Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,184,686	C→T	7.2%	R275C (CGT→TGT)	PP_4564 →	lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,184,686	0	C	T	7.2%	157.9 / 2.8	56	R275C (CGT→TGT)	PP_4564	lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (22/29);  new base T (2/2);  total (25/31)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.33e-01

AACGCAAGGAGAGTTTGTGGACACCCGAATACCGGGCGGCGTATCGGAATAGCGAGCAGCAGGCACGCAGCCTGCTGGTGGACCTGGTGCGGCAGAGCACCCCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGATTCACCGGGCCTTGCGCCGATACGGAAACACATCGATCACTTTCCCCTCACGTATCGCCGCCTGCAGCCCCTTCCAGTAATCCGCGTCA  >  NC_002947/5184543‑5184831                                                                                                                                                |                                                                                                                                                  aaCGCAAGGAGAGTTTGTGGACACCCGAATACCGGGCGGCGTATCGGAATAGCGAGCAGCAGGCACGCAGCCTGCTGGTGGACCTGGTGCGGCAGAGCACCCCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAACGTGCGTAcc                                                                                                                                              >  4:1134/1‑149 (MQ=255)  aCGCAAGGAGAGTTTGTGGACACCCGAATACCGGGCGGCGTATCGGAATAGCGAGCAGCAGGCACGCAGCCTGCTGGTGGACCTGGTGCGGCAGAGCACCCCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTAcc                                                                                                                                              >  5:17344/1‑148 (MQ=255)         gagaGTTTGTGGACACCCGAATACCGGGCGGCGTATCGGAATAGCGAGCAGCAGGCACGCAGCCTGCTGGTGGACCTGGTGCGGCAGAGCACCCCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAg                                                                                                                                      <  7:266810/149‑1 (MQ=255)              tttGTGGACACCCGAATACCGGGCGGCGTATCGGAATAGCGAGCAGCAGGCACGCAGCCTGCTGGTGGACCTGGTGCGGCAGAGCACCCCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGc                                                                                                                                     >  1:270560/1‑145 (MQ=255)                    gACACCCGAATACCGGGCGGCGTATCGGAATAGCGAGCAGCAGGCACGCAGCCTGCTGGTGGACCTGGTGCGGCAGAGCACCCCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAgt                                                                                                                           >  3:296565/1‑149 (MQ=255)                    gACACCCGAATACCGGGCGGCGTATCGGAATAGCGAGCAGCAGGCACGCAGCCTGCTGGTGGACCTGGTGCGGCAGAGCACCCCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAg                                                                                                                            <  2:64230/148‑1 (MQ=255)                         ccGAATACCGGGCGGCGTTTCGGAATAGCGAGCTGGAGGCACGCATCCTGCTGGTGGACCTGGTGCGGCAGAGCACCGCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGtt                                                                                                                        <  3:188031/147‑1 (MQ=255)                         ccGAATACCGGGCGGCGTATCGGAATAGCGAGCAGCAGGCACGCAGCCTGCTGGTGGACCTGGTGCGGCAGAGCACCCCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGttt                                                                                                                       >  4:234834/1‑148 (MQ=255)                            aaTACCGGGCGGCGTATCGGAATAGCGAGCAGCAGGCACGCAGCCTTCTGGTGGACGTGGTGCGGCAGAGCACCCCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAg                                                                                                                   <  6:273370/149‑1 (MQ=255)                             aTACCGGGCGGCGTATCGGAATAGCGAGCAGCAGGCACGCAGCCTGCTGGTGGACCTGGTGCGGCAGAGCACCCCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAgg                                                                                                                  <  1:229675/149‑1 (MQ=255)                              tACCGGGCGGCGTATCGTAATAGCGAGCAGCAGGCATGCAGCATGCTGGTGTACCTTGTGCGGCAGAGCTCCCCGCTGCATCGGATGTTCCTGCAGTAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGc                                                                                                                 <  6:17344/149‑1 (MQ=255)                                ccGGGCGTCGTATCGGAATAGCGAGCAGCAGGCACGGAGCCTGCTGGTGGACCTGGTGCGGCAGAGCACCCCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGt                                                                                                               <  3:261357/149‑1 (MQ=255)                                 cGGGCGGCGTATCGGAATAGCGAGCAGCAGGCACGCAGCCTGCTGGTGGACCTGGTGCGGCAGAGCACCCCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTg                                                                                                              <  4:296565/149‑1 (MQ=255)                                       gcgTATCGTAAACGCGAGCAGCAGGCACGATGCCTGCTGGGGTACCTGGGGCGGAAGAGCACCCCGCAGCAACGTAGGTGCCTGCAGGAACGGTTGGGCCAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGc                                                                                                        <  1:75731/149‑1 (MQ=255)                                       gcgTATCGGAATAGCGAGCAGCAGGCACGCAGCCTGCTGGTGGACCTGGTGCGGCAGAGCACCCCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGc                                                                                                        <  2:270560/149‑1 (MQ=255)                                               gAATAGCGAGCAGCAGGCACGCAGCCTGCTGGTGGACCTGGTGCGGCAGAGCACCCCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTg                                                                                                                      <  5:246647/127‑1 (MQ=255)                                               gAATAGCGAGCAGCAGGCACGCAGCCTGCTGGTGGACCTGGTGCGGCAGAGCACCCCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTg                                                                                                                      >  6:246647/1‑127 (MQ=255)                                               gAATAGCGAGCAGCAGGCACGCAGCCTGCTGGTGGACCTGGTGCGGCAGAGCACCCCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTcgc                                                                                                >  2:240973/1‑149 (MQ=255)                                                    gCGAGCAGCAGGCACGCAGCCTGCTGGTGGACCTGGTGCGGCAGAGCACCCCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGTGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGa                                                                                           >  1:291535/1‑149 (MQ=255)                                                    gCGAGCAGCAGGCACGCAGCCTGCTGGTGGACCTGGTGCGGCAGAGCACCCCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGTGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGa                                                                                           >  5:142352/1‑149 (MQ=255)                                                      gAGCAGCAGGCACGCAGCCTGCTGGTGGACCTGGTGCGGCAGAGCACCCCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGAtt                                                                                         >  1:193066/1‑149 (MQ=255)                                                         cagcagGCACGCAGCCTGCTGGTGGACCTGGTGCGGCAGAGCACCCCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGATTCAc                                                                                      <  3:234834/149‑1 (MQ=255)                                                         cagcagGCACGCAGCCTGCTGGTGGACCTGGTGCGGCAGAGCACCCCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGATTCAc                                                                                      <  1:240973/149‑1 (MQ=255)                                                                        ctgctgGTGGACCTGGTGCGGCAGAGCACCCCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGATTCACCGGGCCTTGCGCCGa                                                                       <  4:232568/149‑1 (MQ=255)                                                                         tgctgGTGGACCTGGTGCGGCAGAGCACCCCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCAGTTCAGCGAGATGAAGTGGTTGAAGGAGTGCAAGGCCTGTTAGCGCTGCTTCACAGCGCCTTGCGCCGa                                                                       >  1:189819/1‑148 (MQ=255)                                                                            tggtggACCTGGTGCGGCAGAGCACCCCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGATTCACCGGGCCTTGCGCCGATACg                                                                   <  2:193066/149‑1 (MQ=255)                                                                                 gACCTGGTGCGGCAGAGCACCCCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGATTCACCGGGCCTTgcgc                                                                          >  3:87657/1‑137 (MQ=255)                                                                                 gACCTGGTGCGGCAGAGCACCCCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGATTCACCGGGCCTTgcgc                                                                          <  4:87657/137‑1 (MQ=255)                                                                                 gACCTGGGCCGGCAGAGCACCCCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGATTCACCGGGCCTTGCGCCGATACGGAAac                                                              <  4:48495/149‑1 (MQ=255)                                                                                      ggTGCGGCAGAGCACCCCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGATTCACCGGGCCTTGCGCCGATACGGAAACACATc                                                         >  8:168637/1‑149 (MQ=255)                                                                                         gCGGCAGAGCACCCCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGATTCACCGGGCCTTGCGCCGATACGGAAACACATCGAt                                                      >  4:239157/1‑149 (MQ=255)                                                                                          cGGAAGAGCAACCTGCATCAACGGAGGTTCCTGCAGGAACGGTTGGGAAAGGTGCGTACCCATTTGATCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGATTCACCGGGCCTTGCGCCGATACGGAAACACATCGAt                                                      <  3:1134/148‑1 (MQ=255)                                                                                           ggCAGAGCACCCCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGATTCACCGGGCCTTGCGCCGATACGGAAACACATCGATCa                                                    <  1:171601/149‑1 (MQ=255)                                                                                            gCAGAGCACCCCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGATTCACCGGGCCTTGCGCCGATACGGAAACACATCGATCAc                                                   >  7:159787/1‑149 (MQ=255)                                                                                               gagCACCCCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGATTCACCGGGCCTTGCGCCGATACGGAAACACATCGATCACttt                                                >  7:229839/1‑149 (MQ=255)                                                                                                agCACCCCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGATTCACCGGGCCTTGCGCCGATACGGAAACACATCGATCACTTTc                                               <  8:159787/149‑1 (MQ=255)                                                                                                 gCACCCCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGTGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGATTCACCGGGCCTTGCGCCGATACGGAAACACATCGATCACTTTcc                                              <  3:204185/149‑1 (MQ=255)                                                                                                     cccGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGATTCACCGTGCCTTGCGCCGATACGGAACCACATCGATCACTTTCCCCt                                           >  7:257160/1‑148 (MQ=255)                                                                                                     cccGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGATTCACCGGGCCTTGCGCCGATACGGAAACACATCGATCACTTTCCCCTc                                          <  8:229839/149‑1 (MQ=255)                                                                                                      ccGCAGGAACGGAGGTTCGTGCAGTAACGGTTGGGCAAGGTGCGTACCCCTTTTAGCGACTGCAAGTGTTTGCAGGCGTGACAGGCCTGTTGGCGCTGATTCACCGGGCCTTGCGCCGATTCGGACACACATCGATCCCTTTCCCCTCa                                         <  2:189819/149‑1 (MQ=255)                                                                                                          agcaACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGATTCACCGGGCCTTGCGCCGATACGGAAacac                                                            <  6:223371/126‑1 (MQ=255)                                                                                                          agcaACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGATTCACCGGGCCTTGCGCCGATACGGAAacac                                                            >  5:223371/1‑126 (MQ=255)                                                                                                              aCGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGATTCACCGGGCCTTGCGCCGATACGGAAACACATCGATCACTTTCCCCTCACGTATcgc                                 >  3:245020/1‑149 (MQ=255)                                                                                                                 gAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGATTCACCGGGCCTTGCGCCGATACGGAAACACATCGATCACTTTCCCCTCACGTATcgccgc                              <  3:239157/149‑1 (MQ=255)                                                                                                                        cTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGATTCACCGGGCCTTGCGCCGATACGGAAACACATCGATCACTTTCCCCTCACGTATCGCCGCCTGCAGc                       <  4:245020/149‑1 (MQ=255)                                                                                                                         tGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGATTCACCGGGCCTTGCGCCGATACGGAAACACATCGATCACTTTCCCCTCACGTATCGCCGCCTGCAGcc                      >  7:202197/1‑149 (MQ=255)                                                                                                                           cAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGATTCACCGGGCCTTGCGCCGATACGGAAACACATCGATCACTTTCCCCTCACGTATCGCCGCCTGCAGcccc                    <  8:202197/149‑1 (MQ=255)                                                                                                                            aGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGATTCACCGGGCCTTGCGCCGATACGGAAACACATCGATCACTTTCCCCTCACGTATCGCCGCCTGCAGCCCCt                   <  8:28058/149‑1 (MQ=255)                                                                                                                              gAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGATTCACCGGGCCTTGCGCCGATACGGAAACACATCGATCACTTTCCCCTCACGTATCGCCGCCTGCAGCCCCTTc                 >  6:92521/1‑149 (MQ=255)                                                                                                                                 cGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGATTCACCGGGCCTTGCGCCGATACGGAAACACATCGATCACTTTCCCCTCACGTATCGCCGCCTGCAgacaacgg                 >  7:249835/1‑139 (MQ=255)                                                                                                                                 cGGTTGGGAAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGATTCACCGGGCCTTGCGCCGATACGGAAACACATCGATCACTTTCCCCTCACGTATCGCCGCCTGCa                         <  8:249835/138‑1 (MQ=255)                                                                                                                                  ggTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTATTTGAAGGCGTGACAGGCCTGTTCGCGCTGATTCACCGGGCCTTGCGCCGATACGGAAACACATCGATCACTTTCCCCTCACGTATCGCCGCCTGCAGCCCCTTCCAg              >  3:97659/1‑148 (MQ=255)                                                                                                                                      gggCAAGGTGTGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGATTCACCGGGCCTTGCGCCGATACGGAAACACATCGATCACTTTCCCCTCACGTATCGCCGCCTGCAGCCCCTTCCAGTAAt          <  2:291535/148‑1 (MQ=255)                                                                                                                                      gggCAAGGTGTGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGATTCACCGGGCCTTGCGCCGATACGGAAACACATCGATCACTTTCCCCTCACGTATCGCCGCCTGCAGCCCCTTCCAGTAAt          <  6:142352/148‑1 (MQ=255)                                                                                                                                          aaGGTGAGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGATTCACCGGGCCTTGCGCCGATACGGAAACACATCGATCACTTTCCCCTCACGTATCGCCGCCTGCAGCCCCTTCCAGTAATCcgcg     >  5:289536/1‑149 (MQ=255)                                                                                                                                              tGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGATTCACCGGGCCTTGCGCCGATACGGAAACACATCGATCACTTTCCCCTCACGTATCGCCGCCTGCAGCCCCTTCCAGTAATCCGCGTCa  >  2:302313/1‑148 (MQ=255)                                                                                                                                                |                                                                                                                                                  AACGCAAGGAGAGTTTGTGGACACCCGAATACCGGGCGGCGTATCGGAATAGCGAGCAGCAGGCACGCAGCCTGCTGGTGGACCTGGTGCGGCAGAGCACCCCGCAGCAACGGAGGTTCCTGCAGGAACGGTTGGGCAAGGTGCGTACCCATTTGAGCGAGATGAAGTGTTTGAAGGCGTGACAGGCCTGTTCGCGCTGATTCACCGGGCCTTGCGCCGATACGGAAACACATCGATCACTTTCCCCTCACGTATCGCCGCCTGCAGCCCCTTCCAGTAATCCGCGTCA  >  NC_002947/5184543‑5184831

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: ‑