Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,491,225	G→A	9.1%	L56F (CTC→TTC)	clpV ←	protein ClpV1

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,491,225	0	G	A	9.1%	119.2 / 2.2	44	L56F (CTC→TTC)	clpV	protein ClpV1
Reads supporting (aligned to +/- strand):  ref base G (20/20);  new base A (2/2);  total (22/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.60e-01

GTAATGTGCGGCGACAGCGCCGGGGTGCGGGTATTACCTTTCTTGAAGGTGCCCAGGGCGGTGACCAGCTGCGCTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGG‑TCGCTGTCGTTG‑TTGTCGAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACAGAGACTTCAGGTTCACAAGGCGACCCCATCGTAAGGAA  >  NC_002947/3491083‑3491373                                                                                                                                                 |                                                                                                                                                     gTAATGTGCGGCGACAGCGCCGGGGTGCGGGTATTACCTTTCTTGAAGGTGCCCAGGGCGGTGACCAGCTGCGCTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGG‑TCGCTGTCGTTG‑TTGTCGAGCAACTg                                                                                                                                                >  1:105088/1‑149 (MQ=255)    aTGTGCGGCGACAGCGCCGGGGTGCGGGTATTACCTTTCTTGAAGGTGCCCAGGGCGGTGACCAGCTGCGCTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGG‑TCGCTGTCGTTG‑TTGTCGAGCAACTgca                                                                                                                                              <  5:39180/148‑1 (MQ=255)       tgCGGCGACAGCGCCGGGGTGCGGGTATTACCTTTCTTGAAGGTGCCCAGGGCGGTGACCAGCTGCGCTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGG‑TCGCTGTCGTTG‑TTGTCGAGCAACTgcagc                                                                                                                                            >  6:221424/1‑147 (MQ=255)       tgCGGCGACAGCGCCGGGGTGCGGGTATTACCTTTCTTGAAGGTGCCCAGGGCGGTGACCAGCTGCGCTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGG‑TCGCTGTCGTTG‑TTGTCGAGCAACTgcagc                                                                                                                                            <  5:221424/147‑1 (MQ=255)                      ggggTGCGGGTATTACCTTTCTTGAAGGTGCCCAGGGCGGTGACCAGCTGCGCTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGG‑TCGCTGTCGTTG‑TTGTCGAGCAACTGCAGCAGCAGGTGCTCCACTTc                                                                                                                           <  4:141371/149‑1 (MQ=255)                         gTGCGGGTATTACCTTTCTTGAAGGTGCCCAGGGCGGTGACCAGCTGCGCTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGG‑TCGCTGTCGTTG‑TTGTCGAGCAACTgcagca                                                                                                                                           >  7:125232/1‑130 (MQ=255)                         gTGCGGGTATTACCTTTCTTGAAGGTGCCCAGGGCGGTGACCAGCTGCGCTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGG‑TCGCTGTCGTTG‑TTGTCGAGCAACTgcagca                                                                                                                                           <  8:125232/130‑1 (MQ=255)                          tGCGGGTATTACCTTTCTTGAAGGTGCCCAGGGCGGTGACCAGCTGCGCTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGG‑TCGCTGTCGTTG‑TTGTCGAGCAACTGCAGCAGCAGGTGCTCCACTTCCAcc                                                                                                                       <  2:105088/149‑1 (MQ=255)                                    aCCTTTCTTGAAGGTGCCCAGGGCGGTGACCAGCTGCGCTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGG‑TCGCTGTCGTTGCTTGTCGAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATg                                                                                                               <  1:76101/148‑1 (MQ=255)                                          cTTGAAGGTGCCCAGGGCGGTGACCAGCTGCGCTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGG‑TCGCTGTCGTTG‑TTGTCGAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTcc                                                                                                        <  3:39025/148‑1 (MQ=255)                                             gAAGGTGCCCAGGGCGGTGACCAGCTGCGCTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGG‑TCGCTGTCGTTG‑TTGTCGAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGAc                                                                                                     <  7:96497/148‑1 (MQ=255)                                               aGGTGCCCAGGGCGGTGACCAGCTGCGCTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGG‑TCGCTGTCGTTG‑TTGTCGAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAgg                                                                                                  <  6:315556/149‑1 (MQ=255)                                               aGGTGCCCAGGGCGGTGACCAGCTGCGCTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGG‑TCGCTGTCGTTG‑TTGTCGAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAgg                                                                                                  <  6:249324/149‑1 (MQ=255)                                                         ggCGGTGACCAGCTGCGCTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGG‑TCGCTGTCGTTG‑TTGTCGAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGgccg                                                                                        >  1:345687/1‑149 (MQ=255)                                                               gACCAGCTGCGCTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGGTTGGCTGTCGTTG‑TTGTCGAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCGCAGGGCCGCcgcg                                                                                   >  1:103683/1‑149 (MQ=255)                                                                               aGGCGTTCGGAGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGG‑TCGCTGTCGTTG‑TTGTCGAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCg                                                                  >  8:36822/1‑149 (MQ=255)                                                                                   gTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGG‑TCGCTGTCGTTG‑TTGTCGAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTg                                                              >  3:292979/1‑149 (MQ=255)                                                                                       ggCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGG‑TCGCTGTCGTTG‑TTGTCGAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGttt                                                          <  6:92585/149‑1 (MQ=255)                                                                                       ggCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGG‑TCGCTGTCGTTG‑TTGTCGAACAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTg                                                              <  3:189885/145‑1 (MQ=255)                                                                                       ggCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGG‑TCGCTGTCGTTG‑TTGTCGAACAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTg                                                              <  7:119032/145‑1 (MQ=255)                                                                                       ggCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGG‑TCGCTGTCGTTG‑TTGTCGAACAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTg                                                              >  4:189885/1‑145 (MQ=255)                                                                                       ggCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGG‑TCGCTGTCGTTG‑TTGTCGAACAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTg                                                              >  8:119032/1‑145 (MQ=255)                                                                                          gacgacCTGGTAGTGGCGAAGGATCGGCGCCAGG‑TCGCTGTCGTTG‑TTGTCGAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGAACAGGGCCGCCGCGCGTTCCGTGGCCGTGAGGCTGGTTTCGt                                                       >  8:152466/1‑149 (MQ=255)                                                                                                           gcAGGATCGGCGCCAGG‑TCGCTGTCGTTG‑TTGTCGAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCt                                                               >  7:159562/1‑124 (MQ=255)                                                                                                           gcAGGATCGGCGCCAGG‑TCGCTGTCGTTG‑TTGTCGAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCt                                                               <  8:159562/124‑1 (MQ=255)                                                                                                            cAGGATCGGCGCCAGG‑TCGCTGTCGTTG‑TTGTCGAGCAACTGCAGCAGCAGGTGCTCCGCTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACagag                                     <  7:272767/149‑1 (MQ=255)                                                                                                              ggATCGGCGCCAGG‑TCGCTGTCGTTG‑TTGTCGAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCGCAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACAGAGAc                                   <  2:103683/149‑1 (MQ=255)                                                                                                                 tCGGCGCCAGG‑TCGCTGTCGTTG‑TTGTCGAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGc                                                  >  6:239817/1‑131 (MQ=255)                                                                                                                 tCGGCGCCAGG‑TCGCTGTCGTTG‑TTGTCGAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGc                                                  <  5:239817/131‑1 (MQ=255)                                                                                                                 tCGGCGCCAGG‑TCGCTGTCGTTG‑TTGTCGAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACAGAGACTTc                                <  4:292979/149‑1 (MQ=255)                                                                                                                        cAGG‑TCGCTGTCGTTG‑TTGTCGAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACAGAGACTTCAGGTTca                         >  5:354198/1‑149 (MQ=255)                                                                                                                           g‑TCGCTGTCGTTG‑TTGTCGAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACAGAGACTTCAGGTTcac                        >  5:92095/1‑147 (MQ=255)                                                                                                                                     gttg‑ttGTCGAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACAGAGACTTCAGGTTCACAAg                     >  7:207602/1‑141 (MQ=255)                                                                                                                                     gttg‑ttGTCGAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACAGAGACTTCAGGTTCACAAg                     <  8:207602/141‑1 (MQ=255)                                                                                                                                      ttg‑ttgTCGAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACAGAGACTTCAGGTTCACAAGGCGACCCCa            <  2:345687/149‑1 (MQ=255)                                                                                                                                        g‑ttgtCGAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACAGAGACTTCAGGTTCACAAGGCGACCCCATc          >  6:82953/1‑149 (MQ=255)                                                                                                                                            gtCGAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACAGAGACTTCAGGTTCACAAg                     <  7:195456/135‑1 (MQ=255)                                                                                                                                            gtCGAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACAGAGACTTCAGGTTCACAAg                     >  8:195456/1‑135 (MQ=255)                                                                                                                                            gtCGAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACAGAGACTTCAGGTTCACAAGGCGACCCCATCGt        >  1:246505/1‑148 (MQ=255)                                                                                                                                             tggAGCACCTGCTGCTGCAGTTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACAGAGACTTCAGGTTCACAAGGCGACCCCATCGt        >  7:242514/3‑147 (MQ=255)                                                                                                                                             tCGAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACAGAGACTTCAGGTTCACAAGGCGACCCCATCGTaa      <  1:20936/149‑1 (MQ=255)                                                                                                                                             tCGAGAAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCAGACAGGCACAGGGCCGACGCGCTTTCGGTGGACGTGCGGCTGGGTTCGTTTAGCTTGGCGAACAGAGAATTCAGGATCACAAGGCGACACCATCGTaa      >  8:95169/1‑149 (MQ=255)                                                                                                                                               gAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACAGAGACTTCAGGTTCACAAGGCGACCCCATCGTAAg     >  6:103509/1‑148 (MQ=255)                                                                                                                                               gAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGCGCGGCTGGTTTCGTTGAGCTTGGCGAACAGAGACTTCAGGTTCACAAGGCGACCCCATCGTAAg     >  2:87379/1‑148 (MQ=255)                                                                                                                                                 gCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACAGAGACTTCAGGTTCACAAGGCGACCCCa            >  2:303005/1‑139 (MQ=255)                                                                                                                                                 gCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACAGAGACTTCAGGTTCACAAGGCGACCCCa            <  1:303005/139‑1 (MQ=255)                                                                                                                                                 gCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCAAACAGAGACTTCAGGTTCACAAGGCGACCCCATCGTAAGGaa  >  8:12735/1‑149 (MQ=255)                                                                                                                                                 |                                                                                                                                                     GTAATGTGCGGCGACAGCGCCGGGGTGCGGGTATTACCTTTCTTGAAGGTGCCCAGGGCGGTGACCAGCTGCGCTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGG‑TCGCTGTCGTTG‑TTGTCGAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACAGAGACTTCAGGTTCACAAGGCGACCCCATCGTAAGGAA  >  NC_002947/3491083‑3491373

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: ‑