Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,610,342	C→G	8.2%	I261M (ATC→ATG)	PP_4081 →	type IV/VI secretion system protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,610,342	0	C	G	8.2%	148.4 / 5.1	49	I261M (ATC→ATG)	PP_4081	type IV/VI secretion system protein
Reads supporting (aligned to +/- strand):  ref base C (20/25);  new base G (2/2);  total (22/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.45e-01

ACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCCTACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGTGCTGGAGTCGCTGAACGGCATTTTGCAGCAATAGCCAACCGTGTCACAGCACCACTGAGTTCAACGAATTCGCGAGGTTTTTGCC  >  NC_002947/4610195‑4610486                                                                                                                                                    |                                                                                                                                                 aCTGATTCACCAACTGCACGGGATCATCAGCGAACTGCCCGGCCCCACCCGCTAAGAAGTCTGCGACCCGTACAACAATGACGGGTGGACAAACAGCCGCATTAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCACcgccatcgc                                                                                                                                                >  1:678664/1‑150 (MQ=17)    gATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCCTACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCcgccatcgccat                                                                                                                                             <  2:678664/150‑1 (MQ=255)           cAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCCTACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTg                                                                                                                                      <  1:804111/150‑1 (MQ=255)              cTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCCTACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATGGCGATGGCggagatg                                                                                                                                   <  1:125460/150‑6 (MQ=255)               tGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCCTACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCt                                                                                                                                  >  2:811279/1‑150 (MQ=255)                 cACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCCTACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTAc                                                                                                                                <  1:232616/150‑1 (MQ=255)                             cgcgAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCCTACACCACCGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGc                                                                                                                    >  2:516262/1‑150 (MQ=255)                                         ggCCCCACCCCCGAAGAAGTCTGCGACCCCTACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCAc                                                                                                        <  1:634853/150‑1 (MQ=255)                                             ccACCCCCGAAGAAGTCTGCGACCCCTACACCCACGTAACCCCCTGAAACTTCCGCATGAGCCGGATATAGCCGTGGTGGCGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAACTACCGCCTGCACCTGa                                                                                                    >  1:811390/1‑150 (MQ=17)                                                    cGAAGAAGTCTGCGACCCCTACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTa                                                                                                                                 <  1:1038583/114‑1 (MQ=255)                                                    cGAAGAAGTCTGCGACCCCTACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTa                                                                                                                                 >  2:1038583/1‑114 (MQ=255)                                                    cGAAGAAGTCTGCGACCCCTACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAAc                                                                                             <  2:266118/150‑1 (MQ=255)                                                        gaagTCTGTGACCCCTACACCAACGTCGCCCACAGAAACTTCCGCATGAGAGCGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGTGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAg                                                                                         <  2:120815/150‑1 (MQ=18)                                                            tCTGCGACCCCTACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGTGc                                                                                     >  1:539506/1‑150 (MQ=255)                                                                  aCCCCTACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGc                                                                                                              >  2:523159/1‑119 (MQ=255)                                                                  aCCCCTACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGc                                                                                                              <  1:523159/119‑1 (MQ=255)                                                                     ccTACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGTGCTGGAGTCGc                                                                            >  1:135885/1‑150 (MQ=255)                                                                     ccTACACCAACGAAACCCCCAGAAACTTCCGCATGAGCCGGATATCTCCGTGGGGGAGCCCGATGGTCATCTCCGCCATCACCATGGCAGTGGCCTACGGGATTTACAGCTATCTCCTCTACCTGATCACAACCAAGGTTCTGAAGgcgc                                                                            >  2:372786/1‑150 (MQ=255)                                                                      cTACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGTGCTGGAGTCGCt                                                                           <  1:772808/150‑1 (MQ=255)                                                                         cacCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGTGCTGGAGTCGCTGaa                                                                        <  2:254689/150‑1 (MQ=255)                                                                            cAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGt                                                                                       <  1:702189/132‑1 (MQ=255)                                                                            cAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGt                                                                                       >  2:702189/1‑132 (MQ=255)                                                                            cAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGTGCTg                                                                                   >  1:220357/1‑136 (MQ=255)                                                                            cAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGTGCTg                                                                                   <  2:220357/136‑1 (MQ=255)                                                                             aaCGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCAcc                                                                                                       >  1:317074/1‑115 (MQ=255)                                                                             aaCGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCAcc                                                                                                       <  2:317074/115‑1 (MQ=255)                                                                                    cccccAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGTGCTg                                                                                   >  1:206779/1‑128 (MQ=255)                                                                                    cccccAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGTGCTg                                                                                   <  2:206779/128‑1 (MQ=255)                                                                                     ccccAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAg                                                                                         <  1:1083847/121‑1 (MQ=255)                                                                                     ccccAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAg                                                                                         >  2:1083847/1‑121 (MQ=255)                                                                                            aaCTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGTGCTGGAGTCGCTGAACGGCATTTTGCAGCAATAg                                                     <  1:516262/150‑1 (MQ=255)                                                                                             aCTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGTGCTGGAGTCGCTGAACGGCATTTTGCAGCAATAGc                                                    <  1:662255/150‑1 (MQ=255)                                                                                             aCTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGTGCTGGAGTCGCTGAACGGCATTTTGCAGCAATAGc                                                    <  2:135885/150‑1 (MQ=255)                                                                                                      tGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGTGCTGGAGTCGCTGAACGGCATCTTGCAGCAATAGCCAACCgtgt                                           <  2:1195874/150‑1 (MQ=255)                                                                                                         gCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGTGCTGGAGTCGCTGAACGGCAt                                                                  >  2:500398/1‑124 (MQ=255)                                                                                                         gCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGTGCTGGAGTCGCTGAACGGCAt                                                                  <  1:500398/124‑1 (MQ=255)                                                                                                         gCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGTGCTGGAGTCGCTGAACGGCATTTTGCAGCAATAGCCAACCgtg                                            <  1:858624/146‑1 (MQ=255)                                                                                                         gCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGTGCTGGAGTCGCTGAACGGCATTTTGCAGCAATAGCCAACCgtg                                            >  2:858624/1‑146 (MQ=255)                                                                                                                    ccGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGTGCTGGAGTCGCTGAACGGCATTTTGCAGCAATAGc                                                    <  1:529109/127‑1 (MQ=255)                                                                                                                    ccGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGTGCTGGAGTCGCTGAACGGCATTTTGCAGCAATAGc                                                    >  2:529109/1‑127 (MQ=255)                                                                                                                     cGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGTGCTGGAGTCGCTGAACCGCATTTTGCAGCAATAGCCAACCGTGTCACAGCACCACTGAg                            <  1:890657/150‑1 (MQ=255)                                                                                                                           ggAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGTGCTGGAGTCGCTGAACGGCATTTTGCAGCAATAGCCAACCGTGTCACAGCACCACTGAGTTCAAc                      <  2:539506/150‑1 (MQ=255)                                                                                                                               cccGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGTGCTGGAGTCGCTGAACGGCATTTTGCAGCAATAGCCAACCGTGTCACAGCACCACTGAGTTCAACGAAt                  >  2:1357584/1‑150 (MQ=40)                                                                                                                                 cGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGTGCTGGAGTCGCTGAACGGCATTTTGCAGCAATAGCCAACCGTGTCACAGCACCACTGAGTTCAACGAATTc                >  1:962347/1‑150 (MQ=40)                                                                                                                                           caccGCCATGGCGATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGTGCTGGAGTCGCTGAACGGCATTTTGCAGCAATAGCCAACCGTGTCACAGCACCACTGAGTTCAACGAATTCGCGAGGtttt      >  2:1210953/3‑150 (MQ=12)                                                                                                                                           caccGCCATGGCGATGGCGGAGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGTGCTGGAGTCGCTGAACGGCATTTTGCAGCAATAGCCAACCGTGTCACAGCACCACTGAGTTCAACGAAt                  >  1:971500/3‑138 (MQ=11)                                                                                                                                           caccGCCATGGCGATGGCGGAGGCCTACGCGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGTGCTGGAGTCGCTGAACGGCATTTTGCAGCAATAGCCAACCGTGTCACAGCACCACTGAGTTCAACGAAt                  <  2:971500/136‑1 (MQ=11)                                                                                                                                            tcCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGTGCTGGAGTCGCTGAAc                                                                       <  2:861544/84‑1 (MQ=35)                                                                                                                                            tcCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGTGCTGGAGTCGCTGAAc                                                                       >  1:861544/1‑84 (MQ=35)                                                                                                                                            tcCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGTGCTGGAGTCGCTGAACGGCATTTTGCAGCAATAGCCAACCGTGTCACAGCACCACTGAGTTCAACGAATTCGCGAGGttttt     >  2:451238/1‑150 (MQ=32)                                                                                                                                            tcCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGTGCTGGAGTCGCTGAACGGCATTTTGCAGCAATAGCCAACCGTGTCACAGCACCACTGAGTTCAACGAATTCGCGAGGttttt     <  2:811390/150‑1 (MQ=32)                                                                                                                                               gccatcgccatGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGTGCTGGAGTc                                                                              >  1:322430/1‑74 (MQ=34)                                                                                                                                               gccatcgccatGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGTGCTGGAGTc                                                                              <  2:322430/74‑1 (MQ=35)                                                                                                                                               gccaccgccatGGCGATGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGTGCTGGAGTCGCTGAACGGCATTTTGCAGCAATAGCCAACCGTGTCACAGCACCACTGAGTTCAACGAATTCGCGAGGTTTTTGcc  >  1:757361/1‑150 (MQ=12)                                                                                                                                                    |                                                                                                                                                 ACTGATTCACCAACTGCACGGGATCATCCGCGAACTGCGCGGCCCCACCCCCGAAGAAGTCTGCGACCCCTACACCAACGTCGCCCCCAGAAACTTCCGCATGAGCCGGATATGGCCGTGGTGGAGCCCGTTGGTCATCTCCGCCATCGCCATGGCGGTGGCCTACGGGATTTACAGCTACCGCCTGCACCTGATCACAACCGAGGTGCTGGAGTCGCTGAACGGCATTTTGCAGCAATAGCCAACCGTGTCACAGCACCACTGAGTTCAACGAATTCGCGAGGTTTTTGCC  >  NC_002947/4610195‑4610486

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑