Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	554,157	Δ1 bp	7.8%	coding (97/714 nt)	rpsC →	30S ribosomal protein S3

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	554,157	0	G	.	7.8%	157.0 / 7.2	51	coding (97/714 nt)	rpsC	30S ribosomal protein S3
Reads supporting (aligned to +/- strand):  ref base G (23/24);  new base . (2/2);  total (25/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.68e-01

CCGTGCTGATCGCATCGTCAAGCGGTCTTGCCATATCACTGTCAAGGTTGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGATATTCATCGTCCGGCTCAAACTGCACGCATCACCATCCACACCGCTCGTC  >  NC_002947/554014‑554304                                                                                                                                                  |                                                                                                                                                    ccGTGCTGATCGCATCGTCAAGCGGTCTTGCCATATCACTGTCAAGGTTGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGAc                                                                                                                                                >  1:127504/1‑149 (MQ=255)   gTGCTGATCGCATCGTCAAGCGGTCTTGCCATATCACTGTCAAGGTTGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACgg                                                                                                                                              <  1:81787/149‑1 (MQ=255)             cATCGTCAAGCGGTCTTGCCATATCACTGTCAAGGTTGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTAc                                                                                                                                    >  7:179331/1‑149 (MQ=255)              aTCGTCAAGCGGTCTTGCCATATCACTGTCAAGGTTGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACg                                                                                                                                   >  5:342401/1‑149 (MQ=255)                  tCAAGCGGTCTTGCCATATCACTGTCAAGGTTGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACg                                                                                                                                   >  7:168275/1‑145 (MQ=255)                  tCAAGCGGTCTTGCCATATCACTGTCAAGGTTGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACg                                                                                                                                   >  5:259273/1‑145 (MQ=255)                      gCGGTCTTGCCATATCACTGTCAAGGTTGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTAc                                                                                                                           <  8:168275/149‑1 (MQ=255)                        ggTCTTGCCATATCACTGTCAAGGTTGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCt                                                                                                                         <  1:170866/149‑1 (MQ=255)                         gTCTTGCCATATCACTGTCAAGGTTGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTa                                                                                                                                         >  4:293800/1‑132 (MQ=255)                         gTCTTGCCATATCACTGTCAAGGTTGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTa                                                                                                                                         <  3:293800/132‑1 (MQ=255)                         gTCTTGCCATATCACTGTCAAGGTTGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTg                                                                                                                        <  2:127504/149‑1 (MQ=255)                              gCCATATCACTGTCAAGGTTGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGa                                                                                                                               >  8:335235/1‑137 (MQ=255)                              gCCATATCACTGTCAAGGTTGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGa                                                                                                                               <  7:335235/137‑1 (MQ=255)                               ccATATCACTGTCAAGGTTGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAg                                                                                                                  <  7:116589/149‑1 (MQ=255)                                cATATCACTGTCAAGGTTGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGTGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAg                                                                                                                  >  5:204669/1‑148 (MQ=255)                                    tCACTGTCAAGGTTGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCTCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCt                                                                                                             <  4:307229/149‑1 (MQ=255)                                    tCACTGTCAAGGTTGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTGCGTAC‑CAGACgga                                                                                                                                             >  3:228500/1‑116 (MQ=255)                                    tCACTGTCAAGGTTGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTGCGTAC‑CAGACgga                                                                                                                                             <  4:228500/117‑2 (MQ=255)                                    tCACTGTCAAGGTTGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATc                                                                                                              <  3:216284/148‑1 (MQ=255)                                    tCACTGTCAAGGTTGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCt                                                                                                             <  6:342401/149‑1 (MQ=255)                                          tCAAGGTTGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGTCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGaaaa                                                                                                        <  8:179331/148‑1 (MQ=255)                                              ggTTGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGt                                                                                                   <  6:259273/149‑1 (MQ=255)                                                ttGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGa                                                                                                 <  3:2477/149‑1 (MQ=255)                                                    ggACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTAc                                                                                             >  5:353485/1‑149 (MQ=255)                                                    ggACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CACCGTCTGCGTAC‑CAGACggaggt                                                                                                                                          <  3:168330/104‑5 (MQ=255)                                                    ggACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CACCGTCTGCGTAC‑CAGACggaggt                                                                                                                                          >  4:168330/1‑100 (MQ=255)                                                          gTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGTGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCaa                                                                                       <  6:204669/149‑1 (MQ=255)                                                             aCGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGt                                                                                               <  8:11407/138‑1 (MQ=255)                                                             aCGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGt                                                                                               >  7:11407/1‑138 (MQ=255)                                                                 aGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAAc                                                                                <  6:353485/149‑1 (MQ=255)                                                                       tCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACACAATCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTaaa                                                                            >  1:274291/1‑148 (MQ=255)                                                                               gTCAGAAAGTACATCCCACTTGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCTTGAGTACCTCCAAGACAAACTAAAAAGCGCGTcc                                                                  <  7:190923/149‑1 (MQ=255)                                                                                   gAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTaaaaa                                                                          <  4:7800/137‑1 (MQ=255)                                                                                   gAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTaaaaa                                                                          >  3:7800/1‑137 (MQ=255)                                                                                             cccACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGa                                                    >  3:188452/1‑149 (MQ=255)                                                                                                 cTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GGACGCAGACGGTGCTACTTACGCAGATTACCTGTAGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGATAtt                                                <  4:15285/149‑1 (MQ=255)                                                                                                    gCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGat                                                   <  8:163989/143‑1 (MQ=255)                                                                                                    gCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGat                                                   >  7:163989/1‑143 (MQ=255)                                                                                                          gCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGATATTCATCGTCCg                                       >  5:112750/1‑149 (MQ=255)                                                                                                               ggAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGATATTCATCGTCCGGCt                                    <  4:188452/147‑1 (MQ=255)                                                                                                                           gAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGATATTCATCGTCCGGCTCAAACTGCACGCAt                      >  2:111552/1‑149 (MQ=255)                                                                                                                           gAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGATATTCATCGTCCGGCTCAAACTGCACGCAt                      >  6:343138/1‑149 (MQ=255)                                                                                                                            aGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGATATTCATCGTCCGGCTCAAACTGCACGCAt                      >  2:286160/1‑148 (MQ=255)                                                                                                                            aGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGATATTCATCGTCCGGCTCAAACTGCACGCATc                     <  2:274291/149‑1 (MQ=255)                                                                                                                                cac‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTAACTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGATATTCATCGTCCGGCTCAAACTGCACGCATCAcc                  >  6:355348/1‑148 (MQ=255)                                                                                                                                 ac‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGATATTCATCGTCCGGCTCAAACTGCACGCATCACCAt                >  6:347533/1‑149 (MQ=255)                                                                                                                                  c‑cTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGATATTCATCGTCCGGCTCAAACTGCACGCATCACCATc               <  5:355348/149‑1 (MQ=255)                                                                                                                                    cTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGATATTCATCGTCCGGCTCAAACTGCACGCATCACCATcc              >  7:253240/1‑149 (MQ=255)                                                                                                                                         tCTG‑GTACGCAGACGGTGCTACATACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTaaaaa                                                                          >  7:222116/1‑84 (MQ=255)                                                                                                                                         tCTG‑GTACGCAGACGGTGCTACATACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTaaaaa                                                                          <  8:222116/84‑1 (MQ=255)                                                                                                                                                 cGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGATATTCATCGTCCGGCTCAAACTGCACGCATCACCATCCACACCGCTCGTc  >  1:47568/1‑149 (MQ=255)                                                                                                                                                  |                                                                                                                                                    CCGTGCTGATCGCATCGTCAAGCGGTCTTGCCATATCACTGTCAAGGTTGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGATATTCATCGTCCGGCTCAAACTGCACGCATCACCATCCACACCGCTCGTC  >  NC_002947/554014‑554304

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: ‑