Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	103,820	T→A	11.8%	intergenic (+118/‑22)	PP_0098 → / → PP_0099	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	103,820	0	T	A	11.8%	122.9 / 8.3	51	intergenic (+118/‑22)	PP_0098/PP_0099	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (27/18);  new base A (4/2);  total (31/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.74e-01

TGCAGTGCTGCAGCCCTAAGCGCTGTCTGTCTGGGATGGGCGGCAATCGAGCCAGGCAGCGTATGTGCGCTGGCATGGCCTGAAGTAGTCAGACCAGAGGTGCTGGTAAGATCCCGGTGTGCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAACCGCTTTGCCCCTGGTCATTCGGTGGCGGAAGATGATGGCTGGTACCAGGAAGTGCCGCAAACCCAGGGTAC  >  NC_002947/103684‑103966                                                                                                                                         |                                                                                                                                                   tGCAGTGCTGCAGCCCTAAGCGCTGTCTGTCTGGGATGGGCGGCAATCGAGCCAGGCAGCGTATGTGCGCTGGCATGGCCTGAAGTAGTCAGACCAGAGGTGCTGGTAAGATCCCGGTGTGCACGATACCGTATATTAATACAGTAtt                                                                                                                                         >  2:212821/1‑148 (MQ=255)               ccTAAGCGCTGTCTGTCTGGGATGGGCGGCAATCGAGCCAGGCAGCGTATGTGCGCTGGCATGGCCTGAAGTAGTCAGACCAGAGGTGCTGGTAAGATCCCGGTGTGCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGAt                                                                                                                          >  4:241711/1‑149 (MQ=255)                cTAAGCGCTGTCTGTCTGGGATGGGCGGCAATCGAGCCAGGCAGCGTATGTGCGCTGGCATGGCCTGAAGTAGTCAGACCAGAGGTGCTGGTAAGATCCCGGTGTGCACGATACTGTATTAATATACAGTAtcg                                                                                                                                        <  8:95220/134‑3 (MQ=255)                cTAAGCGCTGTCTGTCTGGGATGGGCGGCAATCGAGCCAGGCAGCGTATGTGCGCTGGCATGGCCTGAAGTAGTCAGACCAGAGGTGCTGGTAAGATCCCGGTGTGCACGATACTGTATTAATATACAGTAtcg                                                                                                                                        >  7:95220/1‑132 (MQ=255)                                  ggATGGGCGGCAATCGAGCCAGGCAGCGTATGTGCGCTGGCATGGCCTGAAGTAGTCAGACCAGAGGTGCTGGTAAGCTCCCGGTGTGCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAg                                                                                                       >  6:299956/1‑149 (MQ=255)                                   gATGGGCGGCAATCGAGCCAGGCAGCGTATGTGCGCTGGCATGGCCTGAAGTAGTCAGACCAGACGTGCTGGTAAGATCCCGGTGTGCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAgg                                                                                                      <  8:131967/149‑1 (MQ=255)                                    aTGGGCGGCAATCGAGCCAGGCAGCGTATGTGCGCTGGCATGGCCTGAAGTAGTCAGACCAGAGGTGCTGGTAAGATCCCGGTGTGCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAggg                                                                                                     <  3:138177/149‑1 (MQ=255)                                        gcggcAATCGACCCAGGCAGCGTATGTGCGCTGGCATGGCCTGAAGTAGTCAGACCAGAGGTGCTGGTAAGATCCCGGTGTGCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGt                                                                                                 >  4:179088/1‑149 (MQ=255)                                          ggcAATCGAGCCAGGCAGCGTATGTGCGCTGGCATGGCCTGAAGTAGTCAGACCAGAGGTGCTGGTAAGATCCCGGTGTGCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTgg                                                                                               >  4:308487/1‑149 (MQ=255)                                             aaTCGAGCCAGGCAGCGTATGTGCGCTGGCATGGCCTGAAGTAGTCAGACCAGAGGTGCTGGTAAGATCCCGGTGTGCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCAc                                                                                            >  7:201463/1‑149 (MQ=255)                                                 gAGCCAGGCAGCGTATGTGCGCTGGCATGGCCTGAAGTAGTCAGACCAGAGGTGCTGGTAAGATCCCGGTGTGCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGgcg                                                                                        >  7:25993/1‑149 (MQ=255)                                                    ccAGGCAGCGTATGTGCGCTGGCATGGCCTGAAGTAGTCAGACCAGAGGTGCTGGTAAGATCCCGGTGTGCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGca                                                                                      >  8:42833/1‑148 (MQ=255)                                                      aGGCAGCGTATGTGCGCTGGCATGGCCTGAAGTAGTCAGACCAGAGGTGCTGGTAAGATCCCGGTGTGCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGAGCACaa                                                                                   >  2:222404/1‑149 (MQ=255)                                                       ggCAGCGTATGTGCGCTGGCATGGCCTGAAGTAGTCAGACCAGAGGTGCTGGTAAGATCCCGGTGTGCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAAt                                                                                  <  3:179088/149‑1 (MQ=255)                                                         cAGCGTATGTGCGCTGGCATGGCCTGAAGTAGTCAGACCAGAGGTGCTGGTAAGATCCCGGTGTGCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATcc                                                                                <  3:241711/149‑1 (MQ=255)                                                                tgtgCGCTGGCATGGCCTGAAGTAGTCAGACCAGAGGTGCTGGTAAGATCCCGGTGTGCACGATACCGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAAc                                                                         <  1:212821/149‑1 (MQ=255)                                                                 gtgCGCTGGCATGGCCTGAAGTAGTCAGACCAGAGGTGCTGGTAAGATCCCGGTGTGCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAAcc                                                                        >  6:90614/1‑149 (MQ=255)                                                                   gcgcTGGCATGGCCTGAAGTAGTCAGACCAGAGGTGCTGGTAAGATCCCGGTGTGCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAACCGc                                                                      >  7:99526/1‑149 (MQ=255)                                                                      cTGGCATGGCCTGAAGTAGTCAGACCAGAGGTGCTGGTAAGATCCCGGTGTGCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAACCGCttt                                                                   >  2:338596/1‑149 (MQ=255)                                                                           aTGGCCTGAAGTAGTCAGACCAGAGGTGCTGGTAAGATCCCGGTGTGCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAACCGCTTTGcccc                                                              >  3:294312/1‑149 (MQ=255)                                                                              gCCTGAAGTAGTCAGACCAGAGGGGCTGGTAAGATCCCGGTGTGCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAACCGCTTTGCCCCTgg                                                           <  8:25993/149‑1 (MQ=255)                                                                                cTGAAGTAGTCAGACCAGAGGTGCTGGTAAGATCCCGGTGTGCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAACCGCTTTGCCCCTGGt                                                          >  6:140553/1‑148 (MQ=255)                                                                                 tGAAGTAGTCAGACCAGAGGTGGTGGTAAGATCCCGGTGTGCAAGATTATTTATATTAATACAGTATTCAGGTGAGCCATGATACCTCCAGAACCGCAAAAGGGCCGTGGCCCGGCGCACAAACCACACAACCGATTTGCCCATgtgaa                                                        >  7:227576/1‑145 (MQ=255)                                                                                        gtCAGACCAGAGGTGCTGGTAAGATCCCGGTGTGCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAACCGCTTTGCCCCTGGTCATTCGGTg                                                 <  5:140553/149‑1 (MQ=255)                                                                                        gtCAGACCAGAGGTGCTGGTAAGATCCCGGTGTGCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAACCGCTTTGCCCCTGGTCATTCGGTg                                                 >  6:227140/1‑149 (MQ=255)                                                                                        gtCAGACCAGAGGTGCTGGTAAGATCCCGGTGTGCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAACCGCTTTGCCCCTGGTCATTCGGTg                                                 >  8:196229/1‑149 (MQ=255)                                                                                         tCAGACCAGAGGTGCTGGTAAGATCCCGGTGTGCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAACCGCTTTGCCCCTGGTCATTCGGTgg                                                >  4:249824/1‑149 (MQ=255)                                                                                           aGACCAGAGGTGCTGGTAAGATCCCGGTGTGCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAACCGCTTTGCCCCTGGTCATTCGGTGGCg                                              <  5:90614/149‑1 (MQ=255)                                                                                              ccAGAGGTGCTGGTAAGATCCCGGTGTGCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAACCGCTTTGCCCCTGGTCATTCGGTGGCGGaa                                           <  7:46719/149‑1 (MQ=255)                                                                                                agagGTGCTTGTAAGATCACGGTGTGCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAACCGCTTTGCCCCTGGTCATTCGGTGGCGGAAga                                         <  4:108582/149‑1 (MQ=255)                                                                                                agagGTGCTGGTAAGATCCCGGTGTGCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAACCGCTTTGCCCCTGGTCATTCGGTGGCgg                                             >  6:134556/1‑145 (MQ=255)                                                                                                        tGGTAAGATCCCGGTGTGCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAACCGCTTTGCCCCTGGTCATTCGGTGGCGGAAGATGATGGCt                                 >  6:53434/1‑149 (MQ=255)                                                                                                          gTAAGATCCCGGTGTGCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAACCGCTTTGCCCCTGGTCATTCGGTGGCGGAAGATGATGGCt                                 <  8:201463/147‑1 (MQ=255)                                                                                                          gTAAGATCCCGGTGTGCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAACCGCTTTGCCCCTGGTCATTCGGTGGCGGAAGATGATGGCTg                                <  5:227140/148‑1 (MQ=255)                                                                                                           tAAGATCCCGGTGTGCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAACCGCTTTGCCCCTGGTCATTCGGTGGCGGAAGATGATGGCTgg                               >  7:35938/1‑148 (MQ=255)                                                                                                           tAAGATCCCGGTGTGCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAACCGCTTTGCCCCTGGTCATTCGGTGGCGGAAGATGATGGCTGGt                              <  8:99526/149‑1 (MQ=255)                                                                                                                  ccGGTGTGCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGTGCCGTGGCACGGCGCACAATCCACACACCCGCTTTGCCCCTGGTCATTCGGTGGCGGAAGATGATGGCTGGTACCAgg                        <  5:299956/148‑1 (MQ=255)                                                                                                                   cgttgtgCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAACCGCTTTGCCCCTGGTCATTCGGTGGCGGAAGATGATGGCTGGTACCAGGaa                      <  1:338596/146‑1 (MQ=255)                                                                                                                      tgtgCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAACCGCTTTGCCCCTGGTCATTCGGTg                                                 >  7:127802/1‑119 (MQ=255)                                                                                                                      tgtgCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAACCGCTTTGCCCCTGGTCATTCGGTg                                                 <  8:127802/119‑1 (MQ=255)                                                                                                                        tgCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAACCGCTTTGCCCCTGGTCATTCGGTGGCGGAAGATGATGGCTGGTACCAGGAAGTGcc                 <  4:294312/149‑1 (MQ=255)                                                                                                                         cctgaaTACTGTATTAATATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAACCGCTTTGCCCCTGGTCATTCGGTGGCGGAAGATGATGGCTGGTACCAGGaa                      >  7:241537/6‑143 (MQ=255)                                                                                                                         cctgaaTACTGTATTAATATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAACCGCTTTGCCCCTGGTCATTCGGTGGCGGAAGATGATGGCTGGTACCAGGaa                      <  8:241537/138‑1 (MQ=255)                                                                                                                          ctgaaTACTGTATTAATATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAACCGCTTTGCCCCTGGTCATTCGGTGGCGGAAGATGATGGCTGGTACCAGGAAGTGCCg                >  6:32194/5‑148 (MQ=255)                                                                                                                          ctgaaTACTGTATTAATATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAACCGCTTTGCCCCTGGTCATTCGGTGGCGGAAGATGATGGCTGGTACCAGGAAGTGCCg                >  5:326820/5‑148 (MQ=255)                                                                                                                                  tatataTTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAACCGCTTTGCCCCTGGTCATTCGGTGGCGGAAGATGATGGCTGGTACCAGGAAGTGCCGCAAACCCAg       >  1:166359/3‑149 (MQ=255)                                                                                                                                  tGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAACCGCTTTGCCCCTGGTCATTCGGTGGCGGAAGATGATGGCTGGTACCAGGAAGTGCCGCAAACCCAg       >  2:233462/1‑149 (MQ=255)                                                                                                                                     atatTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAACCGCTTTGCCCCTGGTCATTCGGTGGCGGAAGATGATGGCTGGTACCAGGAAGTGCCGCAAACCCAggg     <  3:308487/148‑1 (MQ=255)                                                                                                                                       atTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAACCGCTTTGCCCCTGGTCATTCGGTGGCGGAAGATGATGGCTGGTACCAGGAAGTGCCGCAAACCCAGGGTAc  >  7:174081/1‑149 (MQ=255)                                                                                                                                       atTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAACCGCTTTGCCCCTGGTCATTCGGTGGCGGAAGATGATGGCTGGTACCAGGAAGTGCCGCAAACCCAGGGTAc  >  8:131014/1‑149 (MQ=255)                                                                                                                                       atTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAACCGCTTTGCCCCTGGTCATTCGGTGGCGGAAGATGATGGCTGGTACCAGGAAGTGCCGCAAACCCAGGGTAc  >  1:178840/1‑149 (MQ=255)                                                                                                                                         |                                                                                                                                                   TGCAGTGCTGCAGCCCTAAGCGCTGTCTGTCTGGGATGGGCGGCAATCGAGCCAGGCAGCGTATGTGCGCTGGCATGGCCTGAAGTAGTCAGACCAGAGGTGCTGGTAAGATCCCGGTGTGCACGATACTGTATATTAATACAGTATTCAGGTGAGCCATGATTCCTCCAGTACCGCAAAAGGGCCGTGGCACGGCGCACAATCCACACAACCGCTTTGCCCCTGGTCATTCGGTGGCGGAAGATGATGGCTGGTACCAGGAAGTGCCGCAAACCCAGGGTAC  >  NC_002947/103684‑103966

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑