Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	97,594	A→C	20.5%	intergenic (+23/+13)	PP_0090 → / ← PP_0091	hypothetical protein/putative lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	97,594	0	A	C	20.5%	60.1 / 9.5	38	intergenic (+23/+13)	PP_0090/PP_0091	hypothetical protein/putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base A (17/12);  new base C (3/5);  total (20/18)
Fisher's exact test for biased strand distribution p-value = 4.28e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAGGGGTTTCGTCCTACACGCTGGAGATCGTGCCCAACAGCGAGGTCAAGGACCAGAACATGGTCGTCGGGACCTGCGATGGCGGGACGAAGAAGATCATCTATCAGAAGAACGATCGATAAGCATCAGGGCCCGGGGCTGCGAAGCAGCCCCACACTCACGGGATGCAGAACACTTCGCTAGGCTCGTTCACCACCACCTTGCGGTTGGCGTCATATAGCAGCACCTGCGGCTCCATCACCGGCGCCCGCGCTTCCAGGCGATAGCGCTCGCCGGCCTTGAAGTTGTCAAAG  >  NC_002947/97450‑97742                                                                                                                                                 |                                                                                                                                                     aaGGGGTTTCGTCCTACACGCTGGAGATCGTGCCCAACAGCGAGGTCAAGGACCAGAACATGGTCGTCGGGACCTGCGATGGCGGGACGAAGAAGATCATCTATCAGAAGAACGATCGATAAGCATCAGGGCCCGGGGCTGCGAagcag                                                                                                                                                  >  6:108005/1‑149 (MQ=255) aaGGGGTTTCGTCCTACACGCTGGAGATCGTGCCCAACAGCGAGGTCAAGGACCAGAACATGGTCGTCGGGACCTGCGATGGCGGGACGAAGAAGATCATCTATCAGAAGAACGATCGATAAGCAGCAGGGCCCGGGGCTGCCAaccac                                                                                                                                                  >  8:242134/1‑148 (MQ=255)         tCGTCCTACACGCTGGAGATCGTGCCCAACAGCGAGGTCAAGGACCAGAACATGGTCGTCGGGACCTGCGATGGCGGGACGAAGAAGATCATCTATCAGAAGAACGATCGATAAGCATCAGGGCCTGGGGCTGCTTCGCAGccccggg                                                                                                                                           <  6:51918/148‑4 (MQ=255)                              gTGCCCAACAGCGAGGTCAAGGACCAGAACATGGTCGTCGGGACCTGCGATGGCGGGACGAAGAAGATCATGTTTCAGATGAACGATCGATAAGCATCAGGGCCCGGGGCTGGGTAGCAGGCCCAGACTCACGGGATTCAGAACACGTc                                                                                                                     >  6:329748/1‑149 (MQ=255)                                            gctCAAGGACCATAACATGGTCGTCGGGACCTGCGATGGCGGGACGAACAACACCAACTATCACAAGAACGATCTATAACCATCAGCGCCCGGGGCTGCGAAGCAGCCCCACACTCACGGGATGCAGAACACTTCGCTAGGCTCGTTca                                                                                                       <  6:110619/147‑1 (MQ=255)                                             gTCAAGGACCAGAACATGGTCGTCGGGACCTGCGATGGCGGGACGAAGAAGATCATCTATCAGAAGAACGATCGATAAGCATCAGGGCCCGGGGCTGCGAAGCAGCCCCACACTCACGGGATGCAGAACACTTCGCTAGGCTCGTTcac                                                                                                      >  6:133250/1‑149 (MQ=255)                                              tCAAGGACCAGAACATGGTCGTCGGGACCTGCGATGGCGGGACGAAGAAGATCATCTATCAGAAGAACGATCGATAAGCATCAGGGCCCGGGGCTGCGGAGCAGCCCCACACTCACGGGTTGCAGAACCCTTCGCTAGGCTCGTTcacc                                                                                                     >  7:285120/1‑149 (MQ=255)                                                aaGGACCAGAACATGGTCGTCGGGACCTGCGATGGCGGGACGAAGAAGATCATCTATCAGAAGAACGATCGAAAAGCATCAGGGCCCGGGGATGCCAAGCAGCCCCACACTCACGGGATGCAGAAACCGTCCCTAGGCGCGTTcaccac                                                                                                   >  2:77078/1‑149 (MQ=255)                                                           cttGGTCGTCGGGACGTGCTATGGCGGTACGACGAAGATCATCTATCAGAATAACGATCGATAAGCATCAGGGCCGGGGGCTGCGAAGCAGCCCCACACTCACGGGATGCAGAACACTTCGCTAGGCTCGTTCACCACCACCTTGCGGt                                                                                        <  1:77078/147‑1 (MQ=255)                                                              gttggtcgGGACCTGCGATGGGGTGACTAAGAATATCATCTATCAGAAGAACGAGCTATAAGCATCAGGGCCCGGGGCTGGGATGCAGCCCCACACTCACGGGATGCAGAACACTTCGCTATGCTCGTTCACCACCACCTTGCGGTTg                                                                                      <  7:242134/144‑1 (MQ=255)                                                                   tcgGGACCTGCGATGGCGGGACGAAGAAGATCATCTATCAGAAGAACGATCGATAAGCATCAGGGCCCGGGGCTGCGAAGCAGCCCCACACTCACGGGATGCAGAACACTTCGCTAGGCTCGTTCACCACCACCTTGCGGTTGGCGTc                                                                                 >  4:292868/1‑148 (MQ=255)                                                                   tcgGGACCTGCGATGGAGGGACGAAGAAGATCATCTATCAGAAGAACGATCGATAAGCATCAGGGCCCGGGGCTGCGAAGCAGCCCCACACTCACGGGATGCAGAACACTTCGCTAGGCTCGTTCACCACCACCTTGCGGTTGGCGTCa                                                                                >  4:297795/1‑149 (MQ=255)                                                                      tgACCTGCTAGGGCGGGACGAAGAAGATCATCTATCAGAAGAACGATCGATAAGCAGCAGGGCCCGGGGCTGCGACGCAGCCCCACACTCACGGGATGCAGAACACTTCGCTAGGCTCGTTCACCACCACCTTGCGGTTGGCGTCatat                                                                             <  6:236366/148‑1 (MQ=255)                                                                         ccTGCGATGGCGGGACGAAGAAGATCATCTATCAGAAGAACGATCGATAAGCATCAGGGCCCGGGGCTGCGAAGCAGCCCCACACTCACGGGATGCAGAACACTTCGCTAGGCTCGTTCACCACCACCTTGCGGTTGGCGTCATATagc                                                                          <  5:306741/149‑1 (MQ=255)                                                                             cGATGGCTGGACGAAGAAGATCATCTATCAGAAGAACGATCGATAAGCATCAGGGCCCGGGGCTGCGAAGCAGCCCCACACTCACGGGATGCAGAACACTTCGCTAGGCTCGTTCACCACCACCTTGCGGTTGGCGTCATATAgcagca                                                                      <  1:220107/149‑1 (MQ=255)                                                                              gATGGCGGGACGAAGAAGATCATCTATCAGAAGAACGATCGAAAAGCATCAGGCCCCGGGGCTGCTAAGCAGCCCCACACTCACGGGATGCAGAACACTTCGCTAGGCTCGTTCACCACCACCTTGCGGTTGGCGTCATATAGCAGCAc                                                                     <  8:206669/149‑1 (MQ=255)                                                                                  gCGGGACGAAGAAGATCATCTATCAGAAGAACGATCGATAAGCATCAGGTCCCGGGGCTGCGAAGCAGCCCCACACTCACGGGATGCAGAACACTTCGCTAGGCTCGTTCACCACCACCTTGCGGTTGGCGTCATATAGCAGCACCTGc                                                                 <  5:108005/149‑1 (MQ=255)                                                                                     ggACGAAGAAGATCATCTATCAGAAGAACGATCGATAAGCATCAGGGCCCGGGGCTGGGAAGCAGCCCCACACTCACGGGATGCAGAACACTTCGCTAGGCTCGTTCACCACCACCTTGCGGTTGGCGTCATATAGCAGCACCTTCg                                                                >  5:115233/1‑147 (MQ=255)                                                                                         gaagaaGATCATCTATCAGAAGAACGATCGATAAGCATCAGGGCCCGGGGCTGCGAATCAGCCCCACACTAACGGGATTAAGAACACTTCGCTAGGCTCCTTAACCACCACAATGCGGATGGCGTCATAAAGCAGCCCCTGCGGCTcc                                                           >  7:52075/1‑148 (MQ=255)                                                                                         gaagaaGATCATCTATCAGAAGAACGATCGATAAGCATCAGGGCCCGGGGCTGCGAAGCAGCCCCACACTCACGGGATGCAGAACACTTCGCTAGGCTCGTTCACCACCACCTTGCGGTTGGCGTCATATagcagc                                                                       <  3:269891/136‑1 (MQ=255)                                                                                         gaagaaGATCATCTATCAGAAGAACGATCGATAAGCATCAGGGCCCGGGGCTGCGAAGCAGCCCCACACTCACGGGATGCAGAACACTTCGCTAGGCTCGTTCACCACCACCTTGCGGTTGGCGTCATATagcagc                                                                       >  4:269891/1‑136 (MQ=255)                                                                                         gaagaaGATCATCTATCAGAAGAACGATCGATAAGCATCAGGGCCCGGGGCTGCGAAGCAGCCCCACACTCACGGGATGCAGAACACTTCGCTAGGCTCGTTCACCACCACCTTGCGGTTGGCGTCATATAGCAGCACCTGCGGCTcc                                                           >  7:234166/1‑148 (MQ=255)                                                                                               gaTCATCTATCAGAAGAACGATCGATAAGCATCAGGGCCCGGGGCTGCGAAGCAGCCCCACACTCACGGGATGCAGAACACTTCGCTAGGCTCGTTCACCACCACCTTGCGGTTGGCGTCATATAGCAGCACCTGc                                                                 <  1:60319/136‑1 (MQ=255)                                                                                               gaTCATCTATCAGAAGAACGATCGATAAGCATCAGGGCCCGGGGCTGCGAAGCAGCCCCACACTCACGGGATGCAGAACACTTCGCTAGGCTCGTTCACCACCACCTTGCGGTTGGCGTCATATAGCAGCACCTGc                                                                 >  2:60319/1‑136 (MQ=255)                                                                                                        tCAGAAGAACGATCGATAAGCATCAGGGCCCGGGGCTGCGAAGCAGCCCCACACTCACGGGATGCAGAACACTTCGCTAGGCTCGTTCACCACCACCTTGCGGTTGGCGTCATATAGCAGCACCTGCGGCTCCATCACCGGCGCCcgcg                                           >  6:276970/1‑149 (MQ=255)                                                                                                           gaagaaCGATCGATAAGCATCAGGGCCCGGGGCTGCGAAGCACCCCCACACTCACGGGATGCAGAACACTTCGCTAGGCTCGTTCACCACCACCTTGCGGTTGGCGTCATATAGCAGCACCTGc                                                                 <  7:156436/124‑1 (MQ=255)                                                                                                           gaagaaCGATCGATAAGCATCAGGGCCCGGGGCTGCGAAGCACCCCCACACTCACGGGATGCAGAACACTTCGCTAGGCTCGTTCACCACCACCTTGCGGTTGGCGTCATATAGCAGCACCTGc                                                                 >  8:156436/1‑124 (MQ=255)                                                                                                                       atAAGCATCAGGGCCCGGGGCTGCGAAGGAGCCCCACACTCACGGGATGCAGAACACTTCGCTAGGCTCGTTCACCACCACCTTGCGGTTGGCGTCATATAGCAGCACCTGCGGCTCCATCACCGGCGCCCCCGCATCCAGGCGATAgc                            >  1:21558/1‑149 (MQ=255)                                                                                                                       atAAGCATCAGGGCCCGGGGCTGCGAAGCAGCCCCACACTCACGGGATGCAGAACACATCGGTAGGCTCGTTCACCACCACCATGCGGTTGGCGTCATATAGCAGCACCTGCGGCTCCATCACCCGCGCCCGCGCGTCCACGCGATAgc                            >  2:270703/1‑149 (MQ=255)                                                                                                                                  ggCCCGGGGCTGCGACCCAGCCCCACACTCACGGGATGCAGAACACTTCGCTAGGCTCGTTCACCACCACCTTGCGGTTGGCGTCATATAGCAGCACCTGCGGCTCCATCACCGGCGCCCGCGCTTCCAGGCGATAGCGCTCGCCGGcc                 <  8:285120/149‑1 (MQ=255)                                                                                                                                    tgtggggCTGCTTCGCAGCCCCACACTCACGGGATGCAGAACACTTCGCTAGGCTCGTTCACCACCACCTTGCGGTTGGCGTCATATAGCAGCACCTGCGGCTCCATCACCGGCGCCCGCGCTTCCAGGc                                  >  7:235847/4‑130 (MQ=255)                                                                                                                                    tgtggggCTGCTTCGCAGCCCCACACTCACGGGATGCAGAACACTTCGCTAGGCTCGTTCACCACCACCTTGCGGTTGGCGTCATATAGCAGCACCTGCGGCTCCATCACCGGCGCCCGCGCTTCCAGGc                                  <  8:235847/127‑1 (MQ=255)                                                                                                                                    cccGGGGCTGCGAAGCAGCCCCACACTCACGGGATGCAGAACACTTCGCTAGGCTCGTTCACCACCACCTTGCGGTTGGCGTCATATAGCAGCACCTGCGGCTCCATCACCGGCGCCCGCGCTTCCAGGCGATAGCGCTCGCCGGCCtt               <  1:270703/149‑1 (MQ=255)                                                                                                                                     gtggggCTGCTTCGCAGCCCCGCACTCACGGGATGCAGAACACTTCGCTAGGCTCGTTCACCACCACCTTGCGGTTGGCGTCATATAGCAGCACCTGCGGCTCCATCACCGGCGCCCGCGCTTCCAGGCGATAGCGCTCGGCGGCCtg               >  4:207164/3‑147 (MQ=255)                                                                                                                                     ccGTGGCTTCCAAGCAGCCCCACACTCACGGGATGCAGAACACTTCGCTAGGCTCGTTCACCACCACCTTGCGGTTGGCGTCATATAGCAGCACCTGCGGCTCCATCACCGGCGCCCGCGCTTCCAGGCGATAGCGCTCGCCGGCCTTg              <  5:329748/149‑1 (MQ=255)                                                                                                                                     ccGGGGCTGCGAAGCAGCCCCACACTCACGGGATGCAGAACACTTCGCTAGGCTCGTTCACCACCACCTTGCGGTTGGCGTCATATAGCAGCACCTGCGGCTCCATCACCGGCGCCCGCGCTTCCAGGCGATAGCGCTCGCCGGCCtt               >  2:105566/1‑148 (MQ=255)                                                                                                                                       ggggCTGCGAAGCAGCCCCACACTCACGGGATGCAGAACACTTCGCTAGGCTCGTTCACCACCACCTTGCGGTTGGCGTCATATAGCAGCACCTGCGGCTCCATCACCGGCGCCCGCGCTTCCAGGCGATAGCGCTCGCCGGCCTTGaa            <  5:133250/149‑1 (MQ=255)                                                                                                                                        gggCTGCTTCGCAGCCCAGCACTCACGGGATGCAGAACACTTCGCTAGGCTCGTTCACCACCACCTTGCGGTTGGCGTCATATAGCAGCACCTGCGGCTCCATCACCGGCGCCCGCGCTTCCAGGCGATAGCGCTCGCCGGCCTTGAAg           >  6:104973/1‑149 (MQ=255)                                                                                                                                          ggggCGACGCAGCCCCACACTCACGGGATGCAGAACACTTCGCTAGGCTCGTTCACCACCACCTTGCGGTTGGCGTCATATAGCAGCACCTGCGGCTCCATCACCGGCGCCCGCGCTTCCAGGCGATAGCGCTCGCCGGCCTTGAAGtt         <  1:150151/146‑1 (MQ=255)                                                                                                                                               gAAGCAGCCCCACACTCACGGGATGCAGAACACTTCGCTAGGCTCGTTCACCACCACCTTGCGGTTGGCGTCATATAGCAGCACCTGCGGCTCCATCACCGGCGCCCGCGCTTCCAGGCGATAGCGCTCGCCGGCCTTGAAGTTGTCa     >  2:24135/1‑148 (MQ=255)                                                                                                                                                 agcagcCCCACACTCACGGGATGCAGAACACTTCGCTAGGCTCGTTCACCACCACCTTGCGGTTGGCGTCATATAGCAGCACCTGCGGCTCCATCACCGGCGCCCGCGCTTCCAGGCGATAGCGCTCGCCGGCCTTGAAGTTGTCAAAg  <  6:115233/149‑1 (MQ=255)                                                                                                                                                 agcagcCCCACACTCACGGGATGCAGAACACTTCGCTAGGCTCGTTCACCACCACCTTGCGGTTGGCGTCATATAGCAGCACCTGCGGCTCCATCACCGGCGCCCGCGCTTCCAGGCGATAGCGCTCGCCGGCCTTGAAGTTGTCAAAg  >  3:119655/1‑149 (MQ=255)                                                                                                                                                 |                                                                                                                                                     AAGGGGTTTCGTCCTACACGCTGGAGATCGTGCCCAACAGCGAGGTCAAGGACCAGAACATGGTCGTCGGGACCTGCGATGGCGGGACGAAGAAGATCATCTATCAGAAGAACGATCGATAAGCATCAGGGCCCGGGGCTGCGAAGCAGCCCCACACTCACGGGATGCAGAACACTTCGCTAGGCTCGTTCACCACCACCTTGCGGTTGGCGTCATATAGCAGCACCTGCGGCTCCATCACCGGCGCCCGCGCTTCCAGGCGATAGCGCTCGCCGGCCTTGAAGTTGTCAAAG  >  NC_002947/97450‑97742

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: ‑