >  2:318405/1‑148 (MQ=255)                 ggTTCGATGCGGAACAGCGGGTGAGTGTTGTTATCGCCTTGGTAGAAGCAGGTC‑TTGCCGACTGTGCTGGGTTCTGGTGTGTTCTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCT‑GGCCTCTTCGCGGGCACGc                                                                                                                               <  5:334142/149‑1 (MQ=255)                   ttCGATGCGGAACAGCGGGTTCGTGTTGTTTTCGCCTTGGTAGAAGCAGGTC‑TTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCT‑GGCCTCTTCGCGGGCACGc‑cc                                                                                                                            <  6:284209/149‑1 (MQ=255)                      gATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGTTG‑TTGCCGTCTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTCTTTCCCTGGATTCTGGGTTGCGTGGGGT‑GGCCTCTTAGCGGGCACGC‑CCGca                                                                                                                         >  3:337018/1‑148 (MQ=255)                        tGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCGTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCT‑GGCCTCTTCGCGGGCACGC‑CCGCTc                                                                                                                        >  1:293404/1‑149 (MQ=255)                           ggAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTC‑TTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCT‑GGCCTCTTCGCGGGCACGC‑CCGCTCCcac                                                                                                                    <  7:204093/149‑1 (MQ=255)                           ggAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTC‑TTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCT‑GGCCTCTTCGCGGGCACGC‑CCGCTCCcac                                                                                                                    <  4:52115/149‑1 (MQ=255)                                  cGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTC‑TTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCT‑GGCCTCTTCGCGGGCACGC‑CCGCTCCCACA‑GGTACt                                                                                                            <  8:270700/149‑1 (MQ=255)                                   gggTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTC‑TTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCT‑GGCCTCTTCGCGGGCACGC‑CCGCTCCCACA‑GGTACtg                                                                                                           <  1:176869/149‑1 (MQ=255)                                    ggTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTC‑TTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTGGCCTGGGCT‑GGCCTCTTCGCGGGCACGC‑CCGCTCCCACA‑GGTACtgt                                                                                                          <  2:62784/149‑1 (MQ=255)                                       gctggttgtgTGCGCCTGGGGCGCAGCAGGGC‑TTGCGGACTTGTGTGGGTGCTGTTGTTTTGGCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCT‑GGCCTCTTCGCGGGCACGC‑CCGCTCCCACA‑GGTACTGTGCa                                                                                                       <  8:177525/145‑1 (MQ=25)                                       gAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTC‑TTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCT‑GGCCTCTTCGCGGGCACGC‑CCGCTCCCACA‑GGTACTGTGCa                                                                                                       <  1:213485/149‑1 (MQ=255)                                            ttgttTTCGCCTTGGTAGAAGCAGGTC‑TTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCT‑GGCCTCTTCGCGGGCACGC‑CCGCTCCCACA‑GGTACTGGGCAGTGCg                                                                                                  >  4:94019/1‑149 (MQ=255)                                            ttgttTTCGCCTTGGTAGAAGCAGGTC‑TTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCT‑GGCCTCTTCGCGGGCACGC‑CCACTCCCACA‑GGTACTGTGCAGTGCg                                                                                                  >  2:124666/1‑149 (MQ=255)                                              gttTTCGCCTTGGTAGAAGCAGGTC‑TTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCT‑GGCCTCTTCGCGGGCACGC‑CCGCTCCCACA‑GGTACTGTGCAGTGCgg                                                                                                 <  5:286312/148‑2 (MQ=255)                                              gttTTCGCCTTGGTAGAAGCAGGTC‑TTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCT‑GGCCTCTTCGCGGGCACGC‑CCGCTCCCACA‑GGTACTGTGCAGTGCGt                                                                                                 <  6:191793/148‑1 (MQ=255)                                               ttttCGCCTTGGTCGATGCTGGTC‑TTGCCGACTGTGGTGGGTTGTGTTGTGTTGTCGGTGGTCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCT‑GGCCTCTTCGCGGGCACGC‑CCGCTCCCACA‑GGTACTGTGCAGTGCGTGa                                                                                               <  4:57005/149‑1 (MQ=38)                                               ttttCGCCTTGGTAGAAGCAGGTC‑TTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCT‑GGCCTCTTCGCGGGCACGC‑CCGCTCCCACA‑GGTACTGTGCAGTGCGTg                                                                                                <  2:239567/148‑1 (MQ=255)                                               ttttCGCCTTCGTAGAAGCAGGTC‑TTGCCGACTGTGGTGGGTTCAGTTGTGTTGTCGGTGTGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCT‑GGCCTCTTCGCGGGCACGC‑CCGCTCCCACA‑GGTACTGTGCAGTGCGTGa                                                                                               >  3:57005/1‑149 (MQ=39)                                                    gCCTTGGTAGAAGCAGGTC‑TTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCT‑GGCCTCTTCGCGGGCACGC‑CCGCTCCCACA‑GGTACTGTGCAGTGCGTGACGGCt                                                                                          >  5:8988/1‑149 (MQ=255)                                                         ggTAGAAGCAGGTC‑TTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCT‑GGCCTCTTCGCGGGCACGC‑CCGCTCCCACA‑GGTACTGTGCAGTGCGTGACGGCtgtg                                                                                       <  7:356802/147‑1 (MQ=255)                                                         ggTAGAAGCAGGTC‑TTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCT‑GGCCTCTTCGCGGGCACGC‑CCACTCCCACA‑GGTACTGTGCAGTGCGTGACGGCtgtg                                                                                       <  1:124666/147‑1 (MQ=255)                                                          gTAGAAGCAGGTC‑TTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCT‑GGCCTCTTCGCGGGCACGC‑CCGCTCCCACA‑GGTACTGTGCAGTGCGTGACGGCTgtggt                                                                                     <  5:348765/148‑1 (MQ=255)                                                             gAAGCAGGTC‑TTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCT‑GGCCTCTTCGCGGGCACGC‑CCGCTCCCACA‑GGTACTGTGCAGTGCGTGACGGCTGTGGTGAcc                                                                                 <  6:8988/149‑1 (MQ=255)                                                                            cGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCT‑GGCCTCTTCGCGGGCACGC‑CCGCTCCCACA‑GGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGCGGGc                                                                   <  6:162458/149‑1 (MQ=255)                                                                            cGACTGTGGTGGGTTCTGTTGTGTGGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCT‑GGCCTCTTCGCGGGCACGC‑CCGCTCCCACA‑GGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGCGGGc                                                                   <  8:309189/149‑1 (MQ=255)                                                                              aCTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCT‑GGCCTCTTCGCGGGCACGC‑CCGCTCCCACA‑GGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGCGGGCGt                                                                 <  1:174580/149‑1 (MQ=255)                                                                              aCTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCT‑GGCCTCTTCGCGGGCACGC‑CCGCTCCCACA‑GGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGCGGGCGt                                                                 >  5:207799/1‑149 (MQ=255)                                                                               cTGTGGTGGGGTCCGTTGGGTTGGCGGGGGGCATTGTTTTGTTTCCCTGGAATCCGGGGTGCCTGGGCT‑GGCCTCTTCGCGGGCACGCTCCGCTCCCACA‑GGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGCGGGCGt                                                                 <  1:318405/149‑1 (MQ=37)                                                                                    gtggGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCT‑GGCCTCTTCGCGGGCACGC‑CCGCTACCACA‑GGTTCTGTTCAGTGCGTGCCGGGTGTGGTGACCCGGTGGGCGCGGGCGTTCCcgc                                                           >  5:220423/1‑149 (MQ=255)                                                                                     tggGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCT‑GGCCTCTTCGCGGGCACGC‑CCGCTCCCACA‑GGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGCGGGCGTGCCcgc                                                           >  8:67466/1‑148 (MQ=255)                                                                                             gttgtgttgtCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCT‑GGCCTCTTCGCGGGCACGC‑CCGCTCCCACA‑GGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGCGGGCGTGCCCGCGAAGAGGcc                                                  >  2:127921/1‑149 (MQ=255)                                                                                                   ttgtCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCT‑GGCCTCTTAGCGGGGCCCC‑CCCCGCCCCCACGGTA‑AGTTGAGTGGGGGGCCGCGGTGGGGGCCCCGTGGGGGGGGGGGGGGCCGCGGAGAGGCCGGAccc                                            >  2:370238/1‑148 (MQ=255)                                                                                                                     ttgtttCCCTGGATTCTGGGTTGCCTGGGCT‑GGCCTCTTCGCGGGCACGC‑CCGCTCCCACA‑GGTACTGTGCAGTGCGTGACGGCTTTGGTTACCCTGTGGTAGCGGGCGTGCCCGCGAAGAGGCCTGACCTGCTAATGCAAGGTGTGa                           <  2:293404/148‑1 (MQ=37)                                                                                                                            ccTGGATTCTGGGTTGCCTGGGCT‑GGCCTCTTCGCGGGCACCC‑CCCCTCCCACA‑GGGAAGGTGGAGTGGGGGGCGGGGGTGGTGGCCCGGTGGGGGCGGGCGTGCCCGCGAAGAGGCCTGACCGGGGAATGCAATGTGTGAGGgtgtgt                   >  2:342599/1‑149 (MQ=255)                                                                                                                               ggATTCTGGGTTGCCTGGGCT‑GGCCTCTTCGCGGGCACGC‑CCGCTCCCACA‑GGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGCGGGCGTGCCCGCGAAGAGGc                                                   <  4:110086/114‑1 (MQ=255)                                                                                                                               ggATTCTGGGTTGCCTGGGCT‑GGCCTCTTCGCGGGCACGC‑CCGCTCCCACA‑GGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGCGGGCGTGCCCGCGAAGAGGc                                                   >  3:110086/1‑114 (MQ=255)                                                                                                                                  ttCTGGGTGGCCGGGGCT‑GGCCTCTTCGCGGGCACGC‑CCGCTCCCACA‑GGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGCGGGCGTGCCcgc                                                           <  7:17392/103‑1 (MQ=21)                                                                                                                                     tGGGTTGCCTGGGCT‑GGCCTCTTCGCGGGCACGC‑CCGCTCCCACA‑GGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTgg                                                                           <  2:199340/84‑1 (MQ=255)                                                                                                                                     tGGGTTGCCTGGGCT‑GGCCTCTTCGCGGGCACGC‑CCGCTCCCACA‑GGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTgg                                                                           >  1:199340/1‑84 (MQ=255)                                                                                                                                           gCCTGGGCTCGC‑CTCTTCGCGGGCACGC‑CCGCTCCCACA‑GGTACTGTTCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGCCGGCGTGCCCGCGAAGAGGCCTGACCTGCTAATGCAAGGTGTGAGGCTCTGTGGCTAAAAGCGACCg    >  6:203261/1‑149 (MQ=37)                                                                                                                                             cTGGGCT‑GGCCTCTTCGCGGGCACGC‑CCGCTCCCACA‑GGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGCGGGCGTGCCCGCGAAGAGGCCTGACCTGCTAATGCAAGGTGTGAGGCTCTGTGGGTAAATGCGACCGCa  >  6:314136/1‑149 (MQ=255)                                                                                                                                                       |                                                                                                                                              CTGGCAGGGGATGCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTC‑TTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCT‑GG‑CTCTTCGCGGGCACGC‑CCGCTCCCACA‑GGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGCGGGCGTGCCCGCGAAGAGGCCTGACCTGCTAATGCAAGGTGTGAGGCTCTGTGGGTAAATGCGACCGCA  >  NC_002947/1419401‑1419687

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: ‑