Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,419,548:1	+C	52.3%	intergenic (‑37/+99)	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	52.3%	72.9 / 80.7	44	intergenic (‑37/+99)	PP_1242/PP_1244	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (8/13);  new base C (13/10);  total (21/23)
Fisher's exact test for biased strand distribution p-value = 2.46e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.88e-01

CTGGCAGGGGATGCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGT‑GGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTG‑TTTCCCTGGATTCTGGGTTGCCTGGGCTG‑G‑C‑TCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGCGGGCGTG‑CCCGCGAAGAGGCCTGACCTGCTAATGCAAGGTGTGAGGCTCTGTGGGTAAATG  >  NC_002947/1419401‑1419679                                                                                                                                                        |                                                                                                                                      cTGGCAGGGGATGCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGT‑GGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTG‑TTTCCCTGGATTCTGGGTTGCCTGGGCTG‑G‑C                                                                                                                                      <  3:76733‑M1/149‑1 (MQ=255) cTGGCAGGGGATGCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGT‑GGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTG‑TTTCCCTGGATTCTGGGTTGCCTGGGCTG‑G‑C                                                                                                                                      <  2:249659‑M1/149‑1 (MQ=255)           aTGCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGT‑GGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTG‑TTTCCCTGGATTCTGGGTTGCCTGGGCTG‑G‑Cctcttcgcgg                                                                                                                            <  3:227806‑M1/149‑11 (MQ=255)             gCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGT‑GGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTG‑TTTCCCTGGATTCTGGGTTGCCTGGGCTG‑G‑Cctcttcgcgggc                                                                                                                          <  2:114298‑M1/149‑13 (MQ=255)                gggTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGT‑GGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTG‑TTTCCCTGGATTCTGGGTTGCCTGGGCTG‑G‑Cctcttcgcgggcacg                                                                                                                       >  3:18381‑M1/1‑134 (MQ=255)                  ggtagatgcGGAACTCAGTGTTAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCATGCCGACTGTTGT‑GGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTG‑TTTCCCTGGAATCTGGGTTGCCTGGGCTG‑G‑Cctcttcgctggcacgcc                                                                                                                     <  6:350438‑M1/145‑18 (MQ=255)                       aTGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGT‑GGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTG‑TTTCCCTGGATTCTGGGTTGCCTGGGCTG‑G‑Cctcttcgcgggcacgcccgctc                                                                                                                <  4:18381‑M1/149‑23 (MQ=255)                          cgcaacagCGGGTTCGGGTGGTTTTCGCCTTGGAAGAAGCTGGTCTTGCCGACTGTGGT‑GGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTG‑TTTCCCTGGATTCTGGGTTGCCTGGGCTG‑G‑Cctcttcgcgggcacgcccgctccc                                                                                                              <  2:293777‑M1/145‑25 (MQ=255)                           ggAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGT‑GGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTG‑TTTCCCTGGATTCTGGGTTGCCTGGGCTG‑G‑Cctcttcgcgggcacgcccgctccca                                                                                                             >  6:235627‑M1/1‑123 (MQ=255)                                              gttTTCGCCTTGGTAGAAGCAGGTCTTGCTGACTGTGGT‑GGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTG‑TTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCC‑TCTTCGCGGGCACGCCCGCTCCCACAGGTACtgtg                                                                                                  <  6:19397/140‑1 (MQ=255)                                              gttTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGT‑GGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTG‑TTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCC‑TCTTCGCGGGCACGCCCGCTCCCACAGGTACtgtg                                                                                                  >  5:19397/1‑140 (MQ=255)                                                          gTAGAAGCAGGTCTTGCCGACTGTGGTGGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTG‑TTTCCCTGGATTCTGGGTTGCCTGGGCTG‑G‑Cctcttcgcgggcacgcccgctcccacagggtcaccacagccgtcacgcactgca                                                                                >  1:205819‑M1/1‑93 (MQ=255)                                                           tAGAAGCAGGTCTTGCCGACTGTGGT‑GGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTG‑TTTCCCTGGATTCTGGGTTGCCTGGGCTG‑G‑Cctcttcgcgggcacgcccgctcccacagggtcaccacagccgtcacgcactgcacag                                                                             >  7:96666‑M1/1‑91 (MQ=255)                                                             caaGCAGGTCTTGCAGACTGTGGT‑GGTTTCTGTTGTGTTGTCGGTGGGCATTGTTTTG‑TTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCC‑TCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGAcc                                                                          <  4:241078/148‑1 (MQ=255)                                                               aGCAGGTCTTGCCGACTGTGGT‑GGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTG‑TTTCCATGGATTATGGGTTGCCTGGGCTGCC‑C‑AATTCGCCGGCACGCCCGCTCCCACAGGTACTGTTCAGTGAGTGACGGCTGTGGTGAcc                                                                          >  2:85498/1‑147 (MQ=255)                                                                gCAGGTCTTGCCGACTGTGGT‑GGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTG‑TTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCC‑TCTTCGCGGGCCCGCCCCCTCCCACAGGTACTGTGCAGTGCGTGGCGGCGGTGGGGACCCtg                                                                       >  6:180943/1‑149 (MQ=255)                                                                   ggTCTTGCCGACTGTGGT‑GGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTTCCCTGGATTCTGGGTTGCCTGGGATG‑G‑CATCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCATTGCGTGACGGCTGTGGTGCCCAtgtg                                                                     >  1:85747/1‑149 (MQ=38)                                                                   ggTCTTGCCGACTGTGGT‑GGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTG‑TTTCCCTGGATTCTGGGTTGCCTGGGCTG‑G‑Cctcttcgcgggcacgcccgctcccacagggtcaccacagccgtcacgcactgcacagtacctgtgg                                                                    <  8:96666‑M1/149‑67 (MQ=255)                                                                     tCTTGCCGACTGTGGT‑GGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTG‑TTTCCCTGGATTCTGGGTTGCCTGGGCTG‑G‑Cctcttcgcgggcacgcccgctcccacagggtcaccacagccgtcacgcactgcacagtacctgtggga                                                                  <  5:235627‑M1/149‑69 (MQ=255)                                                                          ccGACTGTGGT‑GGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTG‑TTTCCCTGGATTCTGGGTTGCCTGGGCTG‑G‑Cctcttcgcgggcacgcccgctcccacagggtcaccacagccgtcacgcactgcacagtacctgtgggagcgg                                                              <  2:107695‑M1/148‑73 (MQ=255)                                                                           cGACTGTGGT‑GGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTG‑TTTCCCTGGATTCTGGGTTGCCTGGTCAG‑G‑Cctcttcgcgggcacgcccgctcccacagggtcaccacagccgtcacgcactgcacagtacctgtggga                                                                  <  5:11363‑M1/143‑69 (MQ=255)                                                                           cGACTGTGGT‑GGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTG‑TTTCCCTGGATTCTGGGTTGCCTGGTCAG‑G‑Cctcttcgcgggcacgcccgctcccacagggtcaccacagccgtcacgcactgcacagtacctgtggga                                                                  >  6:11363‑M1/1‑75 (MQ=255)                                                                             aCTGTGGT‑GGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTG‑TTTCCCTGGATTCTGGGTTGCCTGGGCTG‑G‑Cctcttcgcgggcacgcccgctcccacagggtcaccacagccgtcacgcactgcacagtacctgtgggagcgggcgt                                                          <  2:205819‑M1/149‑77 (MQ=255)                                                                                         ttCTGTTGTGTTGTCGGTGGGCATTGTTTTG‑TTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCC‑TCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGGGCGGGTCGGCTGTGGTGACCCTGTGGGAGCGGGCGTG‑CCCGCGAagc                                              >  4:190808/1‑148 (MQ=37)                                                                                                gtgttgtCGGTGGGCATTGTTTTG‑TTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCC‑TCTTCGCGGGCACGCCCGCTCCCACAGTTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGCGGGCGTG‑CCAGCGAAGAGGCCTGa                                       >  5:343129/1‑149 (MQ=255)                                                                                                 tgttgtCGGTGGGCATTGTTTTG‑TTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCC‑TCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCtgtg                                                                     >  3:46594/1‑119 (MQ=255)                                                                                                 tgttgtCGGTGGGCATTGTTTTG‑TTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCC‑TCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCtgtg                                                                     <  4:46594/119‑1 (MQ=255)                                                                                                  gttgtCGGTGGGCATTGTTTTG‑TTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCC‑TCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGCGGGc                                                            <  7:295013/127‑1 (MQ=255)                                                                                                  gttgtCGGTGGGCATTGTTTTG‑TTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCC‑TCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGCGGGc                                                            >  8:295013/1‑127 (MQ=255)                                                                                                   ttgtCGGTGGGCATTGTTTTG‑TTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCC‑TCTTCGCGGGCAAGCCCGCGACCACCGGTACTGTGGAGTGCGTGACGGGGGGGGTGCCGCGGTGGGTGCGGGCGTG‑GCCGGGGAGAGCCCTGACCt                                    >  8:314121/1‑149 (MQ=255)                                                                                                        ggTGGGCATTGTTTTG‑TTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCC‑TCTTCGCGGGCACGCCCGCTACCACAGGTACGGTGCAGTGCGTGACGGCTGTGGGGACCCAGTGGGAGCGGGCGTG‑CCCGCGAAGAGGCCTGACCAGCTaa                               >  2:101317/1‑149 (MQ=38)                                                                                                             gCATTGTTTTG‑TTTCCCTGGATTCTGGGTTGCCTGGGCTG‑G‑Cctcttcgcgggcacgcccgctcccacaggt                                                                                                        <  6:39382‑M1/72‑31 (MQ=255)                                                                                                             gCATTGTTTTG‑TTTCCCTGGATTCTGGGTTGCCTGGGCTG‑G‑Cctcttcgcgggcacgcccgctcccacaggt                                                                                                        >  5:39382‑M1/1‑42 (MQ=255)                                                                                                              cATTGTTTTG‑TTTCCCTGGATTCTGGGTTGCCTGGGCTG‑GCC‑TCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGGTGTGGTGACCCTGTGGGAGCGGGCGTG‑CCCGCGAAGAGGCCTGCCCTGCTAATGGAAg                         >  5:100958/1‑149 (MQ=37)                                                                                                                     ttg‑tttCCCTGCATGCGGGGTTGCCTGGGCGG‑GCC‑TCTTCCCGGCCACGCCCGCGCCCACCGCTACTGGGCAGTGCGGCACGGCTGTGGTGACCCGGTGGGAGCGGGCGTG‑CCCGCGAAGAGGCCTGACCTGCTAATGCAAGGTGTGa                   <  3:251279/148‑1 (MQ=255)                                                                                                                      tcttttCCGTGGATTCTGGTTTGCCTGGGCTG‑GCC‑TCTTCGCTGGCAGGCCCGCTCCCACTGGTACTGTGCTGTGCTTGAGGGGTGTGGTTACCCTGTGGGAGGGGGCTTG‑CCCGCGAAGAGGCCTGACCTGCTAATGCAAGGTGTGa                   <  6:318991/145‑1 (MQ=255)                                                                                                                       g‑ttcCCCTGTATTCTGGGTGGCCGGGGCGG‑GCC‑TCTTCGCGGGCACGCCCGCTCCCACCGGTCCTGTGCAGGGCGGGACGGCTGTGGTGACCCGGTGGGAGCGGGGGTG‑CCCGCGAAGAGGCCTGACCTGCTAATGCAAGGTGTGAgg                 <  6:100958/148‑1 (MQ=25)                                                                                                                          ttCCCTGGATTCTGGGTTGCCTGGGCTG‑GCC‑TCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGGAGTGCGTGACGGCTGTGGTGACCGTGTGGGAGCGGGCGTG‑CCCGCGAAGAGGCCTGACCTGCTAATGGAAGGTGTGa                   >  5:318991/1‑144 (MQ=37)                                                                                                                           tCCCTGGATTCTGGGTTGCCTGGGCTG‑GCC‑TCTTAGCCGGCACCCCCCCTCCCAAACGTAAAGTGCACTTCGTGAAGGCTGTGGTTAACCAGTTGGAGCGGGCCTT‑GCCCCCAAAAAGCCAGACCAGCGAATGAAAAGTGTGAAGcgat             >  4:80873/1‑146 (MQ=255)                                                                                                                                 gATTCTGGGGTGCCTGGGCTG‑GCC‑TCTTCGCGGGCACGCCCGCTCCCCCAGGTACTGTGCAGTGCGTGACGGCTGTGGGGACCCTGTGGGAGCGGGCGTG‑CCCGCGAAGAGGCCTGACCTGCTAATGCAAGGTGTGAGGCTCTGTgg         <  5:180943/147‑1 (MQ=37)                                                                                                                                 gATGCTGGGTTGCCTGGGCGG‑GCC‑TCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGGGGTTACCCTGGGGGAGCGGGCGTG‑CCCGCGAAGAGGCCTGACCTGCTAATGCAAGGTGTGAGGCTCTGTgg         <  1:101317/147‑1 (MQ=37)                                                                                                                                   ttCTGGGTTGCCTGGGCTG‑GCC‑TCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGCGGGCGTG‑CCCGCGAAGAGGCCTGACCTGCTAATGCAAGGTGTGAGGCTCTGTGGGTa      >  1:235406/1‑148 (MQ=255)                                                                                                                                      tGGGTTGCCTGGGCTG‑GCC‑TCTTCGCGGGCACGCCCGCTCCCACAGGTTCTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGCGGGCGGG‑CCCGCGAAGAGGCCTGACCGGCTAATGCAAGGTGTGTGGCTCTGTGGGTAAATg  >  5:315798/1‑149 (MQ=37)                                                                                                                                      tGGGGTGCGTGGGCTG‑GCC‑TCTTCGCGGGCACGCGCGCTCCCAGTGGTACTGTGCAGTGCGTGACGGCTGTGGTGTCCCTGGGGGAGCGGGCGTGCCCCGCGAAGAGGCCTGACCTGCTAATGCAAGGTGTGAGGCTCTGTGGGTAAAt   <  1:85498/149‑1 (MQ=255)                                                                                                                                                        |                                                                                                                                      CTGGCAGGGGATGCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGT‑GGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTG‑TTTCCCTGGATTCTGGGTTGCCTGGGCTG‑G‑C‑TCTTCGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTGACGGCTGTGGTGACCCTGTGGGAGCGGGCGTG‑CCCGCGAAGAGGCCTGACCTGCTAATGCAAGGTGTGAGGCTCTGTGGGTAAATG  >  NC_002947/1419401‑1419679

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: ‑