Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,336,335	A→G	7.7%	L183L (CTA→CTG)	PP_1161 →	lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,336,335	0	A	G	7.7%	147.7 / 2.8	52	L183L (CTA→CTG)	PP_1161	lipoprotein
Reads supporting (aligned to +/- strand):  ref base A (26/22);  new base G (2/2);  total (28/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.55e-01

GCTGTTCGAGGAACGCGAAGGCGAGCAGGGCACTGTGATCGTGATGGAGGAGTGGTGTTTCGGCTACATGCGCGGTACCCAGGTGGCCGGTTGGGGCGAGTTGCCACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGCGATGAGGATATCCAGGCCTGTGTGCCGCAGGTGGTCGAGGCTGCGCGTGGGCTGTACCGACATTTCAAAAAACTGCACTGATCGGATCGTTGGCTAGCGCTCAC  >  NC_002947/1336194‑1336481                                                                                                                                              |                                                                                                                                                   gCTGTTCGAGGAACGCGAAGGCGAGCAGGGCACTGTGATCGTGATGGAGGAGTGGTGTTTCGGCTACATGCGCGGTACCCAGGTGGCCGGTTGGGGCGAGTTGCCACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTACATGGGc                                                                                                                                             >  8:231200/1‑149 (MQ=255)   tGTTCGAGGAACGCGAAGGCGAGCAGGGCACTGTGATCGTGATGGAGGAGTGGTGTTTCGGCTACATGCGCGGTACCCAGGTGGCCGGTTGGGGCGAGTTGCCACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTg                                                                                                                                           >  2:210218/1‑149 (MQ=255)        gAGGAACGCGAAGGCGAGCAGGGCACTGTGATCGTGATGGAGGAGTGGTGTTTCGGCTACATGCGCGGTACCCAGGTGGCCGGTTGGGGCGAGTTGCCACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTgg                                                                                                                                          >  5:164781/1‑145 (MQ=255)        gAGGAACGCGAAGGCGAGCAGGGCACTGTGATCGTGATGGAGGAGTGGTGTTTCGGCTACATGCGCGGTACCCAGGTGGCCGGTTGGGGCGAGTTGCCACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTgg                                                                                                                                          <  6:164781/145‑1 (MQ=255)               gcgAAGGCGAGCAGGGCACTGTCATCGTGATGGAGGAGTGGTGTTTCGGCTACATGCGCGGTACCCAGGTGGCCGGTTGGGGCGAGTTGCCACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTGGAGGATAATTTc                                                                                                                               <  6:68382/149‑1 (MQ=255)                 gAAGGCGAGCAGGGCACTGTGATCGTGATGGAGGAGTGGTGTTTCGGCTACATGCGCGGTACCCAGGTGGCCGGTTGGGGCGAGTTGCCACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTGGAGGATAATTTCGa                                                                                                                             <  8:133177/149‑1 (MQ=255)                         gCAGGGCACTGTGATCGTGATGGAGGAGTGGTGTTTCGGCTACATGCGCGGTACCCAGGTGGCCGGTTGGGGCGAGTTGCCACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTGGAGGATAATTTCGAGCTGCTgg                                                                                                                     <  3:248247/149‑1 (MQ=255)                               cACTGTGATCGTGATGGAGGAGTGGTGTTTCGGCTACATGCGCGGTACCCAGGTGGCCGGTTGGGGCGAGTTGCCACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTGGAGGATAATTTCGAGCTGCTGGAc                                                                                                                   >  2:201035/1‑145 (MQ=255)                                aCTGTGATCGTGATGGAGGAGTGGTGTTTCGGCTACATGCGCGGTACCCAGGTGGCCGGTTGGGGCGAGTTGCCACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGAt                                                                                                              <  5:184438/149‑1 (MQ=255)                                    tgATCGTGATGGAGGAGTGGTGTTTCGGCTACATGCGCGGTACCCAGGTGGCCGGTTGGGGCGAGTTGCCACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGc                                                                                                          >  8:184247/1‑149 (MQ=255)                                     gATCGTTATGTAGGAGTGGTGTGTCGGCTTCATGGGCGGTACCCTGGTGGCCGGTTGGGGCGAGTTGCCACCTGAGCATGACCCGCTGCTAAAGGCAATTTGGCTAGATGTGCTGTAGTATAATTTCGAGCTGCTGTTCCAGATGatc                                                                                                          <  4:194449/148‑3 (MQ=255)                                         gTGATGGAGGAGTGGTGTTTCGGCTACATGCGCGGTACCCAGGTGGCCGGTTGGGGCGAGTTGCCACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGCGATGa                                                                                                     <  1:210218/149‑1 (MQ=255)                                         gTGATGGAGGAGTGGTGTTTCGGCTACATGCGCGGTACCCAGGTGGCCGGTTGGGGCGAGTTGCCACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGCGATGa                                                                                                     <  7:231200/149‑1 (MQ=255)                                           gATGGAGGAGTGGTGTTTCGGCTACATGCGCGGTACCCAGGTGGCCGGTTGGGGCGAGTTGCCACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTGGAGGATAAATTCGAGCTGCTGGACAAGATGAGCTCTGAg                                                                                                    >  4:176805/1‑148 (MQ=255)                                           gATGGAGGAGGGGTGTTTCGGCTACATGCGCGGTACCCAGGTGGCCGGTTGGGGCGAGTTGCCACCGGAGCAGGACCCGCTGCTCACGGCCCTTTCGCTACATGTGCTGGAGGATAACTTAGAGCTGCTGGACCAGATGAGCGagtcg                                                                                                    >  4:180181/1‑144 (MQ=255)                                               gaggagTGGTGTTTCGGCTACATGCGCGGTACCCAGGTGGCCGGTTGGGGCGAGTTGCCACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGCGATGAGGatat                                                                                               >  2:119503/1‑149 (MQ=255)                                                          tttCGGCTACATGCGCGGTACCCAGGTGGCCGGTTGGGGCGAGTTGCCACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGCGATGAGGATATCCAGGCCtgtg                                                                                    >  1:242712/1‑149 (MQ=255)                                                          tttCGGCTACATGCGCGGTACCCAGGTGGCCGGTTGGGCCGAGTTGCCACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGCGATGAGGATATCCAGGCCtgtg                                                                                    >  2:61807/1‑149 (MQ=255)                                                              ggCTACATGCGCGGTACCCAGGTGGCCGGTTGGGGCGAGTTGCCACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGCGATGAGGATATCCAgg                                                                                          <  1:187341/139‑1 (MQ=255)                                                              ggCTACATGCGCGGTACCCAGGTGGCCGGTTGGGGCGAGTTGCCACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGCGATGAGGATATCCAgg                                                                                          >  2:187341/1‑139 (MQ=255)                                                              ggCTACATGCGCGGTACCCAGGTGGCCGGTTGGGGCGAGTTGCCACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGCGATGAGGATATCCAGGCCtgtgtg                                                                                  >  8:112292/1‑147 (MQ=255)                                                                  aCATGCGCGGTACCCAGGTGGCCGGTTGGGGCGAGTTGCCACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTGCATGGGCTGGAGGATAATTTCGAg                                                                                                                            <  4:233931/101‑1 (MQ=255)                                                                  aCATGCGCGGTACCCAGGTGGCCGGTTGGGGCGAGTTGCCACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTGCATGGGCTGGAGGATAATTTCGAg                                                                                                                            <  4:237776/101‑1 (MQ=255)                                                                  aCATGCGCGGTACCCAGGTGGCCGGTTGGGGCGAGTTGCCACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTGCATGGGCTGGAGGATAATTTCGAg                                                                                                                            >  3:233931/1‑101 (MQ=255)                                                                  aCATGCGCGGTACCCAGGTGGCCGGTTGGGGCGAGTTGCCACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTGCATGGGCTGGAGGATAATTTCGAg                                                                                                                            >  3:237776/1‑101 (MQ=255)                                                                  aCATGCGCGGTACCCAGGTGGCCGGTTGGGGCGAGTTGCCACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGCGATGAGGATATCCAGGCCtgtg                                                                                    <  7:155470/141‑1 (MQ=255)                                                                  aCATGCGCGGTACCCAGGTGGCCGGTTGGGGCGAGTTGCCACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGCGATGAGGATATCCAGGCCtgtg                                                                                    >  8:155470/1‑141 (MQ=255)                                                                   cATGCGCGGTACCCAGGTGGCCGGTTGGGGCGAGTTGCCACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGCGATGAGGATATCCAGGCCTGTGTGCCGCa                                                                             <  7:249183/147‑1 (MQ=255)                                                                      gcgcGGTACCCAGGTGGCCGGTTGGGGCGAGTTGCCACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGCGATGAGGATATCCAGGCCTGTGTGCCg                                                                               >  4:119380/1‑142 (MQ=255)                                                                      gcgcGGTACCCAGGTGGCCGGTTGGGGCGAGTTGCCACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGCGATGAGGATATCCAGGCCTGTGTGCCg                                                                               <  3:119380/142‑1 (MQ=255)                                                                      gcgcGGTACCCAGGTGGCCGGTTGGGGCGAGTTGCCACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTGGAGGATAATTTCGAGCTGCTAGACGAGATGAGCGATGAGGATATCCAGGCCTGTGTGCCGCAggtgg                                                                        >  2:68833/1‑149 (MQ=255)                                                                            tACCCAGGTGGCCGGTTGGGGCGAGTTGCCACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGCGATGAGGATATCCAGGCCTGTGTGCCGCAGGTGGTCGAgg                                                                  <  7:112292/149‑1 (MQ=255)                                                                                  ggTGGCCGGTTGGGGCGAGTTGCCACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGCGATGAGGATATCCAGGCCTGTGTGCCGCAGGTGGTCGAGGCTgcgc                                                            <  7:184247/149‑1 (MQ=255)                                                                                               ggCGAGTTGCCACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGCGATGAGGATATCCAGGCCTGTGTGCCGCAGGTGGTCGAGGCTGCGCGTGGGCTGTAcc                                                >  3:160240/1‑148 (MQ=255)                                                                                               ggCGAGTTGCCACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGCGATGAGGATATCCAGGCCTGTGTGCCGCAGGTGGTCGAGGCTGCGCGTGGGCTGTACCg                                               <  1:119503/149‑1 (MQ=255)                                                                                                         cACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTGGAGTATAATTTCGAGCTGCTGGACCAGATGAGCGATGAGGATATCCAGGCCTGTGTGCCGCAGGTGGTCGAGGCTGCGCGTgg                                                        <  2:210674/130‑1 (MQ=255)                                                                                                         cACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGCGATGAGGATATCCAGGCCTGTGTGCCGCAGGTGGTCGAGGCTGCGCGTgg                                                        >  1:210674/1‑130 (MQ=255)                                                                                                          aCCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGCGATGAGGATATCCAGGCCTGTGTGCCGCAGGTGGTCGAGGCTGCGCGTGGGCTGTACCGACAtt                                          <  7:41847/143‑1 (MQ=255)                                                                                                          aCCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGCGATGAGGATATCCAGGCCTGTGTGCCGCAGGTGGTCGAGGCTGCGCGTGGGCTGTACCGACAtt                                          >  8:41847/1‑143 (MQ=255)                                                                                                                   ggACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGCGATGAGGATATCCAGGCCTGTGTGCCGCAGGTGGTCGAgg                                                                  <  2:160718/110‑1 (MQ=255)                                                                                                                   ggACCCGCTGCTCAAGGCCATTTCGCTACAAGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGCGATGAGGATATCCAGGCCTGTGTGCCGCAGGTGGTCGAgg                                                                  >  1:160718/1‑110 (MQ=255)                                                                                                                    gACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGCGATGAGGATATCCAGGCCTGTGTGCCGCAGGTGGTCGAGGCTGCGCGTGGGCTGTACCGACATTTCAAAAAACTGCACt                           >  5:132160/1‑148 (MQ=255)                                                                                                                                aaGGCCATTTCGCTACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGCGATGAGGATATCCAGGCCTGTGTGCCGCAGGTGGTCGAGGCTGCGCGTGGGCTGTACCGACATTTCAAAAAACTGCACTGATCGGATCGtt               <  4:160240/148‑1 (MQ=255)                                                                                                                                  ggCCATTTCGCTACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGCGATGAGGATATCCAGGCCTGTGTGCCGCAGGTGGTCGAGGCTGCGCGTGGGCTGTACCGACATTTCAAAAAACTGCACTGATCGGATCGTTGGc            >  7:20405/1‑149 (MQ=255)                                                                                                                                   gCCATTTCGCTACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGCGATGAGGATATCCAGGCCTGTGTGCCGCAGGTGGTCGAGGCTGCGCGTGGGCTGTACCGACATTTCAAAAAACTGCACTGATCGGATCGTTGGc            >  6:176360/1‑148 (MQ=255)                                                                                                                                   gCCATTTCGCTACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGCGATGAGGATATCCAGGCCTGTGTGCCGCAGGTGGTCGAGGCTGCGCGTGGGCTGTACCGACATTTCAAAAAACTGCACTGATCGGATCGTTGGc            >  8:238528/1‑148 (MQ=255)                                                                                                                                     cATTTCGCTACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGCGATGAGGATATCCAGGCCTGTGTGCCGCAGGTGGTCGAGGCTGCGCGTGGGCTGTACCGACATTTCAAAAAACTGCACTGATCGGATCGTTGGCTAg         >  5:64451/1‑149 (MQ=255)                                                                                                                                     cATTTCGCTACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGCGATGAGGATATCCAGGCCTGTGTGCCGCAGGTGGTCGAGGCTGCGCGTGGGCTGTACCGACATTTCAAAAAACTGCACTGATCGGATCGTTGGCTAg         >  4:262396/1‑149 (MQ=255)                                                                                                                                         tCGCAACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGCGATGAGGATATCCAGGCCTGTGTGCCGCAGGTGGTCGAGGCTGCGCGTGGGCTGTACCGACATTTCAAAAAACTGCACTGATCGGATCGTTGGCTAgcgc      <  4:177345/148‑1 (MQ=255)                                                                                                                                          cGCTACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGCGATGAGGATATCCAGGCCTGTGTGCCGCAGGTGGTCGAGGCTGCGCGTGGGCTGTACCGACATTTCAAAAAACTGCACTGATCGGATCGTTGGCTAGCGCt     <  1:201035/148‑1 (MQ=255)                                                                                                                                          cGCTACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGCGATGAGGATATCCAGGCCTGTGTGCCGCAGGTGGTCGAGGCTGCGCGTGGGCTGTACCGACATTTCAAAAAACTGCACTGATCGGATCGTTGGCTAGCGCTc    >  2:156924/1‑149 (MQ=255)                                                                                                                                            cTACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGCGATGAGGATATCCAGGCCTGTGTGCCGCAGGTGGTCGAGGCTGCGCGTGGGCTGTACCGACATTTCAAAAAACTGCACTGATCGGATCGTTGGCTAGCGCTCAc  <  6:64451/149‑1 (MQ=255)                                                                                                                                              |                                                                                                                                                   GCTGTTCGAGGAACGCGAAGGCGAGCAGGGCACTGTGATCGTGATGGAGGAGTGGTGTTTCGGCTACATGCGCGGTACCCAGGTGGCCGGTTGGGGCGAGTTGCCACCGGAGCAGGACCCGCTGCTCAAGGCCATTTCGCTACATGGGCTGGAGGATAATTTCGAGCTGCTGGACCAGATGAGCGATGAGGATATCCAGGCCTGTGTGCCGCAGGTGGTCGAGGCTGCGCGTGGGCTGTACCGACATTTCAAAAAACTGCACTGATCGGATCGTTGGCTAGCGCTCAC  >  NC_002947/1336194‑1336481

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: ‑