Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,162,570	G→A	12.5%	intergenic (+474/‑106)	PP_2776 → / → PP_2777	homocysteine S‑methyltransferase family protein/acyl carrier protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,162,570	0	G	A	12.5%	98.3 / 5.9	40	intergenic (+474/‑106)	PP_2776/PP_2777	homocysteine S‑methyltransferase family protein/acyl carrier protein
Reads supporting (aligned to +/- strand):  ref base G (17/18);  new base A (3/2);  total (20/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.36e-01

GCTTCTGGAACTATCGTGCTGTTTCAAGCAATCGATTTTGTCATTTTACGACCCCTCTCCAAGCCCCATTGAGCTGCATGAATCAAAGGTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTAGGGAAACACTCAATGAATAATCCGTTGGAATTGGACAGCGTCATCAGCAG  >  NC_002947/3162421‑3162713                                                                                                                                                      |                                                                                                                                                cgatCTGGAACTATCGTGCTGTTTCAAGCAATCGATTTTGTCATTTTACGACCCCTCTCCAAGCCCCATTGAGCTGCATGAATCAAAGGTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAg                                                                                                                                                 <  1:1087457/147‑1 (MQ=255)  cTTCTGGAACTATCGTGCTGTTTCAAGCAATCGATTTTGTCATTTTACGACCCCTCTCCAAGCCCCATTGAGCTGCATGAATCAAAGGTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAgg                                                                                                                                                <  1:962237/150‑1 (MQ=255)      tGGAACTATCGTGCTGTTTCAAGCAATCGATTTTGTCATTTTACGACCCCTCTCCAAGCCCCATTGAGCTGCATGAATCAATGGTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGga                                                                                                                                            <  2:639527/150‑1 (MQ=255)                    tGTTTCAAGCAATCGATTTTGTCATTTTACGACCCCTCTCCAAGCCCCATTGAGCTGCATGAATCAAAGGTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGACAGACAGTAGACGccc                                                                                                                              >  2:63293/1‑150 (MQ=255)                     gTTTCAAGCAATCGATTTTGTCATTTTACGACCCCTCTCCAAGCCCCATTGAGCTGCATGAATCAAAGGTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCg                                                                                                                             >  2:736314/1‑150 (MQ=255)                      tttCAAGCAATCGATTTTGTCATTTTACGACCCCTCTCCAAGCCCCATTGAGCTGCATGAATCAAAGGTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCCTAAGGGgagag                                                                                                                                         <  2:374765/137‑2 (MQ=255)                      tttCAAGCAATCGATTTTGTCATTTTACGACCCCTCTCCAAGCCCCATTGAGCTGCATGAATCAAAGGTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCCTAAGGGgagag                                                                                                                                         >  1:374765/1‑136 (MQ=255)                                                      ccTCTCCAAGCCCCATTGAGCTGCATGAATCAAAGGTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCtttt                                                                                            >  2:645899/1‑150 (MQ=255)                                                       ctctCCAAGCCCCATTGAGCTGCATGAATCAAAGGTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCttttt                                                                                           >  2:280664/1‑150 (MQ=255)                                                        tctcCAAGCCCCATTGAGCTGCATGAATCAAAGGTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCtttttt                                                                                          >  1:144676/1‑150 (MQ=255)                                                         ctcCAAGCCCCATTGAGCTGCATGAATCAAAGGTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCttttttt                                                                                         >  1:326572/1‑150 (MQ=255)                                                          tcCAAGCCCCATTGAGCTGCATGAATCAAAGGTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTg                                                                                        <  1:660354/150‑1 (MQ=255)                                                                             cATGAATCAAAGGTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGccc                                                                                    <  1:883783/135‑1 (MQ=255)                                                                             cATGAATCAAAGGTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGccc                                                                                    >  2:883783/1‑135 (MQ=255)                                                                              aTGAATCAAAGGTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTattcatt                                                                    <  1:205147/150‑1 (MQ=255)                                                                                   tCAAAGGTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTGTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATg                                                               >  2:486785/1‑150 (MQ=255)                                                                                     aaaGGTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCCTAAGGGgaga                                                                                                                                          <  2:90405/73‑1 (MQ=255)                                                                                     aaaGGTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCCTAAGGGgaga                                                                                                                                          >  1:90405/1‑73 (MQ=255)                                                                                      aaGGTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCCAAACCGCTTGTTTTGGCCCGATGACTTTATTCATTCAATGCgg                                                            <  1:486785/150‑1 (MQ=255)                                                                                       aGGTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAgggg                                                                                                                                              <  2:287865/67‑1 (MQ=255)                                                                                       aGGTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAgggg                                                                                                                                              >  1:287865/1‑67 (MQ=255)                                                                                               gggCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTTCCCCCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTAg                                                   <  1:912302/150‑1 (MQ=255)                                                                                               gggCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTAg                                                   <  1:63293/150‑1 (MQ=255)                                                                                                    cgcTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTAGGGaaa                                              <  1:905389/150‑1 (MQ=255)                                                                                                           aTTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTAGGGAAaca                                            <  1:422521/145‑1 (MQ=255)                                                                                                           aTTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTAGGGAAaca                                            >  2:422521/1‑145 (MQ=255)                                                                                                                tcACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTAGTGAAACACTCAATGaat                                  >  2:570094/1‑150 (MQ=255)                                                                                                                        aGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTAGGGAAACACTCAATGAATAATCCGtt                          <  2:144676/150‑1 (MQ=255)                                                                                                                         gCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTAGGGAAACACTCAATGAATAATCCGTTg                         <  1:645899/150‑1 (MQ=255)                                                                                                                              gATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTAGGGAAACACTCAATGAATAATCCGTTGGAAtt                    <  1:736314/150‑1 (MQ=255)                                                                                                                               aTGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTAGGGAAACACTCAATGAATAATCCGTTGGAATTg                   >  2:1093510/1‑150 (MQ=255)                                                                                                                               aTGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTAGGGAAACACTCAATGAATAATCCGTTGGAATTg                   <  1:231563/150‑1 (MQ=255)                                                                                                                                     cGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTAGGGAAACACTCAATGAATAATCCGTTGGAATTGGACAGc             <  2:326572/150‑1 (MQ=255)                                                                                                                                      gTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCaaaa                                                                                                    <  2:592737/62‑1 (MQ=255)                                                                                                                                      gTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCaaaa                                                                                                    >  1:592737/1‑62 (MQ=255)                                                                                                                                        tGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTAGGGAAACACTCAATGAATAATCCGTTGGAATTGGACAGCGtc          <  1:469096/150‑1 (MQ=255)                                                                                                                                          aCTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTAGGGAAACACTCAATGa                                    >  1:604026/1‑122 (MQ=255)                                                                                                                                          aCTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCCATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGTCTTTTGTAGGGAAACACTCAATGa                                    <  2:604026/122‑1 (MQ=255)                                                                                                                                              tcCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTAGGGAAACACTCAATGAATAATCCGTTGGAATTGGACAGCGTCATcagc    >  1:752570/1‑150 (MQ=255)                                                                                                                                              tcCCCCTAAGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTTTCTTTTTTTTTTTATTCATTCAATGCTGCTTTTGTAGGTAAACACTCTATGATTAATCCGTTGGAATTGGACATCGtcatcatc    >  2:287522/1‑148 (MQ=255)                                                                                                                                                cccTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTAGGGAAACACTCAATGAATAATCCGTTGGAATTGGACAGCGTCATcagcag  >  2:837474/1‑150 (MQ=255)                                                                                                                                                cccTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTAGGGAAACACTCAATGAATAATCCGTTGGAATTGGACAGCGTCATcagca   >  2:111112/1‑149 (MQ=255)                                                                                                                                                cccTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTAGGGAAACACTCAATGAATAATCCGTTGGAATTGGACAGCGTCATcagca   <  1:111112/149‑1 (MQ=255)                                                                                                                                                cccTTAGGGGAAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTTTGTATTCAATGCGGCTTTTGTAGAGAAAAATACAATGATTTAACCATCGGAATTGTACAGCGTCATcagcag  >  1:351298/1‑150 (MQ=255)                                                                                                                                                      |                                                                                                                                                GCTTCTGGAACTATCGTGCTGTTTCAAGCAATCGATTTTGTCATTTTACGACCCCTCTCCAAGCCCCATTGAGCTGCATGAATCAAAGGTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTAGGGAAACACTCAATGAATAATCCGTTGGAATTGGACAGCGTCATCAGCAG  >  NC_002947/3162421‑3162713

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑