Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,271,465	A→T	7.0%	R535R (CGA→CGT)	mrdA‑I →	transpeptidase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,271,465	0	A	T	7.0%	159.3 / 3.1	57	R535R (CGA→CGT)	mrdA‑I	transpeptidase
Reads supporting (aligned to +/- strand):  ref base A (23/30);  new base T (2/2);  total (25/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.39e-01

TACGCCGATCGACCCAAACCCCATGCCCGACATCGTGCTGCACGACAAGCATGCCTGGGACCAGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGCAGGGTGAGCGTTACAACCGCAACAAGACCCTTGAGCGCCACCGCGACAACGCCCTGTTTGTCGGCTTTGCTCCGGCTGAGCACCCCAGTGTGGTGGTGGCGG  >  NC_002947/4271324‑4271610                                                                                                                                               |                                                                                                                                                  tACGCCGATCGACCCAAACCCCATGCCCGACATCGTGCTGCACGACAAGCATGCCTGGGACCAGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCg                                                                                                                                            <  5:247142/149‑1 (MQ=255) tACGCCGATCGACCCAAACCCCATGCCCGACATCGTGCTGCACGACAAGCATGCCTGGGACCAGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCg                                                                                                                                            <  3:1047/149‑1 (MQ=255)      cGATCGACCCAAATCCCATGCCCGACATCGTGCTGCACGACAAGCATGCCTGGGACCAGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCaa                                                                                                                                        >  8:79422/1‑148 (MQ=255)         tCGACCCAAATCCCATGCCCGACATCGTGCTGCACGACAAGCATGCCTGGGACCAGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGc                                                                                                                                    <  7:79422/149‑1 (MQ=255)          cGACCCAAACCCCATGCCCGACATCGTGCTGCACGACAAGCATGCCTGGGACCAGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGc                                                                                                                                    <  2:265321/148‑1 (MQ=255)           gACCCAAACCCCATGCCCGACATCGTGCTGCACGACAAGCATGCCTGGGACCAGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCgg                                                                                                                                  >  6:41974/1‑149 (MQ=255)             cccAAACCCCATGCCCGACATCGTGCTGCACGACAAGCATGCCTGGGACCAGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTa                                                                                                                                >  4:185798/1‑149 (MQ=255)              ccAAACCCCATGCCCGACATCGTGCTGCACGACTAGCATGCCTGGGACCAGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCg                                                                                                                                            <  7:89196/136‑1 (MQ=255)              ccAAACCCCATGCCCGACATCGTGCTGCACGACAAGCATGCCTGGGACCAGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCg                                                                                                                                            >  8:89196/1‑136 (MQ=255)              ccAAACCCCATGCCCGACATCGTGCTGCACGACAAGCATGCCTGGGACCAGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTAc                                                                                                                               >  7:65115/1‑149 (MQ=255)                  aCCCCATGCCCGACATCGTGCTGCACGACAAGCATGCCTGGGACCAGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACcgcg                                                                                                                           <  1:63343/149‑1 (MQ=255)                    cccATGCCCGACATCGTGCTGCACGACAAGCATGCCTGGGACCAGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCT‑AATTGCCGGCAAAAGCGGTACCGCGCa                                                                                                                         <  7:237047/149‑1 (MQ=255)                    cccATGCCCGACATCGTGCTGCACGACAAGCATGCCTGGGACCAGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCa                                                                                                                         <  5:41974/149‑1 (MQ=255)                           ccGACATCGTGCTGCACGACAAGCATGCCTGGGACCAGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGgtggtg                                                                                                                  >  1:70758/1‑149 (MQ=255)                            cGACATCGTGCTGCACGACAAGCATGCCTGGGACCAGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGtggtgg                                                                                                                 <  6:8222/149‑1 (MQ=255)                               cATCGTGCTGCACGACAAGCATGCCTGGGACCAGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGa                                                                                                              <  3:185798/149‑1 (MQ=255)                                      ctgcACGACAAGCATGCCTGGGACCAGGTCAGCCTGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATAAAGCa                                                                                                       <  7:6076/149‑1 (MQ=255)                                      ctgcACGACAAGCATGCCTGGGACCAGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGc                                                                                                        <  3:213177/148‑1 (MQ=255)                                      ctgcACGACAAGCATGCCTGGGACCAGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGCa                                                                                                       <  6:275213/149‑1 (MQ=255)                                         cACGACAAGCATGCCTGGGACCAGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGCAgg                                                                                                     <  8:2753/148‑1 (MQ=255)                                           cGACAAGCATGCCTGGGACCAGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGCAGGGt                                                                                                   >  6:63379/1‑148 (MQ=255)                                             aCAAGCATGCCTGGGACCAGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCGCTTTTGCCGGCaattcgg                                                                                                                                   >  4:18006/1‑110 (MQ=255)                                             aCAAGCATGCCTGGGACCAGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCGCTTTTGCCGGCaattcgg                                                                                                                                   <  3:18006/115‑6 (MQ=255)                                             aCAAGCATGCCTGGGACCAGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCGCTTTTGCCGGCaattcgg                                                                                                                                   >  6:1196/1‑110 (MQ=255)                                             aCAAGCATGCCTGGGACCAGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCGCTTTTGCCGGCaattcgg                                                                                                                                   <  5:1196/115‑6 (MQ=255)                                              cAAGCATGCCTGGGACCAGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGCAGGGTGAGc                                                                                               <  3:94269/149‑1 (MQ=255)                                                 gCATGCCTGGGACCAGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGCAGGGTGAGCGt                                                                                             >  5:52904/1‑148 (MQ=255)                                                    tGCCTGGGACCAGGTCAGCCAGGGCATGCAGATGGTAATGCACGACCCGCGCGGCATTGCCCCCGCCGCGGCCGCCGGTGCCCAATAACG‑AATTGCCCGCAAAAGCGGTACCGCGCAGGTGGTTGCGAACAAGCAGGGTGAGCCTTAc                                                                                          >  1:43761/1‑148 (MQ=255)                                                      ccTGGGACCAGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGCAGGGTGAGCGTTACAAc                                                                                       <  4:202597/149‑1 (MQ=255)                                                       cggggCCCAGGTCAGCCAGGGCATGCAGATGGTCATGCACCACCCGCGCGGCATTGCCCCCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGCCGGGTGGGCGTTACAAca                                                                                      >  8:120554/3‑148 (MQ=37)                                                        tGGGACCAGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACGGCGCAGGTGGTGGCGATCAAGCAGGGTGAGCGTTACAACCg                                                                                     >  5:234850/1‑149 (MQ=255)                                                        tGGGACCAGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGCAGGGTGAGCGTTACAACCg                                                                                     >  3:75237/1‑149 (MQ=255)                                                           gACCAGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGCAGGGTGAGCGTTACAACCGca                                                                                   >  4:23755/1‑148 (MQ=255)                                                            aCCAGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGCAGGGTGAGCGTTACAACCGcaa                                                                                  >  8:191832/1‑148 (MQ=255)                                                              cAGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGCAGGGTGAGCGTTACAACCGcaac                                                                                 >  5:52004/1‑147 (MQ=255)                                                               aGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGCAgg                                                                                                     <  8:15515/126‑1 (MQ=255)                                                               aGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGCAgg                                                                                                     >  7:15515/1‑126 (MQ=255)                                                               aGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGCAGGGTGAGCGTTACAACCGCAACAAg                                                                              <  8:65115/149‑1 (MQ=255)                                                                 gTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGCAGGGTGAGCGTTACAACCGCAACAAGAc                                                                            <  5:63379/149‑1 (MQ=255)                                                                     gCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGCAGGGTGAGCGTTACAACCGCAACAAGACCCtt                                                                        <  2:70758/149‑1 (MQ=255)                                                                                 aGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGCAGGGTGAGCGTTACAACCGCAACAAGATCCTTGAGCGCCACcgc                                                            <  4:4926/149‑1 (MQ=255)                                                                                  gATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGCAGGGTGAGCGTTACAACCGCAACAAGACCCTTGAGCTCCAAcgc                                                            >  8:115524/1‑148 (MQ=255)                                                                                   aTGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGCAGGGTGAGCGTTACAACCGCAACAAGACCCTTGAGCGCCACCGCGa                                                          <  3:23755/149‑1 (MQ=255)                                                                                         aTGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGCAGGGTGAGCGTTACAACCGCAACAAGACCCTTGAGCGCCACCGCGACAACGc                                                    >  1:72114/1‑149 (MQ=255)                                                                                              cGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGCAGGGTGAGCGTTACAACCGCAACAAGACCCTTGAGCGCCACCGCGACAACGCCCTGt                                               <  6:52004/149‑1 (MQ=255)                                                                                                   cgcgcgGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGCAGGGTGAGCGTTACAACCGCAACAAGACCCTTGAGCGCCACCGCGACAACGCCCTGTTTGTc                                          <  7:191832/149‑1 (MQ=255)                                                                                                        ggCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGCAGGGTGAGCGTTACAACCGCAACAAGACCCTTGAGCGCCACCGCGACAACGCCCTGTTTGTCGGCtt                                     >  7:37950/1‑149 (MQ=255)                                                                                                               cccGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGCAGGGTGAGCGTTACAACCGCAACAAGACCCTTGAGCGCCACCGCGACAACGCCCTGTTTGTCGGCTTTGCTcc                               <  2:72114/148‑1 (MQ=255)                                                                                                                    gccgcgGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGCAGGGTGAGCGTTACAACCGCAACAAGACCCTTGAGCGCCACCGCGACAACGCCCTGTTTGTCGGCTTTGCTCCGGCTGa                         <  4:75237/149‑1 (MQ=255)                                                                                                                    gccgcgGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGCAGGGTGAGCGTTACAACCGCAACAAGACCCTTGAGCGCCACCGCGACAACGCCCTGTTTGTCGGCTTTGCTCCGGCTGa                         <  8:37950/149‑1 (MQ=255)                                                                                                                     ccgcgGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGCAGGGTGAGCGTTACAACCGCAACAAGACCCTTGAGCGCCACCGCGACAACGCCCTGTTTGTCGGCTTTGCTCCGGCTGAg                        <  7:120554/149‑1 (MQ=255)                                                                                                                       gcgGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGCAGGGTGAGCGTTACAACCGCAACAAGACCCTTGAGCGCCACCGCGACAACGCCCTGTTTGTCGGCTTTGCTCCGGCTGAGCa                      >  6:86967/1‑149 (MQ=255)                                                                                                                                      cAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGCAGGGTGAGCGTTACAACCGCAACAAGACCCTTGAGCGCCACCGCGa                                                          <  2:81174/98‑1 (MQ=255)                                                                                                                                      cAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGCAGGGTGAGCGTTACAACCGCAACAAGACCCTTGAGCGCCACCGCGa                                                          >  1:81174/1‑98 (MQ=255)                                                                                                                                      cAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGCAGGGTGAGCGTTACAACCGCAACAAGACCCTTGAGCGCCACCGCGACAACGCCCTGTTTGTCGGCTTTGCTCCGGCTGAGCACCCCAGTgtggtggt       >  4:185038/1‑149 (MQ=255)                                                                                                                                           ccG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGCAGGGTGAGCGTTACAACCGCAACAAGACCCTTGAGCGCCACCGCGACAACGCCCTGTTTGTCGGCTTTGCTCCGGCTGAGCACCCCAGTGTGGTGGTGGCgg  <  6:52904/149‑1 (MQ=255)                                                                                                                                            cG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGCAGGGTGAGCGTTACAACCGCAACAAGACCCTTGAGCGCCACCGCGACAACGCCCTGTTTGTCGGCTTTGCTCCGGCTGAGCACCCCAGTGTGGTGGTGGCgg  >  1:116614/1‑148 (MQ=255)                                                                                                                                               |                                                                                                                                                  TACGCCGATCGACCCAAACCCCATGCCCGACATCGTGCTGCACGACAAGCATGCCTGGGACCAGGTCAGCCAGGGCATGCAGATGGTCATGCACGACCCGCGCGGCATTGCCCGCGCCGCGGCCGCCGGTGCCCAGTACCG‑AATTGCCGGCAAAAGCGGTACCGCGCAGGTGGTGGCGATCAAGCAGGGTGAGCGTTACAACCGCAACAAGACCCTTGAGCGCCACCGCGACAACGCCCTGTTTGTCGGCTTTGCTCCGGCTGAGCACCCCAGTGTGGTGGTGGCGG  >  NC_002947/4271324‑4271610

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: ‑