Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,166,707	C→A	10.9%	intergenic (‑551/‑230)	PP_5483 ← / → PP_1921	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,166,707	0	C	A	10.9%	112.9 / 6.6	46	intergenic (‑551/‑230)	PP_5483/PP_1921	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (20/21);  new base A (3/2);  total (23/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.03e-01

CCCTCGATCAGAAAGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCCGTTGGCCATTATGTG‑AAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTTGGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACC‑TGGCTTCCAGGTTGCAGGTCGTAGGGAGTAGGGAGTAGGGAGTAGGGAGTAGGGGCAGGGAGAGTCGGCGCGGGTGCAGATTCTGTCGAGCGAAGCAGGAGAGAGGAGGGTTGGTGTTATTTTGCTACTATGACTATGCGCACGACGGGC  >  NC_002947/2166560‑2166853                                                                                                                                                      |                                                                                                                                                   cccTCGATCAGAAAGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCCGTTGGCCATTATGTG‑AAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTTGGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACC‑TGGCt                                                                                                                                                   >  4:77165/1‑149 (MQ=255)   cTCGATCAGAAAGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCCGTTGGCCATTATGTG‑AAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTTGGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACC‑TGGCTTc                                                                                                                                                 >  7:29073/1‑149 (MQ=255)       aTCAGAAAGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCCGTTGGCCATTATGTG‑AAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTTGGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACC‑TGGCTTCCAgg                                                                                                                                             <  3:77165/149‑1 (MQ=255)         cAGAAAGTTACTCTCAGCAACCTATTGCAGAGGGTATAAGGATCGCCGTTGGCCATTATGTG‑AAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTTCGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACA‑TGGCTTCCAGGtt                                                                                                                                           >  5:284921/1‑149 (MQ=255)             aaGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCCGTTGGCCATTATGTG‑AAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTTGGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACC‑TGGAAGCCAGGTTgatt                                                                                                                                       <  1:304005/149‑4 (MQ=255)              aGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCCGTTGGCCATTATGTG‑AAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTTGGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACC‑TGGCTTCCAGGTTGCAgg                                                                                                                                      <  8:29073/149‑1 (MQ=255)                ttACTCTCAGCAACCTATTGCAGAGGGGTTAAGGATCGCCGTTGGCCATTATGTG‑AAACGACACGCTCCTGGAGCGGGATGATCCGAGGGCTGTTGGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACC‑TGGCTTCCAGGTTGCAGGTc                                                                                                                                    <  2:271668/149‑1 (MQ=255)                    tctcAGCAACCTATTGCAGAGGGTATAAGGATCGCCGTTGGCCAATAAGTG‑AAACGACCCGCTCCTGGAGACGGATGATACGAGGGCTGATGGGCTGTCGCTGGTTGAGTGAAGCTCAATCAACC‑ACTCTTCCACGTTGAAGGTCgtag                                                                                                                                >  4:230351/1‑149 (MQ=255)                    tctcAGCAACCTAGTGCAGAGGGTTTAAGGATCGCCGTTGGCCATTATGTG‑AAACGACCCGCTCCGGGAGCGGGATGATCCGAGGGCTGTTGGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACC‑TGGCTTCCAGGTTGCAGGTCgtag                                                                                                                                >  6:152382/1‑149 (MQ=255)                      tcAGCAACCTATTGCTTAGGGTTTAAGGATCGCCGTTGGCCATTATGTG‑AATCGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTTGGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACC‑TGGCTTCCAGGTTGCAGGTCgtag                                                                                                                                <  3:230351/147‑1 (MQ=255)                      tcAGCAACCTATTGCAGAGGGTTTAAGGATCGCCGTTGGCCATTATGTG‑AAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTTGGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACC‑TGGCTTCCAGGTTGCAGGTCgtagg                                                                                                                               >  7:305936/1‑148 (MQ=255)                         gCAACCTATTGCAGAGGGTTTAAGGATCGCCGTTGGCCATTATGTG‑AAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTTGGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACC‑TGGCTTCCAGGTTGCAGGTCgtagggag                                                                                                                            >  1:272208/1‑148 (MQ=255)                           aaCCTATTGCAGAGGGTTTAAGGATCGCCGTTGGCCATTATGTG‑AAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTTGGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACC‑TGGCTTCCAGGTTGCAGGTCgtagggagtag                                                                                                                         >  2:259/1‑149 (MQ=255)                             ccTATTGCAGAGGGTTTAAGGATCGCCGTTGGCCATTATGTG‑AAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTTGGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACC‑TGGCTTCCAGGTTGCAGGTCgtagggagtaggg                                                                                                                       >  5:172062/1‑149 (MQ=255)                               tATTGCAGAGGGTTTAAGGATCGCCGTTGGCCATTATGTG‑AAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTTGGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACC‑TGGCTTCCAGGTTGCAGGTCgtagggagtagggag                                                                                                                     >  4:277368/1‑149 (MQ=255)                                 ttGCAGAGGGTTTAAGGATCGCCGTTGGCCATTATGTG‑AAACGACCCGCTCCTGGAGCGGGATGATACGAGGGCTGTTGGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACC‑TGGCTTCCAGGTTGCAGGTCgtagggagtagggag                                                                                                                     >  7:311656/1‑147 (MQ=255)                                    cactaggTTTAACGCTAGCCCTTTGCCCATAAGTGCAAACAACCCGCCCCTGTCCCGGTAT‑AACCGCAGGCTGTTGGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACC‑TGGCTTCCAGGTTGCAGGTCgtagggagtagggagtagg                                                                                                                 <  4:112809/143‑1 (MQ=255)                                    cAGAGGGTTTAAGGATCGCCGTTGGCCATTATGTG‑AAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTTGGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACC‑TGGCTTCCAGGTTGCAGGTCgtagggagtagggagtagg                                                                                                                 <  3:70192/148‑1 (MQ=255)                                    cAGAGGGTTTAAGGATCGCCGTTGGCCATTATGTG‑AAACGACCCGCTCCTGGAGCGGGATGATCCGAAGGCTGTTGGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACC‑TGGCTTCCAGGTTGCAGGTCgtagggagaagggagtagg                                                                                                                 <  2:129221/148‑1 (MQ=255)                                     agagGGTTTAAGGATCGCCGTTGGCCATTATGTG‑AAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTTGGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACC‑TGGCTTCCAGGTTGCAGGTCgtagggagtagggagtaggga                                                                                                               <  2:150174/149‑1 (MQ=255)                                      gagGGTTTAAGGATCGCCGTTGGCCATTATGTG‑AAACGACCAGCTCATGGAGCTGTATGATACGAGGTCTGTTGGTGTGTAGCTGGTTGAGTGAAGCTCAATAAACC‑TTGCTTCCAGGTTTCAGGTCgtatgtaggagggagtaggtag                                                                                                              >  3:278676/1‑149 (MQ=255)                                          gtgtcaGGAGCGCCGTTGGCAATTATGTG‑AAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTTGGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACC‑TGGCTTCCAGGTTGCAGGTCgtagggagtagggagtagggagtagg                                                                                                          <  8:305936/144‑1 (MQ=255)                                                 gATCGCCGGTGGCCAATATGTG‑AAACGCCCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTTGTGGTGTCGCTGGTGGAGTGAAGCTCAATCAACC‑TGGCTTCCAGGTTGCAGGTCGTAGGgagtagggagtagggagtagggagtagg                                                                                                   <  4:295585/149‑1 (MQ=255)                                                         ttGGCCATTATGTG‑AAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTTGGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACC‑TGGCTTCCAGGTTGCAGGTCgtagggagtagggagtagg                                                                                                                 <  8:207231/127‑1 (MQ=255)                                                                  aTGTC‑AACCGACCCGCTCCTGTAGCTGGATGATCCGAGTGCTGTTGGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACC‑TGGCTTCCAGGTTGCAGGTCGTAGGGAGTAGGGAGTAGGGAGTAGGGAGTAGGGGCAGGGAGAGTCGgc                                                                                   <  8:311656/148‑1 (MQ=255)                                                                             tcccGCTCCAGGAGCGGGATGATCCGAGGGCTGTTGGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACC‑TGGCTTCCAGGTTGCAGGTCGTAGGGAGTAGGGAGTAGGGAGTAGGGAGTAGGGGCAGGGAGAGTCGGCGCggggg                                                                            >  1:94388/2‑143 (MQ=255)                                                                                       ggAGCGGGATGATCCGAGGGCTGTTGGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACC‑TGGCTTCCAGGTTGCAGGTCGTAGGGAGTAGGGAGTAGGGAGTAGGGAGTAGGGGCAGGGAGAGTCGGCGCGGGTGCAGATTCTGTCGAg                                                              >  2:107077/1‑149 (MQ=255)                                                                                        gAGCGGGATGATCCGAGGGCTGTTGGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACC‑TGGCATCCAGGTTGCAGGTCGTAGGGAGTAGGGAGTAGGGAGTAGGGAGTAGGGGCAGGGAGAGTCGGCGCGGGTGCAGATTCTGTCGa                                                               <  5:152382/147‑1 (MQ=255)                                                                                              gatgatCCGAGGGCTGTTGGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACC‑TGGCTTCCAGGTTGCAGGTCGTAGGGAGTAGGGAGTAGGGAGTAGGGAGTAGGGGCAGGGAGAGTCGGCGCGGGTGCAGATTCTGTCGAGCGAAGCa                                                       <  2:272208/149‑1 (MQ=255)                                                                                               atgatCCGAGGGCTGTTGGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACC‑TGGCTTCCAGGTTGCAGGTCGTAGGGAGTAGGGAGTAGGGAGTAGGGAGTAGGGGCAGGGAGAGTCGGCGCGGGTGCAGATTCTGTCGAGCGAAGCAg                                                      >  4:378743/1‑149 (MQ=255)                                                                                                  atCCGAGGGCTGTTGGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACC‑TGGCTTCCAGGTTGCAGGTCGTAGGGAGTAGGGAGTAGGGAGTAGGGAGTAGGGGCAGGGAGAGTCGGCGCGGGCGCAGATTCTGTCGAGCGAAGCAGga                                                    <  2:94388/148‑1 (MQ=255)                                                                                                   tCCGAGGGCTGTTGGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACC‑TGGCTTCCAGGTTGCAGGTCGTAGGGAGTAGGGAGTGGGGAGTAGGGAGTAGGGGCAGGGAGAGTCGGCGCGGGTGCAGATTCTGTCGAGCGAAGCAGgag                                                   <  6:172062/148‑1 (MQ=255)                                                                                                      gAGGGCTGTTGGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACC‑TGGCTTCCAGGTTGCAGGTCGTAGGGAGTAGGGAGTAGGGAGTTGGGAGTAGGGGCAGGGAGAGTCGGCGCGGGTGCAGATTCTGTCGAGCGAAGCAGGagagag                                               <  3:277368/149‑1 (MQ=255)                                                                                                      gAGGGCTGTTGGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACC‑TGGCTTCCAGGTTGCAGGTCGTAGGGAGTAGGGAGTAGGGAGTAGGGAGTAGGGGCAGGGAGAGTCGGCGCGGGTGCAGATTCTGTCGAGCGAAGCAGGagagag                                               >  2:345022/1‑149 (MQ=255)                                                                                                                   gtgtCGCTGGTTGAGTGAAGCTCAATCAACCATGGCTTCAAGGTTGCAGTTCTTAGGGAGTAGGGAGTAGGGAGTAGGTATTAGGGGAAGGGAGAGTCGGCGCGGGTGCAGATTATGTCGAGCGAAGAAGGAGAGAGGAGGGTTGgtgt                                   >  1:238548/1‑149 (MQ=255)                                                                                                                         cTGGTTGAGTGAAGCTCAATCAACC‑TGGCTTCCAGGTTGCAGGTCGTAGGGAGTAGGGAGTAGGGAGTAGGGAGTAGGTGCAGGGAGAGTCGGCGCGGGTGCAGATTCTGTCGAGCGAAGCAGGAGAGAGGAGGGTTGGTGTTATTTTg                            >  8:144756/1‑149 (MQ=255)                                                                                                                         cTGGTTGAGTGAAGCTCAATCAACC‑TGGCTTCCAGGTTGCAGGTCGTAGGGAGTAGGGAGTAGGGAGTAGGGAGTAGGGGCAGGGAGAGTCGGCCCGCGTGGAGATTCTGTCGAGCGAAGCAGGAGAGAGGAGGGTTGGAGatatagg                             >  1:65306/1‑145 (MQ=255)                                                                                                                          tGGTTGAGGGAAGCTCAATCAACC‑TGGCTTCCAGGTTGCAGGTCGTAGGGAGTAGGGAGTAGGGAGTAGGGAGTAGGGGCAGGGAGAGTCGGCGCGGGTGCAGATTCTGTCGAGCGAAGCAGGAGAGAGGAGGGTTGGTGTTATTTTGc                           <  2:238548/149‑1 (MQ=255)                                                                                                                                    aaGCTCAATCAACC‑TGGCTTCATGGTTGAAGGTCGTTGGGAGTTGGTAGTAGGGAGTAGGTAGTCGGGGCTGGGAGAGTCGGCGCGGGTGATGATTCTGTCGAGCGAAGCAGGAGAGAGGAGGGTTGGTGTTATTTTGCTactatgac                  <  1:107077/148‑1 (MQ=255)                                                                                                                                         caatcaaCC‑TGGCTTCCAGGTTGCAGGTCGTAGGGAGTAGGGAGTAGGGAGTAGGGAGTAGGGGCAGGGAGAGTCGGCGCGGGTGCAGATTCTGTCGAGCGAAGCAGGAGAGATGAGGGTTGGTGTTTTTTTGCTACTATGACTATgcg            >  7:75403/1‑149 (MQ=255)                                                                                                                                          ctgcaaCC‑TGGAAGCCAGGTTGCAGGTCGTACGGAGTAGGGAGTAGGGAGTAGGGAGTAGGGGCAGGGAGAGTCGGCGCGGGTGCAGATTCTGTCGAGCGCAGCAGGAGGGAGGAGGGGTGGTGGTATTTTGGTACTATGACTATgcga           >  4:130479/4‑148 (MQ=255)                                                                                                                                           tgcaaCC‑TGGACTCCAGGTTGCAGGTCGTAGGGAGTATGGAGTAGGGAGTAGGGAGTAGGGGCAGGGAGAGTCGGCGCGTGTGCAGATTCTGTCGAGCGAAGCAGGAGAGAGGAGGGTTGGTGTTATTTTGCTACTATGACTATgc             <  8:263962/144‑1 (MQ=255)                                                                                                                                           tgcaaCC‑TGGAAGCCAGGTTGCAGGTCGTAGGGAGTAGGGAGTAGGGAGTAGGGAGTAGGGGCAGGGAGAGTCGGCGCGGGTGCAGATTCTGTCGAGCGAAGCAGGAGAGAGGAGGGTTGGTGTTATTTTGCTACTATGACTATGCGCa          >  2:16532/3‑149 (MQ=255)                                                                                                                                           tgcaaCC‑TGGAAGCCAGGTTGCAGGTCGTAGGGAGTAAGGAGTAGGGAGTAGGGAGTAGGGGCAGGGAGAGTCGGCGCGGGTGCAGATTCTGTCGAGCGAAGCAGGAGAGAGGAGGGTTGGTGGTATTTTGCTACTATGACTATgc             >  7:263962/3‑146 (MQ=255)                                                                                                                                                     gCTTCCCGGTTGCAGGTCGGAGGGAGACGGGCGGAGGGCTTAGGGAGTAGGAGCAGCGAGAGGCTGCGCGTGTGCAGATTCTGTCGAGCGACGCAGGAGAGAGGAGGGTTGGTGTTATTTTGCTACTATGACTATGCGCACGACGGGc  <  4:278676/148‑1 (MQ=255)                                                                                                                                                     gCTTCCAGGTTGCAGGTCGTAGGGAGTAGGGAGTAGGGTGTAGGTAGTAGGTGCAGGGAGAGTCGGCGCGGGTGCAGATTCTGTCGAGCGAAGCAGGAGAGAGGAGGGTTGGTGTTATTTTGCTACTATGACTATGCGCACGACggg   <  7:144756/147‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                   CCCTCGATCAGAAAGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCCGTTGGCCATTATGTG‑AAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTTGGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACC‑TGGCTTCCAGGTTGCAGGTCGTAGGGAGTAGGGAGTAGGGAGTAGGGAGTAGGGGCAGGGAGAGTCGGCGCGGGTGCAGATTCTGTCGAGCGAAGCAGGAGAGAGGAGGGTTGGTGTTATTTTGCTACTATGACTATGCGCACGACGGGC  >  NC_002947/2166560‑2166853

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: ‑