Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	3,288,032	C→A	36.5%	intergenic (+22/‑58)	yraH → / → yraI	putative fimbrial‑like adhesin protein/putative periplasmic pilin chaperone

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,288,032	0	C	A	36.5%	69.1 / 60.3	52	intergenic (+22/‑58)	yraH/yraI	putative fimbrial‑like adhesin protein/putative periplasmic pilin chaperone
Reads supporting (aligned to +/- strand):  ref base C (17/16);  new base A (9/10);  total (26/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

TCCAATGGTATTGTCAATGTTGACCTCATCGCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATAACTATGTCAAAACGAACATTCGCGGTGATATTAACCTTGTTGTGTAGCTTCTGTATTGGCCAG  >  NC_000913/3287894‑3288149                                                                                                                                           |                                                                                                                      tCCAATGGTATTGTCAATGTTGACCTCATCGCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGTCAg                                                                                                                 >  4:74620/1‑145 (MQ=255) tCCAATGGTATTGTCAATGTTGACCTCATCGCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGTCAg                                                                                                                 <  3:74620/145‑1 (MQ=255)  ccAATGGTATTGTCAATGTTGACCTCATCGCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACAGGTCAGATaa                                                                                                             <  2:193765/148‑1 (MQ=255)    aaTGGTATTGTCAATGTTGACCTCATCGCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACAGGTCAGATa                                                                                                              >  3:454467/1‑145 (MQ=255)    aaTGGTATTGTCAATGTTGACCTCATCGCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACAGGTCAGATa                                                                                                              <  4:454467/145‑1 (MQ=255)     aTGGTATTGTCAATGTTGACCTCATCGCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGTCAGATaa                                                                                                             <  1:733751/145‑1 (MQ=255)     aTGGTATTGTCAATGTTGACCTCATCGCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGTCAGATaa                                                                                                             >  2:733751/1‑145 (MQ=255)     aTGGTATTGTCAATGTTGACCTCATCGCTTACCACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGTc                                                                                                                   <  3:16655/139‑1 (MQ=255)     aTGGTATTGTCAATGTTGACCTCATCGCTTACCACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGTc                                                                                                                   >  4:16655/1‑139 (MQ=255)               cAATGTTGACCTCATCGCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGTCAGATa                                                                                                              >  3:62786/1‑134 (MQ=255)               cAATGTTGACCTCATCGCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGTCAGATa                                                                                                              <  4:62786/134‑1 (MQ=255)               cAATGTTGACCTCATCGCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACAGGTCAGAt                                                                                                               >  4:559194/1‑133 (MQ=255)               cAATGTTGACCTCATCGCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACAGGTCAGAt                                                                                                               <  3:559194/133‑1 (MQ=255)                       aCCTCATCGCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACACTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGTCAGAt                                                                                                               >  2:709181/1‑125 (MQ=255)                       aCCTCATCGCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACACTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGTCAGAt                                                                                                               <  1:709181/125‑1 (MQ=255)                           cATCGCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGt                                                                                                                    >  2:396443/1‑116 (MQ=255)                           cATCGCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGt                                                                                                                    <  2:22276/116‑1 (MQ=255)                           cATCGCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGt                                                                                                                    <  1:396443/116‑1 (MQ=255)                           cATCGCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGt                                                                                                                    >  1:22276/1‑116 (MQ=255)                           cATCGCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGTCAGATa                                                                                                              >  4:789215/1‑122 (MQ=255)                           cATCGCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACAGGTCAGATaa                                                                                                             <  2:1002401/123‑1 (MQ=255)                           cATCGCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACAGGTCAGATaa                                                                                                             >  1:1002401/1‑123 (MQ=255)                           cATCGCTTACTACGTATCAACCGTAGTTCCATCACAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGTCAGATa                                                                                                              <  3:789215/122‑1 (MQ=255)                              cGCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTGGGGCGTTATCTGACCTGTCAGATaa                                                                                                             <  2:454210/120‑1 (MQ=255)                              cGCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTGGGGCGTTATCTGACCTGTCAGATaa                                                                                                             <  2:411218/120‑1 (MQ=255)                              cGCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTGGGGCGTTATCTGACCTGTCAGATaa                                                                                                             >  1:454210/1‑120 (MQ=255)                              cGCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTGGGGCGTTATCTGACCTGTCAGATaa                                                                                                             >  1:411218/1‑120 (MQ=255)                                      acGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGTCAGa                                                                                                                <  3:373289/109‑1 (MQ=255)                                      acGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGTCAGa                                                                                                                >  4:373289/1‑109 (MQ=255)                                              aCCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGAcc                                                                                                                       <  1:110779/94‑1 (MQ=255)                                              aCCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGAcc                                                                                                                       >  2:110779/1‑94 (MQ=255)                                              aCCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACAGGTCAg                                                                                                                 <  4:124757/100‑1 (MQ=255)                                              aCCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACAGGTCAg                                                                                                                 >  3:124757/1‑100 (MQ=255)                                                  tAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACAGGTCAGATa                                                                                                              <  1:902761/99‑1 (MQ=255)                                                  tAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACAGGTCAGATa                                                                                                              >  2:902761/1‑99 (MQ=255)                                                           cAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACAGGTCAGAt                                                                                                               <  1:988654/89‑1 (MQ=255)                                                           cAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACAGGTCAGAt                                                                                                               >  2:988654/1‑89 (MQ=255)                                                                  cACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGt                                                                                                                    >  1:772457/1‑77 (MQ=255)                                                                  cACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGt                                                                                                                    <  2:772457/77‑1 (MQ=255)                                                                                                                           tAGGGCGTTATCTGACCTGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGt                                                                          >  4:1052314/1‑62 (MQ=255)                                                                                                                           tAGGGCGTTATCTGACCTGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGt                                                                          <  3:1052314/62‑1 (MQ=255)                                                                                                                                  ttATCTGACAGGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATAACTATGTCAAAACGAACATTCGCGGTGATATTAACCTTGTTGTGTAGCTTCTGTAt         >  1:343754/1‑120 (MQ=255)                                                                                                                                  ttATCTGACAGGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATAACTATGTCAAAACGAACATTCGCGGTGATATTAACCTTGTTGTGTAGCTTCTGTAt         <  2:343754/120‑1 (MQ=255)                                                                                                                                   tATTTGACAGGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATAACTATGTCAAAACGAACATTCGCGGTGATATTAACCTTGTTGTGTAGCTTc              >  1:955893/1‑114 (MQ=255)                                                                                                                                   tATCTGACCTGTCAGATACCGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATAACTATGTCAAAACGAACATTCGCGGTGATATTAACCTTGTTGTGTAGCTTCTGTATTGGCCAg  <  2:379889/126‑1 (MQ=255)                                                                                                                                   tATCTGACCTGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATAACTATGTCAAAACGAACATTCGCGGTGATATTAACCTTGTTGTGTAGCTTCTGTATTGGCCAg  >  1:379889/1‑126 (MQ=255)                                                                                                                                   tATCTGACAGGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATAACTATTTCAAAACGAACATTCGCGGTGATATTAACCTTGTTGTGTAGCTTc              <  2:955893/114‑1 (MQ=255)                                                                                                                                   tATCTGACAGGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATAACTATGTCAAAACGAACATTCGCGGTGATATTAACCttg                          >  1:1084979/1‑102 (MQ=255)                                                                                                                                   tATCTGACAGGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATAACTATGTCAAAACGAACATTCGCGGTGATATTAACCttg                          <  2:1084979/102‑1 (MQ=255)                                                                                                                                      ctgtcctgtcAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATAACTATGTCTAAACGAACATTCGCGGTGATATTaa                               <  2:199587/94‑1 (MQ=255)                                                                                                                                      cTGACCTGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATAACTATGTCAAAACGAACATTCGCGGTGatat                                  >  3:1058388/1‑91 (MQ=255)                                                                                                                                      cTGACCTGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATAACTATGTCAAAACGAACATTCGCGGTGatat                                  <  4:1058388/91‑1 (MQ=255)                                                                                                                                      cTGACCTGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATAACTATGTCAAAACGAACATTCGCGGTGATATTaa                               >  1:199587/1‑94 (MQ=255)                                                                                                                                      cTGACCTGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATAACTATGTCAAAACGAACATTCGCGGTGATATTGACCTTGTTGTGTAGCTTc              <  1:292298/111‑1 (MQ=255)                                                                                                                                      cTGACCTGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATAACTATGTCAAAACGAACATTCGCGGTGATATTGACCTTGTTGTGTAGCTTc              >  2:292298/1‑111 (MQ=255)                                                                                                                                          ccTGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATAACTa                                                             >  1:646426/1‑60 (MQ=255)                                                                                                                                          ccTGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATAACTa                                                             <  2:646426/60‑1 (MQ=255)                                                                                                                                          ccTGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATAACTATGTCAAAACGAACATTCGCGGTGat                                    >  1:688545/1‑85 (MQ=255)                                                                                                                                          ccTGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATAACTATGTCAAAACGAACATTCGCGGTGat                                    <  2:970777/85‑1 (MQ=255)                                                                                                                                          ccTGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATAACTATGTCAAAACGAACATTCGCGGTGat                                    >  1:970777/1‑85 (MQ=255)                                                                                                                                          ccTGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATAACTATGTCAAAACGAACATTCGCGGTGat                                    <  2:688545/85‑1 (MQ=255)                                                                                                                                           |                                                                                                                      TCCAATGGTATTGTCAATGTTGACCTCATCGCTTACTACGTATCAACCGTAGTTCCATCAGAAATCACCCCAGGGGAAGCAGACGCTATCGTTAACGTAACGCTGGATTACCGTTAATACGTTAGGGCGTTATCTGACCTGTCAGATAACGCCCTTTTCCTTCCTCTTTCTCGTTGTATCAGGTTGAAAAATAACTATGTCAAAACGAACATTCGCGGTGATATTAACCTTGTTGTGTAGCTTCTGTATTGGCCAG  >  NC_000913/3287894‑3288149

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑