Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,273,066	A→T	16.4%	intergenic (+31/+260)	PP_2003 → / ← PP_2004	hypothetical protein/AraC family transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,273,066	0	A	T	16.4%	103.3 / 14.6	49	intergenic (+31/+260)	PP_2003/PP_2004	hypothetical protein/AraC family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base A (18/22);  new base T (3/5);  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 = 5.87e-01

GGCGCCGGTGGTGGATGACAGCCAGGGTTCGCAGCCTGTGGCCCCGCCGGCCGAAGCTGCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCC‑GAGGCCGCCGCCCCCTCCCTTTGATGGGT‑C‑GCCT‑GAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCGATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGTCATCATCCCTTCATCCCACCTGCTTAGGCTGAAGGCGAT  >  NC_002947/2272918‑2273204                                                                                                                                                         |                                                                                                                                           ggcgCCGGTGGTGGATGACAGCCAGGGTTCGCAGCCTGTGGCCCCGCCGGCCGAAGCTGCACCCATTCAGGTGCAGCAGGAGGCCCAGCCGGCC‑GAGGCCGCCGCCCCCTCCCTTTGATGGGT‑C‑GCCT‑GAACCGACCCTTTCGCCGGCa                                                                                                                                            <  2:171052/149‑1 (MQ=255)    gcCGGTGGTGGATGACAGCCAGGGTTCGCAGCCTGTGGCCCCGCCGGCCGAAGCTGCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCC‑GAGGCCGCCGCCCCCTCCCTTTGATGGGT‑C‑GCCT‑GAACCGACCCTTTCGCCGGCAGcc                                                                                                                                         <  6:190176/149‑1 (MQ=255)        gtggtgGATGACAGCCAGGGTTCGCAGCCTGTGGCCCCGCCGGCCGAAGCTGCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCC‑GAGGCCGCCGCCCCCTCCCTTTGATGGGT‑C‑GCCT‑GAACCGACCCTTTCGCCGGCAGCCcgcg                                                                                                                                     <  6:31963/149‑1 (MQ=255)         tggtggATGACAGCCAGGGTTCGCAGCCTGTGGCCCCGCCGGCCGAAGCTGCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCC‑GAGGCCGCCGCCCCCTCCCTTTGATGGGT‑C‑GCCT‑GAACCGACCCTTTCGCGGGCTGCCGGCGa                                                                                                                                    <  4:128284/149‑1 (MQ=255)           gtggATGACAGCCAGGGTTCGCAGCCTGTGGCCCCGCCGGCCGAAGCTGCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCC‑GAGGCCGCCGCCCCCTCCCTTTGATGGGT‑C‑GCCT‑GAACCGACCCTTTCGCCGGCAGCCCGCGaaa                                                                                                                                  <  3:210408/149‑1 (MQ=255)            tggATGACAGCCAGGGTTCGCAGCCTGTGGCCCCGCCGGCCGAAGCTGCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCC‑GAGGCCGCCGCCCCCTCCCTTTGATGGGT‑C‑GCCT‑GAACCGGCCCTTTCGCGGGCTGCCGGCGAAAg                                                                                                                                 <  5:173938/149‑1 (MQ=255)                    aGCCAGGGTTCGCAGCCTGTGGCCCCGCCGGCCGAAGCTGCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCC‑GAGGCCGCCGCCCCCTCCCTTTGATGGGT‑C‑GCCT‑GAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGt                                                                                                                          >  3:54680/1‑148 (MQ=255)                      ccAGGGTTCGCAGCCTGTGGCCCCGCCGGCCGAAGCTGCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCC‑GAGGCCGCCGCCCCCTCCCTTTGATGGGT‑C‑GCCT‑GAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCa                                                                                                                       <  4:54680/149‑1 (MQ=255)                       cAGGGTTCGCAGCCTGTGGCCCCGCCGGCCGAAGCTGCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCC‑GAGGCCGCCGCCCCCTCCCTTTGATGGGT‑C‑GCCT‑GAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAg                                                                                                                      <  6:290284/149‑1 (MQ=255)                               gCAGCCTGTGGCCCCGCCGGCCGAAGCTGCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCC‑GAGGCCGCCGCCCCTTCCCTTTGATGGGT‑C‑GCCTCGAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTaa                                                                                                               <  1:85845/149‑1 (MQ=255)                               gCAGCCTGTGGCCCCGCCGGCCGAAGCTGCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCC‑GAGGCCGCCGCCCCCTCCCTTTGATGTTTACAGCCT‑GAACCGGCCCTTTCGCGGGCTGCCGGCGaaa                                                                                                                                  >  8:104636/1‑131 (MQ=25)                               gCAGCCTGTGGCCCCGCCGGCCGAAGCTGCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCC‑GAGGCCGCCGCCCCCTCCCTTTGATGTTTACAGCCT‑GAACCGGCCCTTTCGCGGGCTGCCGGCGaaa                                                                                                                                  <  7:104636/131‑1 (MQ=25)                               gCAGCCTGTGGCCCCGCCGGCCGAAGCTGCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCC‑GAGGCCGCCGCCCCCTCCCTTTGATGGGT‑C‑GCCT‑GAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTaa                                                                                                               >  6:147532/1‑148 (MQ=255)                                       tgGCCCCGCCGGCCGAAGCTGCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCC‑GAGGCCGCCGCCCCCTCCCTTTGATGGGT‑C‑GCCT‑GAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATcccc                                                                                                       <  8:223260/148‑1 (MQ=255)                                          ccccGCCGGCCGAAGCTGCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCC‑GAGGCCGCCGCCCCCTCCCTTTGATGGGT‑C‑GCCT‑GAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGtt                                                                                                   <  8:7401/149‑1 (MQ=255)                                          ccccGCCGGCCGAAGCTGCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCC‑GAGGCCGCCGCCCCCTCCCTTTGATGGGT‑C‑GCCT‑GAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGt                                                                                                    >  4:281532/1‑148 (MQ=255)                                           cccGCCGGCCGAAGCTGCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCC‑GAGGCCGCCGCCCCCTCCCTTTGATGGGT‑C‑GCCT‑GAACCCACCCATTCCCCGGCCGCCCCCGAAAGGGCCGGTTCAGGGGGTAAAAAACCCCTGtt                                                                                                   >  4:118171/1‑148 (MQ=255)                                                cggccgAAGCTGCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCC‑GAGGCCGCCGCCCCCTCCCTTTGATGGGT‑C‑GCCT‑GAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGAc                                                                                             <  3:238405/149‑1 (MQ=255)                                                        gCTGCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCC‑GAGGCCGCCGCCCCCTCCCTTTGATGGGT‑C‑GCCT‑GAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCcgcg                                                                                     <  5:147532/149‑1 (MQ=255)                                                           gCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCC‑GAGGCCGCCGCCCCCTCCCTTTGATGGGT‑C‑GCCT‑GAACCGACCCTTTCGCCGGCAGccc                                                                                                                                        >  6:15578/1‑95 (MQ=255)                                                           gCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCC‑GAGGCCGCCGCCCCCTCCCTTTGATGGGT‑C‑GCCT‑GAACCGACCCTTTCGCCGGCAGccc                                                                                                                                        <  5:15578/95‑1 (MQ=255)                                                                 aTTCAGGTGCAGCAGGATGCCCAGCCGTCC‑GAGGCCGACGCCACCTCCCTTTGATGGGT‑A‑GCAG‑GAACCCACCCATTATCCAGCAACCCGAGAAATGGCCGGTAAAGGGTGTAAACATACCCTGTTTAACAAGCCCAGCGaaaaaaata                                                                            >  8:291049/1‑144 (MQ=255)                                                                  ttCAGGTGCAGCAGGATGCCCAGCCGGCC‑GAGGCCGCCGCCCCCTCCCTTTGATGGGT‑C‑GCCT‑GAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATACCCAGTTACAGACGCCCCGCGATAACTTTCt                                                                           >  2:29110/1‑149 (MQ=255)                                                                     aGGTGCAGCAGGATGCCCAGCCGGCCGGAGGCCGCCGCCCCCGCCCTTTGATGGGT‑C‑GCCT‑GAACCCCCCCTTTAGCCGGCACCCCGCGCAAGGGCCGGGTCAGGCGGTAAACATCCCCGGTTACAGCCGCCCCGCGCTAACGTTATg                                                                          >  1:3412/1‑148 (MQ=255)                                                                     aGGTGCAGCAGGATGCCCAGCCGGCC‑GAGGCCGCCGCCCCCTCCCTTTGATGGGT‑C‑GCCT‑GAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACAGCCCCTGTTACAGCCGCCCCGCGATAACTTTCTgca                                                                        >  5:242351/1‑147 (MQ=255)                                                                                     ccAGCCGGCC‑GAGGCCGCCGCCCCCTCCCTTTGATGGGT‑C‑GCCT‑GAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGGGATAACTTTCTGAACACCTGCTACGTTTAc                                                        <  1:29110/149‑1 (MQ=255)                                                                                      cAGCCGGCC‑GAGGCCGCCGCCCCCTCCCTTTGATGGGT‑C‑GCCT‑GAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCGATAACTTTCTGAACACCTGCTACGTTTAc                                                        >  1:61326/1‑148 (MQ=255)                                                                                          cggcc‑gAGGCCGCCGCCCCCTCCCTTTGATGGGT‑C‑GCCT‑GAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCGATAACTTTCTGAACACCTGCTACGTTTACCACTc                                                   <  7:194444/149‑1 (MQ=255)                                                                                          cggcc‑gAGGCCGCCGCCCCCTCCCTTTGATGGGT‑C‑GCCT‑GAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCGATAACTTTCTGAACACCTGCTACGTTTACCACTc                                                   <  2:61326/149‑1 (MQ=255)                                                                                            gcc‑gAGGCCGCCGCCCCCTCCCTTTGATGGGT‑C‑GCCT‑GAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCGATAACTTTCTGAACACCTGCTACGTTTACCACTCAt                                                 <  6:73066/149‑1 (MQ=255)                                                                                            gcc‑gAGGCCGCCGCCCCCTCCCTTTGATGGGT‑C‑GCCT‑GAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCGAAAACTTTCTGAACACCTGCTACGTTTACCACTCa                                                  >  6:332962/1‑148 (MQ=255)                                                                                                   gccgccgccCCCTCCCTTTGATGGGT‑C‑GCCT‑GAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCGATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCtt                                           <  3:118171/149‑1 (MQ=255)                                                                                                    ccgccgccCCCTCCCTTTGATTGGT‑A‑GCAT‑GAACCTAACATTTCTCCGGCATCCAGCGAAATGGCAGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCTATAACTTTCTTAACACCTGCTACGTTTACCACTCATAAGCtt                                           <  7:291049/148‑1 (MQ=255)                                                                                                            ccctccctTTGATGGGT‑C‑GCCT‑GAACCGACCCTTTCGCCGGCAGCCCGCGAAACGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCGATAACTTTGTGAACACCTGCGACGTTTACCACTCATTAGCTTGTGatcatc                                  >  3:21210/1‑149 (MQ=255)                                                                                                               tccgtTTGATGGGT‑C‑GCCT‑GAAGCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCGATAACTTTCTGAACACCTGCTACGTTTACCACTCAt                                                 <  6:109253/131‑1 (MQ=255)                                                                                                               tccctTTGATGGGT‑C‑GCCT‑GAACCGACCCTTTAGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCGATAACTTTCTGAAGACCTGCTACGTTTACCACTCAt                                                 >  5:109253/1‑131 (MQ=255)                                                                                                                 cctTTGATGGGT‑C‑GCCT‑GAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCGATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGTCATCATCCCtt                              >  8:176980/1‑148 (MQ=255)                                                                                                                  ctTTGATGGGT‑C‑GCCT‑GAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCGATAACTTTCTGAACACCTGCTACGTTTACCACt                                                    <  4:82510/125‑1 (MQ=255)                                                                                                                  ctTTGATGGGT‑C‑GCCT‑GAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCGATAACTTTCTGAACACCTGCTACGTTTACCACt                                                    >  3:82510/1‑125 (MQ=255)                                                                                                                                  cT‑GAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCGATAACTTTCTGAACACCTGCTACGtt                                                           >  6:188744/1‑104 (MQ=255)                                                                                                                                  cT‑GAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCGATAACTTTCTGAACACCTGCTACGtt                                                           <  5:188744/104‑1 (MQ=255)                                                                                                                                   t‑GAACCGGCCCTTTCGCGGGCTGCCGGCGAAAGGGTCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCGATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGTCATCATCCCTTCATCCCACCTGCTTa               <  2:32515/147‑1 (MQ=38)                                                                                                                                   t‑GAACCGGCCCTTTCGCGGGCTGCCGGCGAAAGGGTCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCGATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGTCATCATCCCTTCATCCCACCTGCTTa               >  1:32515/1‑147 (MQ=38)                                                                                                                                       aCCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCGATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGTCATCATCCCTTCATCCCACCTGCTTAGGCt           >  6:172114/1‑148 (MQ=255)                                                                                                                                        ccGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCGATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGTCATCATCCCTTCATCCCACCTGCTTAGGCTg          >  1:257445/1‑148 (MQ=255)                                                                                                                                         cggcccTTTCGCGGGCTGCCGGCGAAAGGGTCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCGATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGTCATCATCCCTTCATCCCACCTGCTTAgg             <  3:48605/141‑1 (MQ=38)                                                                                                                                         cggcccTTTCGCGGGCTCCCGGCGAAAGGGTCGGTTCAGGCTGTAAACATCCCCTCTAACAGACGCCCCGCGATAACTTTCTGAACACCAGCAACCTTTACCACTCATAAGCTAGTCATCATCCATTCATCCCACCTGCTTAGGcacat        >  4:48605/4‑145 (MQ=25)                                                                                                                                              cTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCGATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGTCATCATCCCTTCATCCCACCTGCTTAGGCTGAAGGCGa   <  3:281532/149‑1 (MQ=255)                                                                                                                                               tttCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCGATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGTCATCATCCCTTCATCCCACCTGCTTAGGCTGAAGGCGa   >  3:91637/1‑148 (MQ=255)                                                                                                                                                 tCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCGATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGTCATCATCCCTTCATCCCACCTGCTTAGGCTGAAGGCGAt  <  7:176980/147‑1 (MQ=255)                                                                                                                                                         |                                                                                                                                           GGCGCCGGTGGTGGATGACAGCCAGGGTTCGCAGCCTGTGGCCCCGCCGGCCGAAGCTGCACCCATTCAGGTGCAGCAGGATGCCCAGCCGGCC‑GAGGCCGCCGCCCCCTCCCTTTGATGGGT‑C‑GCCT‑GAACCGACCCTTTCGCCGGCAGCCCGCGAAAGGGCCGGTTCAGGCTGTAAACATCCCCTGTTACAGACGCCCCGCGATAACTTTCTGAACACCTGCTACGTTTACCACTCATAAGCTTGTCATCATCCCTTCATCCCACCTGCTTAGGCTGAAGGCGAT  >  NC_002947/2272918‑2273204

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑