Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,156,030	T→A	10.0%	Y158N (TAT→AAT)	plsX →	phosphate acyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,156,030	0	T	A	10.0%	106.6 / 3.4	40	Y158N (TAT→AAT)	plsX	phosphate acyltransferase
Reads supporting (aligned to +/- strand):  ref base T (18/18);  new base A (2/2);  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 = 7.01e-01

CTGATGGCGTTGTCGCGCTTCGTGCTCAAGACCTTGCCGGGTATCGACCGGCCGGCCATGGTGGCGGCGATCCCGACCCAGACAGGTTACTGTCAACTGCTCGATCTGGGCGCCAATGTCGACTGCAGTGCCGAAAACCTCTATCAGTTCGCGGTAATGGGCTCGGTGGCCGCTCAGGCCCTGGGTGTGCATCGGCCACGCGTGGCGCTGTTGAACATCGGTACCGAGGACATCAAGGGTAACCAGCAGGTCAAGCTGGCTGCCACGCTGTTGCAGA  >  NC_002947/2155889‑2156165                                                                                                                                              |                                                                                                                                        cTGATGGCGTTGTCGCGCTTCGTGCTCAAGACCTTGCCGGGTATCGACCGGCCGGCCATGGTGGCGGCGATCCCGACCCAGACAGGTTACTGTCAACTGCTCGATCTGGGCGCCAATGTCGACTGCAGTGCCGAAAACCTCTATCAGtt                                                                                                                                  >  1:362335/1‑149 (MQ=255)             tCGCGCTTCGTGCTCAAGACCTTGCCGGGTATCGACCGGCCGGCCATGGTGGCGGCGATCCCGACCCAGACAGGTTACTGTCAACTGCTCGATCTGGGCGCCAATGTCGACTGCAGTGCCGAAAACCTCTATCAg                                                                                                                                    >  7:300775/1‑135 (MQ=255)             tCGCGCTTCGTGCTCAAGACCTTGCCGGGTATCGACCGGCCGGCCATGGTGGCGGCGATCCCGACCCAGACAGGTTACTGTCAACTGCTCGATCTGGGCGCCAATGTCGACTGCAGTGCCGAAAACCTCTATCAg                                                                                                                                    <  8:300775/135‑1 (MQ=255)             tCGCGCTTCGTGCTCAAGACCTTGCCGGGTATCGACCGGCCGGCCATGGTGGCGGCGATCCCGACCCAGACAGGTTACTGTCAACTGCTCGATCTGGGCGCCAATGTCGACTGCAGTGCCGAAAACCTCTATCAGTTCGCGGTAATggg                                                                                                                      <  1:36139/149‑1 (MQ=255)               gcgcTTCGTGCTCAAGACCTTGCCGGGTATCGACCGGCCGGCCATGGTGGCGGCGATCCCGACCCAGACAGGTTACTGTCAACTGCTCGATCTGGGCGCCAATGTCGACTGCAGTGCCGAAAACCTCTATCAGTTCGCGGTAATGGGCt                                                                                                                    >  7:187183/1‑149 (MQ=255)                   ttCGTGCTCAAGACCTTGCCGGGTATCGACCGGCCGGCCATGGTGGCGGCGATCCCGACCCAGACAGGTTACTGTCAACTGCTCGATCTGGGCGCCAATGTCGACTGCAGTGCCGAAAACCTCTATCAGTTCGCGGTAATGGGCTCGGt                                                                                                                >  1:239073/1‑149 (MQ=255)                   ttCGTGCTCAAGACCTTGCCGGGTATCGACCGGCCGGCCATGGTGGCGGCGATCCCGACCCAGACAGGTTACTGTCAACTGCTCGATCTGGGCGCCAATGTCGACTGCAGTGCCGAAAACCTCTATCAGTTCGCGGTAATGGGCTCGGt                                                                                                                >  6:125395/1‑149 (MQ=255)                     cGTGCTCAAGACCTTGCCGGGTATCGACCGGCCGGCCATGGTGGCGGCGATCCCGACCCAGACAGGTTACTGTCAACTGCTCGATCTGGGCGCCAATGTCGACTGCAGTGCCGAAAACCTCTATCAGTTCGCGGTAATGGGCTCGGTg                                                                                                               <  2:239073/148‑1 (MQ=255)                        gCTCAAGACCTTGCCGGGTATCGACCGGCCGGCCATGGTGGCGGCGATCCCGACCCAGACAGGTTACTGTCAACTGCTCGATCTGGGCGCCAATGTCGACTGCAGTGCCGAAAACCTCTATCAGTTCGCGGTAATGGGCTCGGTGGCCg                                                                                                           >  1:219863/1‑149 (MQ=255)                         cTCAAGACCTTGCCGGGTATCGACCGGCCGGCCATGGTGGCGGCGATCCCGACCCAGACAGGTTACTGTCAACTGCTCGATCTGGGCGCCAATGTCGACTGCAGTGCCGAAAACCTCAATCAGTTCGCGGTAATGGGCTCGGTGGCCGc                                                                                                          >  5:153078/1‑149 (MQ=255)                         cTCAAGACCTTGCCGGGTATCGACCGGCCGGCCATGGTGGCGGCGATCCCGACCCAGACAGGTTACTGTCAACTGCTCGATCTGGGCGCCAATGTCGACTGCAGTGCCGAAAACCTCAATCAGTTCGCGGTAATGGGCTCGGTGGCCGc                                                                                                          >  5:147560/1‑149 (MQ=255)                          tCAAGACCTTGCCGGGTATCGACCGGCCGGCCATGGTGGCGGCGATCCCGACCCAGACAGGTTACTGTCAACTGCTCGATCTGGGCGCCAATGTCGACTGCAGTGCCGAAAACCTCTATCAGTTCGCGGTAATGGGCTCGGTGGCCGc                                                                                                          >  4:184135/1‑148 (MQ=255)                          tCAAGACCTTGCCGGGTATCGACCGGCCGGCCATGGTGGCGGCGATCCCGACCCAGACAGGTTACTGTCAACTGCTCGATCTGGGCGCCAATGTCGACTGCAGTGCCGAAAACCTCTATCAGTTCGCGGTAATGGGCTCGGTGGCCGCt                                                                                                         >  1:215644/1‑149 (MQ=255)                           cAAGACCTTGCCGGGTATCGACCGGCCGGCCATGGTGGCGGCGATCCCGACCCAGACAGGTTACTGTCAACTGCTCGATCTGGGCGCCAATGTCGACTGCAGTGCCGAAAACCTCTATCAGTTCGCGGTAATGGGCTCGGTGGCCGCt                                                                                                         >  5:54284/1‑148 (MQ=255)                               aCCTTGCCGGGTATCGACCGGCCGACCATGGTGGCGGCGATCCCGACCCAGACAGGTTACTGTCAACTGCTCGATCTGGGCGCCAATGTCGACTGCAGTGCCGAAAACCTCTATCAGTTCGCGGTAATGGGc                                                                                                                     >  3:9170/1‑132 (MQ=255)                               aCCTTGCCGGGTATCGACCGGCCGACCATGGTGGCGGCGATCCCGACCCAGACAGGTTACTGTCAACTGCTCGATCTGGGCGCCAATGTCGACTGCAGTGCCGAAAACCTCTATCAGTTCGCGGTAATGGGc                                                                                                                     <  4:9170/132‑1 (MQ=255)                                    gCCGGGTATCGACCGGCCGGCCATGGTGGCGGCGATCCCGACCCAGACAGGTTACTGTCAACTGCTCGATCTGGGCGCCAATGTCGACTGCAGTGCCGAAAACCTCTATCAGTTCGCGGTAATGGGCTCGGTGGCCGCTCAGGCCCTg                                                                                                <  3:100718/148‑1 (MQ=255)                                     ccGGGTATCGACCGGCCGGCCATGGTGGCGGCGATCCCGACCCAGACAGGTTACTGTCAACTGCTCGATCTGGGCGCCAATGTCGACTGCAGTGCCGAAAACCTCTATCAGTTCGCGGTAATGGGCTCGGTGGCCGCTCAGGCCCTggg                                                                                              <  2:215644/149‑1 (MQ=255)                                      cGGGTATCGACCGGCCGGCCATGGTGGCGGCGATCCCGACCCAGACAGGTTACTGTCAACTGCTCGATCTGGGCGCCAATGTCGACTGCAGTGCCGAAAACCTCTATCAGTTCGCGGTAATGGGCTCGGTGGCCGCTCAGGCCCTGGgt                                                                                             <  2:219863/149‑1 (MQ=255)                                                 cggccggcCATGGTGGCGGCGATCCCGACCCAGACAGGTTACTGTCAACTGCTCGATCTGGGCGCCAATGTCGACTGCAGTGCCGAAAACCTCAATCAGTTCGCGGTAATGGGCTCGGTGGCCGCTCAGGCCCTGGGTGTGCATCGGcc                                                                                  <  6:153078/149‑1 (MQ=255)                                                 cggccggcCATGGTGGCGGCGATCCCGACCCAGACAGGTTACTGTCAACTGCTCGATCTGGGCGCCAATGTCGACTGCAGTGCCGAAAACCTCAATCAGTTCGCGGTAATGGGCTCGGGGGCCGCTCAGGCCCTGGGTGTGCATCGGcc                                                                                  <  6:147560/149‑1 (MQ=255)                                                   gccggccATGGTGGCGGCGATCCCGACCCAGACAGGTTACTGTCAACTGCTCGATCTGGGCGCCAATGTCGACTGCAGTGCCGAAAACCTCTATCAGTTCGCGGTAATGGGCTCGGTGGCCGCTCAGGCCCTGGGTGTGCATCGGCCAc                                                                                <  2:362335/149‑1 (MQ=255)                                                                 cggcgATCCCGACCCAGACAGGTTACTGTCAACTGCTCGATCTGGGCGCCAATGTCGACTGCAGTGCCGAAAACCTCTATCAGTTCGCGGTAATGGGCTCGGTGGCCGCTCAGGCCCTGGGTGTGCATCGGCCACGCGTGGCGCTGTTg                                                                  <  5:125395/149‑1 (MQ=255)                                                                   gcgATCCCGACCCAGACAGGTTACTGTCAACTGCTCGATCTGGGCGCCAATGTCGACTGCAGTGCCGAAAACCTCTATCAGTTCGCGGTAATGGGCTCGGTGGCCGCTCAGGCCCTGGGTGTGCATCGGCCACGCGTGGCGCTGTTGaa                                                                >  5:342275/1‑149 (MQ=255)                                                                       tCCCGACCCAGACAGGTTACTGTCAACTGCTCGATCTGGGCGCCAATGTCGACTGCAGTGCCGAAAACCTCTATCAGTTCGCGGTAATGGGCTCGGTGGCCGCTCAGGCCCTGGGTGTGCATCGGCCACGCGTGGCGCTGTTGAACATc                                                            <  6:245588/149‑1 (MQ=255)                                                                         ccGACCCAGACAGGTTACTGTCAACTGCTCGATCTGGGCGCCAATGTCGACTGCAGTGCCGAAAACCTCTATCAGTTCGCGGTAATGGGCTCGGTGGCCGCTCAGGCCCTGGGTGTGCATCGGCCACGCGTGGCGCTGTTGAACATCg                                                           <  3:184135/148‑1 (MQ=255)                                                                          cGACCCAGACAGGTTACTGTCAACTGCTCGATCTGGGCGCCAATGTCGACTGCAGTGCCGAAAACCTCTATCAGTTCGCGGTAATGGGCTCGGTGGCCGCTCAGGCCCTGGGTGTGCATCGGCCACGCGTGGCGCTGTTGAACATCgg                                                          >  7:63428/1‑148 (MQ=255)                                                                                aGACAGGTTACTGTCAACTGCTCGATCTGGGCGCCAATGTCGACTGCAGTGCCGAAAACCTCTATCAGTTCGCGGTAATGGGCTCGGTGGCCGCTCAGGCCCTGGGTGTGCATCGGCCACGCGTGGCGCTGTTGAACATCGGTACCGAg                                                   <  8:187183/149‑1 (MQ=255)                                                                                               aaCTGCTCGATCTGGGCGCCAATGTCGACTGCAGTGCCGAAAACCTCTATCAGTTCGCGGTAATGGGCTCGGTGGCCGCTCAGGCCCTGGGTGTGCATCGGCCCCGCGTGGCGCTGTTGAACATCGGTACCGAGGACATCAAGGGTAAc                                    >  2:82712/1‑149 (MQ=255)                                                                                                     tCGATCTGGGCGCCAATGTCGACTGCAGTGCCGAAAACCTCTATCAGTTCGCGGTAATGGGCTCGGTGGCCGCTCAGGCCCTGGGTGTGCATCGGCCACGCGTGGCGCTGTTGAACATCGGTACCGAGGACATCAAGGGTAACcagcag                              >  2:108779/1‑149 (MQ=255)                                                                                                       gATCTGGGCGCCAATGTCGACTGCAGTGCCGAAAACCTCTATCAGTTCGCGGTAATGGGCTCGGTGGCCGCTCAGGCCCTGGGTGTGCATCGGCCACGCGTGGCGCTGTTGAACATCGGTACCGAGGACATCAAGGGTAACCAGCAGGt                            >  8:42586/1‑149 (MQ=255)                                                                                                           tGGGCGCCAATGTCGACTGCAGTGCCGAAAACCTCTATCAGTTCGCGGTAATGGGCTCGGTGGCCGCTCAGGCCCTGGGTGTGCATCGGCCACGCGTGGCGCTGTTGAACATCGGTACCGAGGACATCAAGGGt                                       <  5:294407/134‑1 (MQ=255)                                                                                                           tGGGCGCCAATGTCGACTGCAGTGCCGAAAACCTCTATCAGTTCGCGGTAATGGGCTCGGTGGCCGCTCAGGCCCTGGGTGTGCATCGGCCACGCGTGGCGCTGTTGAACATCGGTACCGAGGACATCAAGGGt                                       >  6:294407/1‑134 (MQ=255)                                                                                                             ggCGCCAATGTCGACTGCAGTGCCGAAAACCTCTATCAGTTCGCGGTAATGGGCTCGGTGGCCGCTCAGGCCCTGGGTGTGCATCGGCCACGCGTGGCGCTGTTGAACATCGGTACCGAGGACATCAAGGGTAACCAGCAGGTCa                          <  7:42586/145‑1 (MQ=255)                                                                                                             ggCGCCAATGTCGACTGCAGTGCCGAAAACCTCTATCAGTTCGCGGTAATGGGCTCGGTGGCCGCTCAGGCCCTGGGTGTGCATCGGCCACGCGTGGCGCTGTTGAACATCGGTACCGAGGACATCAAGGGTAACCAGCAGGTCAAgc                       <  2:15875/148‑1 (MQ=255)                                                                                                                           cTGCAGTGCCGAAAACCTCTATCAGTTCGCGGTAATGGGCTCGGTGGCCGCTCAGGCCCTGGGTGTGCATCGGCCACGCGTGGCGCTGTTGAACATCGGTACCGAGGACATCAAGGGTAACCAGCAGGTCAAGCTGGCTGCCACGCTGt        <  6:54284/149‑1 (MQ=255)                                                                                                                               aGTGCCGAAAACCTCTATCAGTTCGCGGTAATGGGCTCGGTGGCCGCTCAGGCCCTGGGTGTGCATCGGCCACGCGTGGCGCTGTTGAACATCGGTACCGAg                                                   >  7:180084/1‑102 (MQ=255)                                                                                                                               aGTGCCGAAAACCTCTATCAGTTCGCGGTAATGGGCTCGGTGGCCGCTCAGGCCCTGGGTGTGCATCGGCCACGCGTGGCGCTGTTGAACATCGGTACCGAg                                                   <  8:180084/102‑1 (MQ=255)                                                                                                                                 tGCCGAAAACCTCTATCAGTTCGCGGTAATGGGCTCGGTGGCCGCTCAGGCCCTGGGTGTGCATCGGCCACGCGTGGCGCTGTTGAACATCGGTACCGAGGACATCAAGGGTAACCAGCAGGTCAAGCTGGCTGCCACGCTGTTGCa    >  1:303135/1‑147 (MQ=255)                                                                                                                                   ccGAAAACCTCTATCAGTTCGCGGTTATGGGCTCGGTGGCCGCTCAGGCCCTGGGTGTGCATCGACCACGCGTGGCGCTGTTGAACATCGGTACCGAGGACATCAAGGGTAAc                                    <  8:4883/113‑1 (MQ=255)                                                                                                                                           ctctATCAGTTCGCGGTAATGGGCTCGGTGGCCGCTCAGGCCCTGGGTGTGCATCGGCCACGCGTGGCGCTGTTGAACATCGGTACCGAGGACATCAAGGGTAACCAGCAGGTCAAGCTGGCTGCCACGCTGTTGCaga  >  7:171843/1‑139 (MQ=255)                                                                                                                                           ctctATCAGTTCGCGGTAATGGGCTCGGTGGCCGCTCAGGCCCTGGGTGTGCATCGGCCACGCGTGGCGCTGTTGAACATCGGTACCGAGGACATCAAGGGTAACCAGCAGGTCAAGCTGGCTGCCACGCTGTTGCaga  <  8:171843/139‑1 (MQ=255)                                                                                                                                              |                                                                                                                                        CTGATGGCGTTGTCGCGCTTCGTGCTCAAGACCTTGCCGGGTATCGACCGGCCGGCCATGGTGGCGGCGATCCCGACCCAGACAGGTTACTGTCAACTGCTCGATCTGGGCGCCAATGTCGACTGCAGTGCCGAAAACCTCTATCAGTTCGCGGTAATGGGCTCGGTGGCCGCTCAGGCCCTGGGTGTGCATCGGCCACGCGTGGCGCTGTTGAACATCGGTACCGAGGACATCAAGGGTAACCAGCAGGTCAAGCTGGCTGCCACGCTGTTGCAGA  >  NC_002947/2155889‑2156165

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: ‑