Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,307,786	G→C	8.2%	intergenic (‑169/‑125)	livK ← / → PP_1142	branched‑chain amino acids ABC transporter substrate‑binding protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,307,786	0	G	C	8.2%	141.8 / 4.6	49	intergenic (‑169/‑125)	livK/PP_1142	branched‑chain amino acids ABC transporter substrate‑binding protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (25/20);  new base C (2/2);  total (27/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.91e-01

ATTCTTATAGTCCTGGCGGCCAGGGCTACAGACCGGGCGGGATTTGCGGCGTGGCCATGCCAACGCGCTAGCCCACCTTCCCCCGGAACATGTCCCGGAACTGTACCGGTACAGTGTAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGCCATCAAACTGCCTGCATCTGCGACCCCGTCCCACAACTTCGGGGCCAATCGACCAAATTACATATTTGAAACCGGGTTTTTCTGC  >  NC_002947/1307641‑1307930                                                                                                                                                   |                                                                                                                                                 aTTCTTATAGTCCTGGCGGCCAGGGCTACAGCCCGGGCGGGATTTGCGGCGTGGCCATGCCAACGCGCTAGCCCACCTTCCCCCGGAACATGTCCCGGAACTGTACCGGTACAGTGTAGAGCGCTG‑TTCGACCGCTTTTCAAGCGCTCg                                                                                                                                               <  5:14375/149‑1 (MQ=255)  ttCTTATAGTCCTGGCGGCCAGGGCTACAGACCGGGCGGGATTTGCGGCGTGGCCATGCCAACGCGCTAGCCCACCTTCCCCCGGAACATGTCCCGGAACTGTACCGGTACAGTGTAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCg                                                                                                                                               >  5:247686/1‑148 (MQ=255)        taGTCCTGGCGGCCAGGGCTACAGACCGGGCGGGATTTGCGGCGTGGCCATGCCAACGCGCTAGCCCACCTTCCCCCGGAACATGTCCCGGAACTGTACCGGTACAGTGTAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTg                                                                                                                                        >  2:270690/1‑149 (MQ=255)        taGTCCTGGCGGCCAGGGCTACAGACCGGGCGGGATTTGCGGCGTGGCCATGCCAACGAGCTAGCCCACCTTACCCCGGAACATGTCCCGGAACTGTACCGGTACAGTGTAGAGAGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTg                                                                                                                                        >  1:294696/1‑149 (MQ=255)           tCCTGGCGGCCAGGGCTACAGACCGGGCGGGATTTGCGGCGTGGCCATGCCAACTCGCTAGCCCACCTTCCCCCGGAACATGTCCCGGAACTGTACCGGTACAGTGTAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGt                                                                                                                                     <  5:205140/149‑1 (MQ=255)           tCCTGGCGGCCAGGGCTACAGACCGGGCGGGATTTGCGGCGTGGCCATGCCAACGCGCTAGCCCACCTTCCCCCGGAACATGTCCCGGAACTGTACCGGTACAGTGTAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGt                                                                                                                                     >  2:245248/1‑149 (MQ=255)            ccTGGCGGCCAGGGCTACAGACCGGGCGCGCTTTGCGGCGTGGCCATGCCAACGCGCTAGCCCACCTTCCCCCGGAACATGTCCCGGAACTGTACCGGTACAGTGTAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTc                                                                                                                                    <  4:249139/149‑1 (MQ=255)             cTGGCGGCCAGGGCTACAGACCGGGCGGGATTTGCGGCGTGGCCATGCCAACGCGCTAGCCCACCTTCCCCCGGAACATGTCCCGGAACTGTACCGGTACAGTGTAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCt                                                                                                                                   >  5:113203/1‑149 (MQ=255)                             cAGACCGGGCGGGATTTGCGGCGTGGCCATGCCAACGCGCTAGCCCACCTTCCCCCGGAACATGTCCCGGAACTGTACCGGTACAGTGTAGAGCGCTGTTTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTc                                                                                                                      <  1:270690/147‑1 (MQ=255)                                        ggATTTGCGGCGTGGCCATGCCAACGCGCTAGCCCACCTTCCCCCGGAACATGTCCCGGAACTGTACCGGTACAGTGTAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAg                                                                                                         >  2:127058/1‑148 (MQ=255)                                               cggcgTGGCCATGCCAACGCGCTAGCCCACCTTCCCCCGTAACATGTCCCGGAACTGTACCGGTACAGTGTAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATAc                                                                                                 <  2:294696/149‑1 (MQ=255)                                                         aTGCCAACGCGCTAGCCCACCTTCCCCCGGAACATGTCCCGGAACTGTACCGGTACAGTGTAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGgcgc                                                                                       >  7:75585/1‑149 (MQ=255)                                                             cAACGCGCTAGCCCACCTTCCCCCGGAACATGTCCCGGAACTGTACCGGTACAGTGTAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGCCAt                                                                                    >  3:257567/1‑148 (MQ=255)                                                             cAACGCGCTAGCCCACCTTCCCCCGGAACATGTCCCGGAACTGTACCGGTACAGTGTAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGACAt                                                                                    >  2:323560/1‑148 (MQ=255)                                                                 gcgcTAGCCCACCTTCCCCCGGAACATGTCCCGGAACTGTACCGGTACAGTGTAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGCCATCAAAc                                                                               <  1:245248/149‑1 (MQ=255)                                                                    cTAGCCCACCTTCCCCCGGAACATGTCCCGGAACTGTACCGGTACAGTGTAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGCCATCAAActgc                                                                            <  4:257567/149‑1 (MQ=255)                                                                       gCCCACCTTCCCCCGGAACATGTCCCGGAACTGTACCGGTACAGTGTAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGCCATCAAActgcct                                                                          <  4:299123/148‑1 (MQ=255)                                                                       gCCCACCTTCCCCCGGAACATGTCCCGGAACTGTACCGGTACAGTGTAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGCCATCAAActgcct                                                                          <  6:247686/148‑1 (MQ=255)                                                                          cACCTTCCCCCGGAACATGTCCCGGAACTGTACCGGTACAGTGTAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGCCATCAAACTGCCTGCAt                                                                      <  1:127058/149‑1 (MQ=255)                                                                             cTTCCCCCGGAACATGTCCCGGAACTGTACCGGTACAGTGTAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGCCATCAAACTGCCTGCATCTg                                                                   >  7:47661/1‑149 (MQ=255)                                                                             cTTCCCCCGGAACATGTCCCGGAACTGTACCGGTACAGTGTAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGCCATCAAACTGCCTGCATCTg                                                                   >  4:20375/1‑149 (MQ=255)                                                                              ttCCCCCGGAACATGTCCCGGAACTGTACCGGTACAGTGTAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGCCATCAAACTGCCTGCATCTGc                                                                  >  5:323168/1‑149 (MQ=255)                                                                                   ccGGAACATGTCCCGGAACTGTACCGGTACAGTGTAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGCCATCAAACTGCCTGCATCTGCGAccc                                                             >  7:144244/1‑149 (MQ=255)                                                                                    cGGAACATGTCCCGGAACTGTACCGGTACAGTGTAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGCCATCAAACTGCCTGCATCTGCGAcccc                                                            >  4:5839/1‑149 (MQ=255)                                                                                        aCATGTCCCGGAACTGTACCGGTACAGTGTAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGCCATCAAACTGCCTGCATCTGCGACCCCGTcc                                                        <  7:131308/149‑1 (MQ=255)                                                                                        aCATGTCCCGGAACTGTACCGGTACAGTGTAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGCCATCAAACTGCCTGCATCTGCGACCCCGTcc                                                        <  6:351771/149‑1 (MQ=255)                                                                                               ccGGAACTGTACCGGTACAGTGTAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGCCATCAAACTGCCTGCATCTGCGACCCCGTCCCACAAc                                                  <  6:323168/148‑1 (MQ=255)                                                                                                   tacagttccGGGACAGTTTAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGCCATCAAACTGCCTGCATCTGCGACCCCGTCCCACAACTTCgg                                             <  7:174180/142‑1 (MQ=255)                                                                                                   aaCTGTACCGGTACAGTGTAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGCCATCAAACTGCCTGCATCTGCGACCCCGTCCCACAACTTCgg                                             <  3:20375/149‑1 (MQ=255)                                                                                                      tGTACCGGTACAGTGTAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGCCATCAAACTGCCTGCATCTGCGACCCCGTCCCACaa                                                   >  6:95066/1‑140 (MQ=255)                                                                                                      tGTACCGGTACAGTGTAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGCCATCAAACTGCCTGCATCTGCGACCCCGTCCCACaa                                                   <  5:95066/140‑1 (MQ=255)                                                                                                       gTACCGGTACAGTGTAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGCCATCAAACTGCCTGCATCTGCGACCCCGTCCCACAACTTCGGGGc                                          >  7:319770/1‑148 (MQ=255)                                                                                                        tACCGGTACAGTGTAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGCCATCAAACTGCCTGCATCTGCGACCCCGTCCCACAACTTCGGGGcc                                         >  6:189029/1‑148 (MQ=255)                                                                                                        tACCGGTACAGTGTAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGCCATCAAACTGCCTGCATCTGCGACCCCGTCCCACAACTTCGGGGcc                                         >  4:103482/1‑148 (MQ=255)                                                                                                             gTACAGTGTAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACATAAAGATACAGAAAGGCGCCATCAAACTGCCTGCATCTGCGACCCCGTCCCACAACTTCggg                                            <  5:70760/140‑1 (MQ=255)                                                                                                             gTACAGTGTAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACATAAAGATACAGAAAGGCGCCATCAAACTGCCTGCATCTGCGACCCCGTCCCACAACTTCggg                                            >  6:70760/1‑140 (MQ=255)                                                                                                                   tgtAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGCCATCAAACTGCCTGCATCTGCGACCCCGTCCCACAACTTCGGGGCCAATCGACCAAAt                             >  7:13025/1‑149 (MQ=255)                                                                                                                     tAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGCCATCAAACTGCCTGCATCTGCGACCCCGTCCCACAACTTCGGGGCCAATCGACCAAAtt                            <  6:198049/148‑1 (MQ=255)                                                                                                                     tAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGCCATCAAACTGCCTGCATCTGCGACCCCGTCCCACAACTTCGGGGCCAATCGACCAAAtt                            >  5:198049/1‑148 (MQ=255)                                                                                                                          cgcTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGCCATCAAACTGCCTGCATCTGCGACCCCGTCCCACAACTTCGGGGCCAATCGACCAAATTACatat                      <  5:181480/149‑1 (MQ=255)                                                                                                                           cacttttCGACCGCTTTTCAAGCGCTCGAACAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGCCATCAAACTGCCTGCATCTGCGACCCCGTCCCACAACTTCGGGGCCAATCGACCAAATTACatat                      >  3:146530/6‑149 (MQ=255)                                                                                                                           cacttttCGACCGCTTTTCAAGCGCTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGCCATCAAACTGCCTGCATCTGCGACCCCGTCCCACAACTTCGGGGCCAATCGACCAAATTACataa                      >  2:336958/6‑148 (MQ=255)                                                                                                                                  cGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGCCATCAAACTGCCTGCATCTGCGACCCCGTCCCACAACTTCGGGGCCAATCGACCAAATTACATATTTGAAAc               >  7:92678/1‑149 (MQ=255)                                                                                                                                   gAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTATCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGCCATCAAACTGCCTGCATCTGCGACCCCGTCCCACAACTTCGGGGCCAATCGACCAAATTACATATTTGAAAcc              >  5:341492/1‑149 (MQ=255)                                                                                                                                       gcTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGCCATCAAACTGCCTGCATCTGCGACCCCGTCCCACAACTTCGGGGCCAATCGACCAAATTACATATTTGAAACCGGGt          >  7:186690/1‑149 (MQ=255)                                                                                                                                        cTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGCCATCAAACTGCCTGCATCTGCGACCCCGTCCCACAACTTCGGGGCCAATCGACCAAATTACATATTTGAAACCGGAtt         >  1:155852/1‑149 (MQ=255)                                                                                                                                         ttGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAATGATACAGAAAGGCGCCATCAAACTGCCTGCATCTGCGACCCCGTCCCACAACTTCGGTGCCAATCGACCAAATTACATATTTGAAACCGGGttt        <  1:323560/149‑1 (MQ=255)                                                                                                                                             aaaGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGCCATCAAACTGCCTGCATCTGCGACCCCGTCCCACAACTTCGGGGCCAATCGACCAAATTACATATTTGAAACCGGGTTTTTCt    <  8:144244/149‑1 (MQ=255)                                                                                                                                               aGCGCTCGAACAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGCCATCAAACTGCCTGCATCTGCGACCCCGTCCCACAACTTCGGGGCCAATCGACCAAATTACATATTTGAAACCGGGTTTTTCTGc  <  4:146530/149‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                 ATTCTTATAGTCCTGGCGGCCAGGGCTACAGACCGGGCGGGATTTGCGGCGTGGCCATGCCAACGCGCTAGCCCACCTTCCCCCGGAACATGTCCCGGAACTGTACCGGTACAGTGTAGAGCGCTG‑TTCGAGCGCTTGAAAAGCGGTCGAAAAGTGCGTCTTTCCTGCGTTGTCGCTTGATCGACAGAAAGATACAGAAAGGCGCCATCAAACTGCCTGCATCTGCGACCCCGTCCCACAACTTCGGGGCCAATCGACCAAATTACATATTTGAAACCGGGTTTTTCTGC  >  NC_002947/1307641‑1307930

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑