Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	554,152:1	+C	8.0%	coding (92/714 nt)	rpsC →	30S ribosomal protein S3

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	554,152	1	.	C	8.0%	186.6 / 11.6	50	coding (92/714 nt)	rpsC	30S ribosomal protein S3
Reads supporting (aligned to +/- strand):  ref base . (22/24);  new base C (2/2);  total (24/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.06e-01

TGCCAAAGGCCGTGCTGATCGCATCGTCAAGCGGTCTTGCCATATCACTGTCAAGGTTGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGATATTCATCGTCCGGCTCAAACTGCACGCATCACCATCC  >  NC_002947/554005‑554292                                                                                                                                                      |                                                                                                                                             tGCCAAAGGCCGTGCTGATCGCATCGTCAAGCGGTCTTGCCATATCACTGTCAAGGTTGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTg‑g                                                                                                                                             <  7:2895/149‑1 (MQ=255)  gCCAAAGGCCGTGCTGATCGCATCGTCAAGCGGTCTTGCCATATCACTGTCAAGGTTGCGGACAAGTAACGGAGTCGATCACATGGGTCAGAAAGTACATCCCACTGCCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CAACGTCTg‑g                                                                                                                                             >  3:137871/1‑148 (MQ=255)          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                                                                                                                             <  3:293800/132‑1 (MQ=255)                                  gTCTTGCCATATCACTGTCAAGGTTGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTa                                                                                                                             >  4:293800/1‑132 (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                                                                                                                              >  4:168330/1‑100 (MQ=255)                                                             ggACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CACCGTCTGCGTAC‑CAGACggaggt                                                                                                                              <  3:168330/104‑5 (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                                       >  7:163989/1‑143 (MQ=255)                                                                                                             gCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGat                                       <  8:163989/143‑1 (MQ=255)                                                                                                                   gCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGATATTCATCGTCCg                           >  5:112750/1‑149 (MQ=255)                                                                                                                        ggAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGATATTCATCGTCCGGCt                        <  4:188452/147‑1 (MQ=255)                                                                                                                                    gAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGATATTCATCGTCCGGCTCAAACTGCACGCAt          >  6:343138/1‑149 (MQ=255)                                                                                                                                    gAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGATATTCATCGTCCGGCTCAAACTGCACGCAt          >  2:111552/1‑149 (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)                                                                                                                                                      |                                                                                                                                             TGCCAAAGGCCGTGCTGATCGCATCGTCAAGCGGTCTTGCCATATCACTGTCAAGGTTGCGGACAAGTAACGGAGTCGATCAGATGGGTCAGAAAGTACATCCCACTGGCATTCGCCTGGGAATCGTCAAGGAGCACAC‑CTCCGTCTG‑GTACGCAGACGGTGCTACTTACGCAGATTACCTGTTGAAGGATCTGAAAACGCGTGAGTACCTCCAAGACAAACTAAAAAGCGCGTCCGTAAGCCGTATCGATATTCATCGTCCGGCTCAAACTGCACGCATCACCATCC  >  NC_002947/554005‑554292

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: ‑