Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,464,291	A→T	9.8%	I58I (ATT→ATA)	lipA ←	lipoyl synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,464,291	0	A	T	9.8%	144.9 / 5.3	51	I58I (ATT→ATA)	lipA	lipoyl synthase
Reads supporting (aligned to +/- strand):  ref base A (25/21);  new base T (2/3);  total (27/24)
Fisher's exact test for biased strand distribution p-value = 6.56e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.12e-01

CCATGATCATGAAGGTGGCGGTACCACCCGAGAAGCACTCGCCCAGGTTCGGGCAGGAGGCCTCTTCGCACACGCTGTGCAGTTTGTGCTTGCGCAGCAGTTGTTTGATGCGGTCTACCTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGCACCACGCAGCTTGACCCCAGCTTCCACCTTCTTCGGCGCTGGGCGCGGGGTGGCATCCTGGGTAGGTATCAGGTTC  >  NC_002947/5464146‑5464438                                                                                                                                                    |                                                                                                                                                     ccATGATCATGAAGGTGGCGGTACCACCCGAGAAGTACTCGCCCAGGTTCGGGCAGGAGGCCTCTTCGCACACGCTGTGCAGTTTGTGCTTGCGCAGCAGTTGTTTGATGCGGTCTACCTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATc                                                                                                                                                  <  8:150753/149‑1 (MQ=255) ccATGATCATGAAGGTGGCGGTACCACCCGAGAAGCACTCGCCCAGGTTCGGGCAGGAGGCCTCTTCGCACACGCTGTGCAGTTTGTGCTTGCGCAGCAGTTGTTTGATGCGGTCTACCTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATc                                                                                                                                                  >  5:163962/1‑149 (MQ=255)  cATGATCATGAAGGTGGCGGTACCACCCGAGAAGCACTCGCCCAGGTTCGGGCAGGAGGCCTCTTCGCACACGCTGTGCAGTTTGTGCTTGCGCAGCAGTTGTTTGATGCGGTCTACCTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATc                                                                                                                                                  >  5:145469/1‑148 (MQ=255)      aTCATGAAGGTGGCGGTACCACCCGAGAAGCACTCGCCCAGGTTCGGGCAGGAGGCCTCTTCGCACACGCTGTGCAGTTTGTGCTTGCGCAGCAGTTGTTTGATGCGGTCTACCTCGGGCGACACCGGGATTCGCGTGC‑‑GT‑ATcccgg                                                                                                                                              <  8:4403/148‑4 (MQ=255)      aTCATGAAGGTGGCGGTACCACCCGAGAAGCACTCGCCCAGGTTCGGGCAGCTCGCCTCTTCGCACACGCTGTGCAGTTTGTGCTTGCGCAGCAGTTGTTTGATGCGGTCTACCTCGGGCGACACCGGGATTCGCGTGC‑‑GT‑ATcccggt                                                                                                                                             <  1:265847/149‑5 (MQ=255)                   cGGTACCACCCGAGAAGCACTCGCCCAGGTTCGGGCAGGAGGCCTCTTCGCACACGTTGTGCAGTTTGTGCTTGCGCAGCAGTTGTTTGATGCGGTCTACCTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGt                                                                                                                                <  6:132543/149‑1 (MQ=255)                       accaccCGAGAAGCACTCGCCCAGGTTCGGGCAGGAGGCCTCTTCGCACACGCTGTGCAGTTTGTGCTTGCGCAGCAGTTGTTTGATGCGGTCTACCTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCt                                                                                                                            >  7:103764/1‑149 (MQ=255)                                         gCCCAGGTTCGGGCAGGAGGCCTCTTCGCACACGCTGTGCAGTTTGTGCTTGCGCAGCAGTTGTTTGATGCGGTCTACCTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGgatgat                                                                                                            <  6:163962/147‑1 (MQ=255)                                               gTTCGGGCAGGAGGCCTCTTCGCACACGCTGTGCAGTTTGTGCTTGCGCAGCAGTTGTTTGATGCGGTCTACCTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGcttctt                                                                                                                                    >  4:40497/1‑117 (MQ=255)                                               gTTCGGGCAGGAGGCCTCTTCGCACACGCTGTGCAGTTTGTGCTTGCGCAGCAGTGGTTTGATGCGGTCTACCTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGcttctt                                                                                                                                    <  3:40497/117‑1 (MQ=255)                                                     gCAGGAGGCCTCTTCGCACACGCTGTGCAGTTTGTGCTTGCGCAGCAGTTGTTTGATGCGGTCTACCTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATgc                                                                                              >  4:208150/1‑149 (MQ=255)                                                          aggCCTCTTCGCACACGCTGTGCAGTTTGTGCTTGCGCAGCAGTTGTTTGATGCGGTCTACCTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGAAGGGATGATCTTCACCGGGATgcgcgc                                                                                          >  6:55213/1‑148 (MQ=255)                                                              ctctTCGCACACGCTGTGCAGTTTGTGCTTGCGCAGCAGTTGTTTGATGCGGTCTACCTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACtt                                                                                     >  6:48074/1‑149 (MQ=255)                                                               tctTCGCACACGCTGTGCAGTTTGTGCTTGCGCAGCAGTTGTTTGATGCGGTCTACCTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACttt                                                                                    >  5:154771/1‑149 (MQ=255)                                                                 ttCGCACACGCTGTGCAGTTTGTGCTTGCGCAGCAGTTGTTTGATGCGGTCTACCTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACttt                                                                                    <  3:208150/147‑1 (MQ=255)                                                                      acacGCTGTGCAGTTTGTGCTTGCGCAGCAGTTGTTTGATGCGGTCTACCTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGca                                                                             >  5:244266/1‑149 (MQ=255)                                                                      acacGCTGTGCAGTTTGTGCTTGCGCAGCAGTTGTTTGATGCGGTCTACCTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGca                                                                             >  8:7734/1‑149 (MQ=255)                                                                       cacGCTGTGCAGTTTGTGCTTGCGCAGCAGTTGTTTGATGCGGTCTACCTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGcac                                                                            <  4:153993/149‑1 (MQ=255)                                                                        acGCTGTGCAGTTTGTGCTTGCGCAGCAGTTGTTTGATGCGGTCTACCTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGcac                                                                            >  5:178903/1‑148 (MQ=255)                                                                            tgtgCAGTTTGTGCTTGCGCAGCAGTTGTTTGATGCGGTCTACCTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATCCGCGCGACTTTGTCGGCACAACg                                                                        >  4:1896/1‑148 (MQ=255)                                                                                cAGTTTGTGCTTGCGCAGCAGTTGTTTGATGCGGTCTACCTCGGGCGACACCGGGATACGCACGCGTGAGATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGCACCACg                                                                        >  1:96380/1‑147 (MQ=255)                                                                                 aGTTTGTGCTTGCGCAGCAGTTGTTTGATGCGGTCTACCTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGCACCACg                                                                        <  7:121093/143‑1 (MQ=255)                                                                                 aGTTTGTGCTTGCGCAGCAGTTGTTTGATGCGGTCTACCTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGCACCACg                                                                        >  8:121093/1‑143 (MQ=255)                                                                                 aGTTTGTGCTTGCGCAGCAGTTGTTTGATGCGGTCTACCTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGCACCACGCAGCtt                                                                  <  5:48074/149‑1 (MQ=255)                                                                                       tgCTTGCGCAGCAGTTGTTTGATGCGGTCTACCTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGCACCACGCAGCTTGAcccc                                                            <  6:178903/149‑1 (MQ=255)                                                                                         cTTGCGCAGCAGTTGTTTGATGCGGTCTACCTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGCACCACGCAGCTTGACCCCa                                                           <  4:66276/148‑1 (MQ=255)                                                                                            gcgcAGCAGTTGTTTGATGCGGTCTACCTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGcaccac                                                                         <  1:7879/131‑1 (MQ=255)                                                                                            gcgcAGCAGTTGTTTGATGCGGTCTACCTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGcaccac                                                                         >  2:7879/1‑131 (MQ=255)                                                                                                agcagTTGTTTGATGCGGTCTACCTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGCACCACGCAGCTTGACCCCAGCTTCCAc                                                   <  6:244266/149‑1 (MQ=255)                                                                                                     ttgttTGATGCGGTCTACCTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGCACCACGCAGCTTGACCCCAGCTTCCACcttct                                              >  7:154899/1‑149 (MQ=255)                                                                                                        tttGATGCGGTCTACCTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGCACCACGCAGCTTGACCCCAGCTTCCACCttcttc                                            <  7:7734/148‑1 (MQ=255)                                                                                                         ttGATGCGGTCTACCTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGCACCACGCAGCTTGAc                                                               <  5:86838/128‑1 (MQ=255)                                                                                                         ttGATGCGGTCTACCTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGCACCACGCAGCTTGAc                                                               >  6:86838/1‑128 (MQ=255)                                                                                                           gATGCGGTCTACCTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGCACCACGCAGCTTGACCCCAGCTTCCACCTTCTTCGgcg                                        >  8:197375/1‑149 (MQ=255)                                                                                                             tGCGGTCTACCTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGCACCACGCAGCTTGACCCCAGCTTCCACCTTCTTCGGCGCt                                      >  5:162843/1‑149 (MQ=255)                                                                                                                ggTCTACCTCGGGCGACACCGGGATACACACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGCACCACGCAGCTTGACCCCAGCTTCCACCTTCTTCGGCGCTggg                                   >  6:146154/1‑149 (MQ=255)                                                                                                                      ccTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGTTTATCTTCACCGGTATGCGCGCGACTTTGTCGGCACCACGCAGCTTGACCCCAGCTTCCACCTTCTTCGgc                                         <  7:48405/137‑1 (MQ=255)                                                                                                                      ccTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGCACCACGCAGCTTGACCCCAGCTTCCACCTTCTTCGGCGCTGGGCGCggg                             <  8:154899/149‑1 (MQ=255)                                                                                                                       cTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGCACCACGCAGCTTGACCCCAGCTTCCACCTTCTTCGGCGCTGGGCGCgggg                            >  5:286762/1‑149 (MQ=255)                                                                                                                       cTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGCACCACGCAGCTTGACCCCAGCTTCCACCTTCTTCGGCGCTGGGCGCgggg                            >  6:140347/1‑149 (MQ=255)                                                                                                                       cTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGCACCACGCAGCTTGACACCAGCTTCCACCTTCTTCGGCGCTGGGCGCgggg                            >  2:235563/1‑149 (MQ=255)                                                                                                                            gCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGCACCACGCAGCTTGACCCCAGCTTCCACCTTCTTCGGCGCTGGGCGCGGGGTGGCa                       >  1:131568/1‑149 (MQ=255)                                                                                                                                cgactggATTCGCGTGC‑‑GT‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGCACCACGCAGCTTGACCCCAGCTTCCACCTTCTTCg                                           >  2:49506/6‑125 (MQ=255)                                                                                                                                cgactggATTCGCGTGC‑‑GT‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGCACCACGCAGCTTGACCCCAGCTTCCACCTTCTTCg                                           <  1:49506/120‑1 (MQ=255)                                                                                                                                 acCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGCACCACGCAGCTTGACCCCAGCTTCCACCTTCTTCGGCGCTGGGCGCGGGGTGGCATCCTg                  <  5:140347/149‑1 (MQ=255)                                                                                                                                  actggATTCGCGTGC‑‑GT‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGCACCACGCAGCTTGACCCCAGCTTCCACCTTCTTCGGCGCTGGGCGCGGGGTGGCATCCTgg                 >  1:198044/4‑149 (MQ=255)                                                                                                                                   cGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGCACCACGCAGCTTGACCCCAGCTTCCACCTTCTTCGGCGCTGGGCGCGGGGTGGCATCCTggg                >  6:302162/1‑149 (MQ=255)                                                                                                                                   cGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGCACCACGCAGCTTGACCCCAGCTTCCACCTTCTTCGGCGCTGGGCGCGGGGTGGCATCCTggg                <  6:286762/149‑1 (MQ=255)                                                                                                                                      gATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGCACCACGCAGCTTGACCCCAGCTTCCACCTTCTTCGGCGCTGGGCGCGGGGTGGCATCCTGggtag             <  5:55213/149‑1 (MQ=255)                                                                                                                                                c‑‑gA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGCACCACGCAGCTTGACCCCAGCTTCCACCTTCTTCGGCGCTGGGCGCGGGGTGGCATCCTGGGTAGGTATCAGGtt   <  6:145469/149‑1 (MQ=255)                                                                                                                                                   gA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGCACCACGCAGCTTGACCCCAGCTTCCACCTTCTTCGGCGCTGGGCGCGGGGGGGCATCCTGGGTAGGTATCAGGTTc  <  2:211742/149‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                     CCATGATCATGAAGGTGGCGGTACCACCCGAGAAGCACTCGCCCAGGTTCGGGCAGGAGGCCTCTTCGCACACGCTGTGCAGTTTGTGCTTGCGCAGCAGTTGTTTGATGCGGTCTACCTCGGGCGACACCGGGATACGCACGC‑‑GA‑ATCCAGTCGGGCTTCTTGGGTAGCTCATCGGTAGGGATGATCTTCACCGGGATGCGCGCGACTTTGTCGGCACCACGCAGCTTGACCCCAGCTTCCACCTTCTTCGGCGCTGGGCGCGGGGTGGCATCCTGGGTAGGTATCAGGTTC  >  NC_002947/5464146‑5464438

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: ‑