Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,521,034	G→A	8.9%	intergenic (+306/‑454)	PP_5582 → / → PP_5583	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,521,034	0	G	A	8.9%	122.7 / 2.6	45	intergenic (+306/‑454)	PP_5582/PP_5583	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (21/20);  new base A (2/2);  total (23/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.21e-01

TAAGCAACAAGTACCATCCCGGTTGTTCGCTTGAATTGAACAGCGGTAAACTCTCCAACTGCCTCGGCGTTAACGTCGCTGCTGGTAGTCTATGCTTACGATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACTTGTAATACGGCTGCGGGCATCTGCACCAGTTGAACCTGGGTGAACATCGTCCTACCCAATCATGCAAGCATTCACACCAATGCTTATAAGTAGATCGTCTGGACGATATAGATAAGAGTGGTGA  >  NC_002947/3520892‑3521172                                                                                                                                               |                                                                                                                                            tAAGCAACAAGTACCATCCCGGTTGTTCGCTTGAATTGAACAGCGGTAAACTCTCCAACTGCCTCGGCGTTAACGTCGCTGCTGGTAGTCTATGCTTACGATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCGCAACCt                                                                                                                                       >  1:216360/1‑149 (MQ=255) tAAGCAACAAGTACCATCCCGGTTGTTCGCTTGAATTGAACAGCGGTAAACTCTCCAACTGCCTCGGCGTTAACGTCGCTGCTGGTAGTCTATGCTTACGATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCGCAACCt                                                                                                                                       <  2:216360/149‑1 (MQ=255)           gTACCATCCCGGTTGTTCGCTTGAATTGAACAGCGGTAAACTCTCCAACTGCCTCGGCGTTAACGTCGCTGCTGGTAGTCTATGCTTACGATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACTTg                                                                                                                            >  1:93880/1‑149 (MQ=255)              ccATCCCGGTTGTTCGCTTGAATTGAACAGCGGTAAACTCTCCAACTGCCTCGGCGTTAACGTCGCTGCTGGTAGTCTATGCTTACGATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACTTGTaa                                                                                                                         >  8:92596/1‑149 (MQ=255)                   ccGGTTGTTCGCTTGAATTGAACAGCGGTAAACTCTCCAACTGCCTCGGCGTTAACGTCGCTGCTGGTAGTCTATGCTTACGATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACTTGTAATACgg                                                                                                                    >  4:9233/1‑149 (MQ=255)                   ccGGTTGTTCGCTTGAATTGAACAGCGGTAAACTCTCCAACTGCCTCGGCGTTAACGTCGCTGCTGGTAGTCTATGCTTACGATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACTTGTAATACgg                                                                                                                    <  4:265469/149‑1 (MQ=255)                   ccGGTTGTTCGCTTGAATTGAACAGCGGTAAACTCTCCAACTGCCTCGGCGTTAACGTCGCTGCTGGTAGTCTATGCTTACGATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACTTGTAATACg                                                                                                                     <  4:129192/148‑1 (MQ=255)                          ttCGCTTGAATTGAACAGCGGTAAACTCTCCAACTGCCTCGGCGTTAACGTCGCTGCTGGTAGTCTATGCTTACGATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCACAACCT‑CAACTACTTGTAATACGGCTGCggg                                                                                                             >  4:122524/1‑149 (MQ=255)                                 gaattgaaCAGCGGTAAACTCTCCAACTGCCTCGGCGTTAACGTCGCTGCTGGTAGTCTATGCTTACGATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACtt                                                                                                                             <  3:125259/126‑1 (MQ=255)                                 gaattgaaCAGCGGTAAACTCTCCAACTGCCTCGGCGTTAACGTCGCTGCTGGTAGTCTATGCTTACGATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACtt                                                                                                                             >  4:125259/1‑126 (MQ=255)                                   attgaaCAGCGGTAAACTCTCCAACTGCCTCGGCGTTAACGTCGCTGCTGGTAGTCTATGCTTACGATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACTTGTAATACGGCTGCg                                                                                                               >  2:183074/1‑138 (MQ=255)                                   attgaaCAGCGGTAAACTCTCCAACTGCCTCGGCGTTAACGTCGCTGCTGGTAGTCTATGCTTACGATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACTTGTAATACGGCTGCg                                                                                                               <  1:183074/138‑1 (MQ=255)                                     tgaaCAGCGGTAAACTCTCCAACTGCCTCGGCGTTAACGTCGCTGCTGGTAGTCTATGCTTACGATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACTTGTAATACGGCTGCGGGCATCTGCAc                                                                                                    >  7:22023/1‑147 (MQ=255)                                          aGCGGTAAACTCTCCAACTGCCTCGGCGTTAACGTCGCTGCTGGTAGTCTATGCTTACGATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCGc                                                                                                                                            <  1:34653/103‑1 (MQ=255)                                          aGCGGTAAACTCTCCAACTGCCTCGGCGTTAACGTCGCTGCTGGTAGTCTATGCTTACGATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCGc                                                                                                                                            >  2:34653/1‑103 (MQ=255)                                              gTAAACTCTCCAACTGCCTCGGCGTTAACGTCGCTGCTGGTAGTCTATGCTTACGATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACTTGTAATACGGCTGCGGGCATCTGCACCAGTTGAACCt                                                                                         >  7:180347/1‑149 (MQ=255)                                               tAAACTCTCCAACTGCCTCGGCGTTAACGTCGCTGCTGGTAGTCTATGCTTACGATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACTTGTAATACGGCTGCGGGCATCTGCACCa                                                                                                  >  2:257705/1‑139 (MQ=255)                                               tAAACTCTCCAACTGCCTCGGCGTTAACGTCGCTGCTGGTAGTCTATGCTTACGATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACTTGTAATACGGCTGCGGGCATCTGCACCa                                                                                                  <  1:257705/139‑1 (MQ=255)                                                  aCTCTCCAACTGCCTCGGCGTTAACGTCGCTGCTGGTAGTCTATGCTTACGATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACTTGTAATACGGCTGCGGGCATCTGCACCAGTTGAACCTGGGt                                                                                     <  2:93880/149‑1 (MQ=255)                                                        cAACTGCCTCGGCGTTAACGTCGCTGCTGGTAGTCTATGCTTACGATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACTTg                                                                                                                            >  8:258452/1‑104 (MQ=255)                                                        cAACTGCCTCGGCGTTAACGTCGCTGCTGGTAGTCTATGCTTACGATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACTTg                                                                                                                            <  7:258452/104‑1 (MQ=255)                                                          aCTGCCTCGGCGTTAACGTCGCTGCTGGTAGTCTATGCTTACGATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACTTGTAATACGGCTGCGGGCATCTGCACCAGTTGAACCTGGGTGAACATCg                                                                             <  1:307885/149‑1 (MQ=255)                                                               cTCGGCGTTAACGTCGCTGCTGGTAGTCTATGCTTACGATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACTTGTAATACGGCTGCGGGCATCTGCACCAGTTGAACCTGGGTGAACATCGTCCTa                                                                        <  8:283641/149‑1 (MQ=255)                                                                  ggCGTTAACGTCGCTGCTGGTAGTCTATGCTTACGATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACTTGTAATACGGCTGCGGGCATCTGCACCAGTTGAACCTGGGTGAACATCGTCCTAcc                                                                      <  8:22023/148‑1 (MQ=255)                                                                      ttAACGTCGCTGCTGGTAGTCTATGCTTACGATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACTTGTAATACGGCTGCGGGCATCTGCACCAGTTGAACCTGGGTGAACATCGTCCTACCCAATc                                                                 <  3:9233/149‑1 (MQ=255)                                                                        aaCGTCGCTGCTGGTAGTCTATGCTTACGATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCACAACCT‑CAACTACTTGTAATAAGGCTGCGGGCATCTGCACCAGTTGAACCTGGGTGAACATCGTCCTACCCAATCAt                                                               >  3:202190/1‑149 (MQ=255)                                                                           gTCGCTGCTGGTAGTCTATGCTTACGATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACTTGTAATACGGCTGCGGGCATCTGCACCAGTTGAACCTGGGTGAACATCGTCCTACCCAATCATGc                                                             >  2:304966/1‑148 (MQ=255)                                                                                    ggTAGTCTATGGTTACGATTCGATCCATCGTCGACACCAGTGCGACCCGACGGATAATCGCAAGCT‑CAACTACTTGTAATACGGCTGCGGGCATCGGCACCAGTTGAACCTGGGTGAACAGCGTCCGACCCAATCATGCAAGCCTTcgc                                                   >  2:226979/1‑147 (MQ=255)                                                                                     gTAGTCTATGCTTACGATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACTTGTAATACGGCTGCGGGCATCTGCACCAGTTGAACCTGGGTGAACATCGTCCTACCCAATCATGCAAGCATTcaca                                                  >  3:109187/1‑149 (MQ=255)                                                                                               cTTACGATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACTTGTAATACGGCTGCGGGCATCTGCACCAGTTGAACCTGGGTGAACATCGTCCTACCCAATCATGCAAGCATTCACACCAATGCtt                                         <  7:92596/148‑1 (MQ=255)                                                                                                ttACGATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACTTGTAATACGGCTGCGGGCATCTGCACCAGTTGAACCTGGGTGAACATCGTCCTACCCAATCATGCAAGCATTCACACCAATGCTta                                        >  7:238304/1‑148 (MQ=255)                                                                                                   cGATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACTTGTAATACGGCTGCGGGCATCTGCACCAGTTGAACCTGGGTGAACATCGTCCTACCCAATCATGCAAGCATTCACACCAATTCTTATaa                                     <  3:30199/148‑1 (MQ=255)                                                                                                   cGATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACTTGTAATACGGCTGCGGGCATCTGCACCAGTTGAACCTGGGTGAACATCGTCCTACCCAATCATGCAAGCATTCACACCAATGCTTATaa                                     <  8:180347/148‑1 (MQ=255)                                                                                                    gATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACTTGTAATACGGCTGCGGGCATCTGCACCAGTTGAACCTGGGTGAACATCGTCCTACCCAATCATGCAAGCATTCACACCAATGCTTATAAg                                    >  7:169214/1‑148 (MQ=255)                                                                                                    gATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACTTGTAATACGGCTGCGGGCATCTGCACCAGTTGAACCTGGGTGAACATCGTCCTACCCAATCATGCAAGCATTCACACCAATGCTTATAAGt                                   <  1:304966/149‑1 (MQ=255)                                                                                                           tCCATCGTCGTCACCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACTTGTAATACGGCTGCGGGCATCTGCACCAGTTGAACCTGGGTGAACATCGTCCTACCCAATCATGCAAGCATTCACACCAATGCTTATAAGTAGATCGt                            >  5:119104/1‑149 (MQ=255)                                                                                                             cATCGTCGTCACCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACTTGTAATACGGCTGCGGGCATCTGCACCAGTTGAACCTGGGTGAACATCGTCCTACCCAAt                                                                  <  7:138812/109‑1 (MQ=255)                                                                                                             cATCGTCGTCACCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACTTGTAATACGGCTGCGGGCATCTGCACCAGTTGAACCTGGGTGAACATCGTCCTACCCAAt                                                                  >  8:138812/1‑109 (MQ=255)                                                                                                               tcgtcgTCACCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACTTGTAATACGGCTGCGGGCATCTGCACAAGTTGAACCTGGGTGAACATAGTCCTACCCAATCATGCAAGCATTCACACCAATGCTTATAAGTAGATAGTCTg                         >  6:306248/1‑148 (MQ=255)                                                                                                                 gtcgtcACCAGTACGACCCGACGGATAATCACAACCT‑CAACTACTTGTAATACGGCTGCGGGCATCTGCACCAGTTGAACCTGGGTGAACATCGTCCTACCCAATCATGCAAGCATTCACACCAATGCTTATAAGTAGATCGTCTGGa                       <  3:122524/148‑1 (MQ=255)                                                                                                                    gtcACCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACTTGTAATACGGCTGCGGGCATCTGCACCAGTTGAACCTGGGTGAACATCGTCCTCCCCAATCATGCAAGCATTCACCCCAATGCTTATAAGTAGATCGTCTGGACGa                    >  5:67039/1‑148 (MQ=255)                                                                                                                       aCCAGTACGACCCGACGGATAATCGCAACCTGCAACTACTTGTAATACGGCTGCGGGCATCTGCACCAGTTGAACCTGGGTGAACATCGTCCTACCCAATCATGCAAGCATTCACACCAATGCTTATAAGTAGATCGTCTGGACGata                  >  1:188334/1‑148 (MQ=255)                                                                                                                       aCCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACTTGTAATACGGCTGCGGGCATCTGCACCAGTTGAACCTGGGTGAACATCGTCCTACCCAATCATGCAAGCATTCACACCAATGCTTATAAGTAGATCGTCTGGACGAtata                <  8:169214/149‑1 (MQ=255)                                                                                                                          aGTACGACCCGACGGATAATCACAACCT‑CAACTACTTGTAATACGGCTGCGGGCATCTGCACCAGTTGAACCTGGGTGAACATCGTCCTACCCAATCATGCAAGCATTCACACCAATGCTTATAAGTAGATCGTCTGGACGATATAGAt             <  4:202190/149‑1 (MQ=255)                                                                                                                                     aCGGATAATCGCAACCT‑CAACTACTTGTAATACGGCTGCGGGCATCTGCACCAGTTGAACCTGGGTGAACATCGTCCTACCCAATCATGCAAGCATTCACACCAATGCTTATAAGTAGATCGTCTGGACGATATAGATAAGAGTGGTGa  <  2:188334/149‑1 (MQ=255)                                                                                                                                               |                                                                                                                                            TAAGCAACAAGTACCATCCCGGTTGTTCGCTTGAATTGAACAGCGGTAAACTCTCCAACTGCCTCGGCGTTAACGTCGCTGCTGGTAGTCTATGCTTACGATTCGATCCATCGTCGTCACCAGTACGACCCGACGGATAATCGCAACCT‑CAACTACTTGTAATACGGCTGCGGGCATCTGCACCAGTTGAACCTGGGTGAACATCGTCCTACCCAATCATGCAAGCATTCACACCAATGCTTATAAGTAGATCGTCTGGACGATATAGATAAGAGTGGTGA  >  NC_002947/3520892‑3521172

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑