Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,321,473	G→A	8.0%	A98T (GCT→ACT)	PP_5629 →	protease/amidase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,321,473	0	G	A	8.0%	140.4 / 2.4	50	A98T (GCT→ACT)	PP_5629	protease/amidase
Reads supporting (aligned to +/- strand):  ref base G (23/23);  new base A (2/2);  total (25/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.85e-01

TGTAACTGTCGATAGTGGCTTGCAACAATGCCTGGACTGGAAACCGGACGTTGTTGTCGTGATTGGAGGAATGGTCTGGGAGCGTACAGAAGCTCCGGATATTCGAGACTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGACACGGTTCCTCATACCTCGAACAGCGCTGACTTTCTGCAAAAAAATGCCGTAGGTTATGACGGGCGCACGCGCTATCGAAGCAGTGCAGTAGCTGTG  >  NC_002947/4321328‑4321619                                                                                                                                                   |                                                                                                                                                   tGTAACTGTCGATAGTGGCTTGCAACAATGCCTGGACTGGAAACCGGACGTTGTTGTCGTGATTGGAGGAATGGTCTGGGAGCGTACAGAAGCTCCGGATATTCGAGACTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTg                                                                                                                                                 >  8:130014/1‑149 (MQ=255)           gATAGTGGCTTGCAACAATGCCTGGACTGGAAACCGGACGTTGTTGTCGTGATTGGAGGAATGGTCTGGGAGCGTACAGAAGCTCCGGATATTCGAGACTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTgtgg                                                                                                                                       >  3:23166/1‑149 (MQ=255)              aGTGGCTTGCAACAATGCCTGGACTGGAAACCGGACGTTGTTGTCGTGATTGGAGGAATGGTCTGGGAGCGTACAGAAGCTCCGGATATTCGAGACTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTgtggtg                                                                                                                                     >  7:153169/1‑148 (MQ=255)               gTGGCTTGCAACAATGCCTGGACTGGAAACCGGTCGTTGTTGTCGTGATTGGTGGAATGGTCTTGGAGCGTAAAGAAGGTCCGGATATTCGAGACTTTCCTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTgtggtg                                                                                                                                     <  1:254392/148‑1 (MQ=255)                      gCATCAATGGCTGGACTGGAAACCGGACGTTGTTGTCGTGATTGGAGGAATGGTCTGGGAGCGTACAGAAGCTCCGGATATTCGAGACTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTGTGGTGGAACGCt                                                                                                                              <  3:95603/147‑1 (MQ=255)                      gCAACAATGCCTGGACTGGAAACCGGACGTTGTTGTCGTGATTGGAGGAATGGTCTGGGAGCGTACAGAAGCTCCGGATATTCGAGACTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTGTGGTGGAACGCTgg                                                                                                                            >  7:148193/1‑149 (MQ=255)                                ctggactggaAACCGGACGTTGTTGTCGTGATTGGAGGAATGGTCTGGGAGCGTACAGAAGCTCCGGATATTCGAGACTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTGTGGGGGAACGCTGGCACTTGCgag                                                                                                                  <  6:279074/149‑1 (MQ=255)                                      tggaAACCGGACGTTGTTGTCGTGATTGGAGGAATGGTCTGGGAGCGTACAGAAGCTCCGGATATTCGAGACTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCgg                                                                                                            >  5:193875/1‑149 (MQ=255)                                        gaAACCGGACGTTGTTGTCGTGATTGGAGGAATGGTCTGGGAGCGTACAGAAGCTCCGGATATTCGAGACTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGc                                                                                                          >  6:311847/1‑149 (MQ=255)                                        gaAACCGGACGTTGTTGTCGTGATTGGAGGAATGGTCTGGGAGCGTACAGAAGCTCCGGATATTCGAGACTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGc                                                                                                          >  6:258193/1‑149 (MQ=255)                                             cGGACGTTGTTGTCGTGATTGGAGGAATGGTCTGGGAGCGTACAGAAGCTCCGGATATTCGAGACTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCt                                                                                                                                           <  6:228841/111‑1 (MQ=255)                                             cGGACGTTGTTGTCGTGATTGGAGGAATGGTCTGGGAGCGTACAGAAGCTCCGGATATTCGAGACTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCt                                                                                                                                           >  5:228841/1‑111 (MQ=255)                                             cGGACGTTGTTGTCGTGATTGGAGGAATGGTCTGGGAGCGTACAGAAGCTCCGGATATTCGAGACTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTc                                                                                                     <  8:153169/149‑1 (MQ=255)                                              ggACGTTGTTGTCGTGATTGGAGGAATGGTCTGGGAGCGTACAGAAGCTCCGGATATTCGAGACTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCg                                                                                                    <  7:118115/149‑1 (MQ=255)                                                aCGTTGTTGTCGTGATTGGAGGAATGGTCTGGGAGCGTACAGAAGCTCCGGATATTCGAGACTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTACTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGa                                                                                                   >  6:224755/1‑148 (MQ=255)                                                aCGTTGTTGTCGTGATTGGAGGAATGGTCTGGGAGCGTACAGAAGCTCCGGATATTCGAGACTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTACTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGa                                                                                                   >  6:219834/1‑148 (MQ=255)                                                  gttgttGTCGTGATTGGAGGAATGGTCTGGGAGCGTACAGAAGCTCCGGATATTCGAGACTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGacac                                                                                                <  1:297310/149‑1 (MQ=255)                                                               ttGGAGGAATGGTCTGGGAGCGTACAGAAGCTCCGGATATTCGAGACTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGACACGGTTCCTCATAcc                                                                                   >  8:251996/1‑149 (MQ=255)                                                                  gaggaATGGTCTGGGAGCGTACAGAAGCTCCGGATATTCGAGACTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGACACGGTTCCTCATACCTc                                                                                 >  6:39087/1‑148 (MQ=255)                                                                  gaggaATGGTCTGGGAGCGTACAGAAGCTCCGGATATTCGAGACTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGACACGGTTCCTCATACCTCg                                                                                <  8:148193/149‑1 (MQ=255)                                                                   aggaATGGTCTGGGAGCGTACAGAAGCTCCGGATATTCGAGACTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGACACGGTTCCTCATAc                                                                                    <  6:336555/144‑1 (MQ=255)                                                                   aggaATGGTCTGGGAGCGTACAGAAGCTCCGGATATTCGAGACTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGACACGGTTCCTCATAc                                                                                    >  5:336555/1‑144 (MQ=255)                                                                     gaATGGTCTGGGAGCGTACAGAAGCTCCGGATATTCGAGACTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGACGGGCTACTCGACACGGTTCCTCATACCTCGaa                                                                              >  8:171009/1‑148 (MQ=255)                                                                           tCTGGGAGCGTACAGAAGCTCCGGATATTCGAGACTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGACACGGTTCCTCATACCTCGAACAGCGCt                                                                       <  5:258193/149‑1 (MQ=255)                                                                           tCTGGGAGCGTACAGAAGCTCCGGATATTCGAGACTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGACACGGTTCCTCATACCTCGAACAGCGCt                                                                       <  7:251996/149‑1 (MQ=255)                                                                                 aGCGTACAGAAGCTCCGGATATTCGAGACTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTACTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGACACGGTTCCTCATACCTCGAACAGCGCTGACttt                                                                 <  5:224755/149‑1 (MQ=255)                                                                                 aGCGTACAGAAGCTCCGGATATTCGAGACTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTACTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGACACGGTTCCTCATACCTCGAACAGCGCTGACttt                                                                 <  5:219834/149‑1 (MQ=255)                                                                                    gTACAGAAGCTCCGGATATTCGAGACTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGACACGGTTCCTCATACCTCGAACAGCGCTGACTTTCTg                                                              >  2:316033/1‑149 (MQ=255)                                                                                        aGAAGCTCCGGATATTCGAGACTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGACACGGTTCCTCATACCTCGAACAGCGCTGACTTTCTGCaa                                                           >  7:108427/1‑148 (MQ=255)                                                                                             cTCCGGATATTCGAGACTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGACACGGTTCCTCATACCTCGAACAGCGCTGACTTTCTGCAAAAAAAt                                                     <  5:311847/149‑1 (MQ=255)                                                                                             cTCCGGATATTCGAGACTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGACACGGTTCCTCATACCTCGAACAGCGCTGACTTTCTGCAAAAAAAt                                                     <  5:39087/149‑1 (MQ=255)                                                                                                cGGATATTCGAGACTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGACACGGTTCCTCATACCTCGAACAGCGCTGACTTTCTGCAAAAAAATGcc                                                  <  6:193875/149‑1 (MQ=255)                                                                                                cGGATATTCGAGACTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGACACGGTTCCTCATACCTCGAACAGCGCTGACTTTCTGCAAAAAAATGcc                                                  <  1:316033/149‑1 (MQ=255)                                                                                                       tCGAGACTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGACACGGTTCCTCATACCTCGAACAGCGCTGACTTTCTGCAAAAAAATGCCGTAGGtt                                           >  6:115242/1‑149 (MQ=255)                                                                                                         gagaCTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGACACGGTTCCTCATACCTCGAACAgcg                                                                         >  5:307502/1‑117 (MQ=255)                                                                                                         gagaCTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGACACGGTTCCTCATACCTCGAACAgcg                                                                         >  5:302143/1‑117 (MQ=255)                                                                                                         gagaCTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGACACGGTTCCTCATACCTCGAACAgcg                                                                         <  6:307502/117‑1 (MQ=255)                                                                                                         gagaCTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGACACGGTTCCTCATACCTCGAACAgcg                                                                         <  6:302143/117‑1 (MQ=255)                                                                                                         gagaCTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGACACGGTTCCTCATACCTCGAACAGCGCTGACTTTCTGCAAAAAAATGCCGTAGGTTAt                                         <  7:171009/149‑1 (MQ=255)                                                                                                                  cttcATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGACACGGTTCCTCATACCTCGAACAGCGCTGACTTTCTGCAAAAAAATGCCGTAGGTTATGACGGgc                                  <  7:130014/148‑1 (MQ=255)                                                                                                                        gCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGACACGGTTCCTCATACCTCGAACAGCGCTGACTTTCTGCAAAAAAATGCCGTAGGTTATGACGGGCGCAcgcg                           >  6:241359/1‑149 (MQ=255)                                                                                                                        gCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGACACGGTTCCTCATACCTCGAACAGCGCTGACTTTCTGCAAAAAAATGCCGTAGGTTATGACGGGCGCAcgcg                           >  8:176071/1‑149 (MQ=255)                                                                                                                         cTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGACACGGTTCCTCATACCTCGAACAGCGCTGACTTTCTGCAAAAAAATGCCGTAGGTTATGACGGGCGCAcgcg                           <  7:176071/148‑1 (MQ=255)                                                                                                                                      tGGAGCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGACACGGTTCCTCATACCTCGAACAGCGCTGACTTTCTGCAAAAAAATGCCGTAGGTTATGACGGGCGCACGCGCTATCGAAgcagtg             <  4:23166/149‑1 (MQ=255)                                                                                                                                       ggAGCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGACACGGTTCCTCATACCTCGAACAGCGCTGACTTTCTGCAAAAAAATGCCGTAGGTTATGACGGGCGCACGCGCTATCGAAgcagtg             >  1:225377/1‑148 (MQ=255)                                                                                                                                          gCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGACACGGTTCCTCATACCTCGAACAGCGCTGACTTTCTGCAAAAAAATGCCGTAGGTTATGACGGGCGCAcg                             <  2:322670/129‑1 (MQ=255)                                                                                                                                          gCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGACACGGTTCCTCATACCTCGAACAGCGCTGACTTTCTGCAAAAAAATGCCGTAGGTTATGACGGGCGCACGCGCTATCGAAgcagtgcag          >  6:192864/1‑148 (MQ=255)                                                                                                                                           cGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGACACGGTTCCTCATACCTCGAACAGCGCTGACTTTCTGCAAAAAAATGCCGTAGGTTATGACGGGCGCACGCGCTATCGAAgcagtgcag          >  5:145292/1‑147 (MQ=255)                                                                                                                                            gACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGACACGGTTCCTCATACCTCGAACAGCGCTGACTTTCTGCAAAAAAATGCCGTAGGTTATGACGGGCGCACGCGCTATCGAAGCAGTGCAGTAg       <  5:192864/149‑1 (MQ=255)                                                                                                                                                 ttGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGACACGGTTCCTCATACCTCGAACAGCGCTGACTTTCTGCAAAAAAATGCCCTAGGTTATGACGGGCGCACGCGCTATCGAAGCAGTGCAGTAGCtgtg  >  7:88588/1‑149 (MQ=255)                                                                                                                                                   |                                                                                                                                                   TGTAACTGTCGATAGTGGCTTGCAACAATGCCTGGACTGGAAACCGGACGTTGTTGTCGTGATTGGAGGAATGGTCTGGGAGCGTACAGAAGCTCCGGATATTCGAGACTTT‑CTTCATGCTAGTCGTTCAAGTGGAGCGACAATTGCTGGCATCTGTGGTGGAACGCTGGCACTTGCGAGAGCCGGGCTACTCGACACGGTTCCTCATACCTCGAACAGCGCTGACTTTCTGCAAAAAAATGCCGTAGGTTATGACGGGCGCACGCGCTATCGAAGCAGTGCAGTAGCTGTG  >  NC_002947/4321328‑4321619

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: ‑