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	97.5%	129.6 / ‑3.1	40	intergenic (‑37/+99)	PP_1242/PP_1244	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base C (18/21);  total (19/21)
Fisher's exact test for biased strand distribution p-value = 4.75e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.60e-01

CTGGCAGGGGATGCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGC‑ATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑G‑CTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGCGGGCGTG‑CCCGCGAAGAGGCCTGACCTGCTAATGCAAGGTGTGAGGCTCTGTGGGTAAATGCGACCGC  >  NC_002947/1419401‑1419686                                                                                                                                                       |                                                                                                                                            cTGGCAGGGGATGCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGC‑ATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGggctg‑g‑c                                                                                                                                            >  7:194111/1‑149 (MQ=255) cTGGCAGGGGATGCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGC‑ATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGggctg‑g‑c                                                                                                                                            <  3:237784/149‑1 (MQ=255)       ggggATGCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGC‑ATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGggctg‑g‑c                                                                                                                                            <  7:38990/143‑1 (MQ=255)       ggggATGCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGC‑ATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGggctg‑g‑c                                                                                                                                            >  8:38990/1‑143 (MQ=255)       ggggATGCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGC‑ATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTc                                                                                                                                       <  3:54078/149‑1 (MQ=255)        gggATGCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGC‑ATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTcg                                                                                                                                      >  1:307424/1‑149 (MQ=255)         ggATGCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGC‑ATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTcgc                                                                                                                                     <  6:241088/149‑1 (MQ=255)                  gtgcGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGC‑ATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGcc                                                                                                                            <  2:234506/146‑1 (MQ=255)                      gATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGGTCTGTTGTGTTGTCGGTGGGC‑ATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCt                                                                                                                        <  3:24364/149‑1 (MQ=255)                        ggCGGCACCGCGGGTGCGTGCGTGTTTCGCCTTGGGAGCAGCCGGGCTGGCCGCCTGTGGGGGGGTCTGGTGTGTTGGCGTGGGGC‑CTTGGGTTGTTTCCCTGGATGCTGGGTTGCCTGGGCTG‑GCCGCTTCGCGGGCACGCCCGCTcc                                                                                                                      <  3:202679/148‑1 (MQ=255)                                aGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGC‑ATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGGCCCCCCCCTCCcaacagg                                                                                                               >  3:14838/1‑143 (MQ=255)                                   gggTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGC‑ATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACtg                                                                                                           <  8:194111/149‑1 (MQ=255)                                     gTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGC‑ATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACtgtg                                                                                                         <  5:43385/149‑1 (MQ=255)                                           gttgttTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGC‑ATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTCCCACAg                                                                                                                 <  6:335454/135‑1 (MQ=255)                                           gttgttTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGC‑ATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTCCCACAg                                                                                                                 >  5:335454/1‑135 (MQ=255)                                               ttttCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGC‑ATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGa                                                                                               >  3:83760/1‑149 (MQ=255)                                                            aGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCAAGTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGa                                                                                   >  1:92245/1‑149 (MQ=39)                                                                gCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGC‑ATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGc                                                                                                   <  8:133778/128‑1 (MQ=255)                                                                gCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGC‑ATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGc                                                                                                   >  7:133778/1‑128 (MQ=255)                                                                   ggTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGC‑ATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTgg                                                                           <  4:83760/149‑1 (MQ=255)                                                                    gTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGC‑ATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTggg                                                                          <  4:196991/149‑1 (MQ=255)                                                                    gTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGC‑ATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTgg                                                                           >  6:161922/1‑148 (MQ=255)                                                                      cTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGC‑ATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAg                                                                        >  7:262664/1‑149 (MQ=255)                                                                         gCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGC‑ATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGc                                                                                                   >  8:62570/1‑119 (MQ=255)                                                                             aCTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGC‑ATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCCCACCCACAGGTACTGTGCAGTGCGTGTCGGCTTTGGTGACCCTGTGGGAGCGGGCGt                                                                 >  1:136419/1‑149 (MQ=255)                                                                                 tggtggGTTCTGTTGTGTTGTCGGTGGGC‑ATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGCGGGCGTG‑c                                                              <  5:161922/147‑1 (MQ=255)                                                                                   tggggTTCTGTTGTGTTGTCGGTGGGC‑TTTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGCGGGCGTG‑CCcgc                                                          <  8:245370/147‑1 (MQ=255)                                                                                        ttCTGTTGTGTTGTCGGTGGGC‑ATTGTTTTGTATCCCTGCAATCTGGGTTGCCTGGGCTGCC‑CTCTTCGCGGGCACGCCCGCTCCCACATGTACAGTGCAGTGCGAGACCGCAGTGGTGACCCTGTGGGAGCCGGCGTG‑CCCGCGaa                                                       >  6:68725/1‑147 (MQ=37)                                                                                           tgttgtgttgTCGGTGGGC‑ATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCCAGCCCGCTCCCACAGGTACTGTGCAGTGGGTGACGGCTGTGGGGTCCCGGTGGGCGCCGGGGTG‑CCCGCGaacgggc                                                  >  3:352851/1‑144 (MQ=255)                                                                                              tgtgttgtCGGTGGGC‑ATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCAACCACACGTACTGTGGAGTGCGTGACGGCTGTGGTGACCCGGTGGGAGCGGGCGTG‑CCCGCGAAGAGGccag                                               >  3:179939/1‑147 (MQ=38)                                                                                                ttttggCGGGGGGC‑ATTTGTTTGTTTCCCTGGTTTCTGGGTTGCCTGGGCTG‑GCCTCTTCGGGGGCACGCCCGCTCCCACAGGTTCTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGCGGGCGTG‑CCCGCGAAGAGGCCTGAc                                             <  8:262664/147‑1 (MQ=25)                                                                                                    gtCGGTGGGC‑ATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGCGGGCGTG‑CCCGCGAAGAGGCCTGACCTg                                          <  2:92245/148‑1 (MQ=255)                                                                                                     tCGGTGGGC‑ATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACCCCCCCACCCACAAGTAAAGTGCAATTCCTGACCGCTGTGGTGACCCTGTTGGATCCGGCCTG‑ACCGCGAAAACGCCAGAccatc                                         >  8:148993/1‑145 (MQ=255)                                                                                                             tctttgttttgttTCCGTGGTTTGTGGGTGGCGTGGGCGG‑GCCTCTTCGGGGGCACGCCGGCGCCCACAGTTACTTTGCAGTGGGTGAGGGGTGTGGTGACCCTGTGGGTGGGGGGGTGCCCCGCTAAGTGGCCTGACCTGCTAATGCa                                  <  2:136419/146‑1 (MQ=255)                                                                                                             c‑ATTGTTTTTTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCGCTTCGCTGGCACCCCCGCTCCCACAGGTACTGTGCTGTGCGTGACGGGTGTGGTGACCCTGTGGGAGCGGGCGTG‑CCCGCGAAGAGGCCTGACCTGCTAATGCAAg                                <  3:357965/149‑1 (MQ=37)                                                                                                             c‑ATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGCGGGc                                                                   >  1:178264/1‑115 (MQ=255)                                                                                                             c‑ATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGCGGGc                                                                   <  2:178264/115‑1 (MQ=255)                                                                                                                            cttgtaTTCTGGGGGGCGTGGGCTG‑GCCTGTTCGGGGGCAGGCCGGGTCCCACTGTTAGTGTGAAGTGCGTTAGGGCTGTGGTGACCGTGTGGGAGGGGGGGTG‑CCCGCGAAGAGGCCTGACCTGCTAATGCAAGGTGTGAGGCTCtgt                  <  7:148993/144‑1 (MQ=255)                                                                                                                             cTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTACCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGCGGGCGTG‑CCCGCGAAGAGGCCTGACCTGCTAATGCAAGGTGTGCGGCTCtgtg                 >  2:12077/1‑149 (MQ=255)                                                                                                                             cTGGATTCTGGGTTGCCTGGGCTG‑GCCTCTTCGCGGGCACCCCCCCAACCACAGGTAAAGTGCAGTGCGTGTCGGCGGTGGTGACCCAGTTGGAGCGGGCGTG‑CCCGCGAAAAGGCCAGACCGTCGAAAGCAACGTGTGAGGcagggtg                 >  6:317035/1‑143 (MQ=255)                                                                                                                                  ttCTGGGTTGCCTGGGCTG‑GCCTCTGCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGGGGTGACCCTGTGGGAGCGGGCGTG‑CCCGCGAAGAGGCCTGACCTGCTAATGCAAGGTGTGAGGCTCTGTGGGTaa            <  2:217343/149‑1 (MQ=255)                                                                                                                                      gggTTGCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGGGGGAGCGGGCGTG‑CCCGCGAAGAGGCCTGACCTGCTAATGCAAGGTGTGAGGCTCTGTGGGTAAATGc        >  5:171687/1‑149 (MQ=255)                                                                                                                                           gCCTGGGCTG‑GCCTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGGAGTGGGGGCCGGCTGTGGTGGCGCGGGGGGAGGGGGCGTG‑GCCGCGCAGAGGGCTGACCGGGTATTGCAAGGGGTGCGGCTCGGGGGGGAAGTGGGAGCg   >  8:263900/1‑149 (MQ=16)                                                                                                                                            ccTGGGCTG‑GCCTCTTGGGGGGCAGGCCCGCTCCCACAGGTACTGTGCTGTGCGTGACGGGTGTGGTGACCCTGGGGGAGCGGGCGTG‑CCCGCGAAGAGGCCTGACCTGCTAATGCAAGGTGTGAGGCTCTGTGGGTAAATGCGACCGc  <  5:317035/149‑1 (MQ=37)                                                                                                                                                       |                                                                                                                                            CTGGCAGGGGATGCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGC‑ATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTG‑G‑CTCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGCGGGCGTG‑CCCGCGAAGAGGCCTGACCTGCTAATGCAAGGTGTGAGGCTCTGTGGGTAAATGCGACCGC  >  NC_002947/1419401‑1419686

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑